Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/infernal-1.1.3/rmark/rmark-create.c
Examining data/infernal-1.1.3/rmark/rmark-rocplot.c
Examining data/infernal-1.1.3/src/cmscan.c
Examining data/infernal-1.1.3/src/cmsearch.c
Examining data/infernal-1.1.3/src/cmstat.c
Examining data/infernal-1.1.3/src/cm_p7_modelconfig_trunc.c
Examining data/infernal-1.1.3/src/cm_trunc.c
Examining data/infernal-1.1.3/src/cmsim.c
Examining data/infernal-1.1.3/src/cp9-test.c
Examining data/infernal-1.1.3/src/cp9.c
Examining data/infernal-1.1.3/src/cp9_dp.c
Examining data/infernal-1.1.3/src/cp9_modelmaker.c
Examining data/infernal-1.1.3/src/cp9_mx.c
Examining data/infernal-1.1.3/src/cp9_trace.c
Examining data/infernal-1.1.3/src/display.c
Examining data/infernal-1.1.3/src/errors.c
Examining data/infernal-1.1.3/src/eweight.c
Examining data/infernal-1.1.3/src/hmmband.c
Examining data/infernal-1.1.3/src/hmmband.h
Examining data/infernal-1.1.3/src/infernal.h
Examining data/infernal-1.1.3/src/itest_brute.c
Examining data/infernal-1.1.3/src/cmbuild.c
Examining data/infernal-1.1.3/src/cmcalibrate.c
Examining data/infernal-1.1.3/src/cmconvert.c
Examining data/infernal-1.1.3/src/cmemit.c
Examining data/infernal-1.1.3/src/cmfetch.c
Examining data/infernal-1.1.3/src/cmpress.c
Examining data/infernal-1.1.3/src/cmalign.c
Examining data/infernal-1.1.3/src/cm_p7_domaindef.c
Examining data/infernal-1.1.3/src/cm_p7_modelmaker.c
Examining data/infernal-1.1.3/src/cm_parsetree.c
Examining data/infernal-1.1.3/src/cm_pipeline.c
Examining data/infernal-1.1.3/src/cm_qdband.c
Examining data/infernal-1.1.3/src/cm_submodel.c
Examining data/infernal-1.1.3/src/logsum.c
Examining data/infernal-1.1.3/src/mpisupport.c
Examining data/infernal-1.1.3/src/prior.c
Examining data/infernal-1.1.3/src/prior.h
Examining data/infernal-1.1.3/src/rnamat.c
Examining data/infernal-1.1.3/src/rnamat.h
Examining data/infernal-1.1.3/src/sub_cm-test.c
Examining data/infernal-1.1.3/src/stats.c
Examining data/infernal-1.1.3/src/stats.h
Examining data/infernal-1.1.3/src/impl_sse/cm_optimized.c
Examining data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c
Examining data/infernal-1.1.3/src/impl_sse/sse_util.c
Examining data/infernal-1.1.3/src/impl_sse/impl_sse.h
Examining data/infernal-1.1.3/src/impl_sse/sse_cm_dpsearch.c
Examining data/infernal-1.1.3/src/impl_sse/sse_cm_dpsmall.c
Examining data/infernal-1.1.3/src/impl_sse/sse_cmcons_hitmx.c
Examining data/infernal-1.1.3/src/impl_sse/sse_cmcons_mscyk.c
Examining data/infernal-1.1.3/src/trcyk.c
Examining data/infernal-1.1.3/src/truncyk.c
Examining data/infernal-1.1.3/src/truncyk_check.c
Examining data/infernal-1.1.3/src/alphabet.c
Examining data/infernal-1.1.3/src/bandcyk-montecarlo-test.c
Examining data/infernal-1.1.3/src/bandcyk-truncation-test.c
Examining data/infernal-1.1.3/src/cm.c
Examining data/infernal-1.1.3/src/cm_alidisplay.c
Examining data/infernal-1.1.3/src/cm_alndata.c
Examining data/infernal-1.1.3/src/cm_dispatch.h
Examining data/infernal-1.1.3/src/cm_dpalign.c
Examining data/infernal-1.1.3/src/cm_dpalign_trunc.c
Examining data/infernal-1.1.3/src/cm_dpsearch.c
Examining data/infernal-1.1.3/src/cm_dpsearch_trunc.c
Examining data/infernal-1.1.3/src/cm_dpsmall.c
Examining data/infernal-1.1.3/src/cm_file.c
Examining data/infernal-1.1.3/src/cm_modelconfig.c
Examining data/infernal-1.1.3/src/cm_mx.c
Examining data/infernal-1.1.3/src/cm_p7_band.c
Examining data/infernal-1.1.3/src/cm_modelmaker.c
Examining data/infernal-1.1.3/src/cm_tophits.c
Examining data/infernal-1.1.3/easel/esl_bitfield.c
Examining data/infernal-1.1.3/easel/esl_bitfield.h
Examining data/infernal-1.1.3/easel/esl_buffer.c
Examining data/infernal-1.1.3/easel/esl_buffer.h
Examining data/infernal-1.1.3/easel/esl_cluster.c
Examining data/infernal-1.1.3/easel/esl_cluster.h
Examining data/infernal-1.1.3/easel/esl_composition.c
Examining data/infernal-1.1.3/easel/esl_composition.h
Examining data/infernal-1.1.3/easel/esl_cpu.c
Examining data/infernal-1.1.3/easel/esl_cpu.h
Examining data/infernal-1.1.3/easel/esl_dirichlet.c
Examining data/infernal-1.1.3/easel/esl_dirichlet.h
Examining data/infernal-1.1.3/easel/esl_distance.c
Examining data/infernal-1.1.3/easel/esl_distance.h
Examining data/infernal-1.1.3/easel/esl_dmatrix.c
Examining data/infernal-1.1.3/easel/esl_dmatrix.h
Examining data/infernal-1.1.3/easel/esl_dsqdata.c
Examining data/infernal-1.1.3/easel/esl_dsqdata.h
Examining data/infernal-1.1.3/easel/esl_exponential.c
Examining data/infernal-1.1.3/easel/esl_exponential.h
Examining data/infernal-1.1.3/easel/esl_fileparser.c
Examining data/infernal-1.1.3/easel/esl_fileparser.h
Examining data/infernal-1.1.3/easel/esl_gamma.c
Examining data/infernal-1.1.3/easel/esl_gamma.h
Examining data/infernal-1.1.3/easel/esl_gencode.c
Examining data/infernal-1.1.3/easel/esl_gencode.h
Examining data/infernal-1.1.3/easel/esl_getopts.c
Examining data/infernal-1.1.3/easel/esl_getopts.h
Examining data/infernal-1.1.3/easel/esl_gev.c
Examining data/infernal-1.1.3/easel/esl_gev.h
Examining data/infernal-1.1.3/easel/esl_graph.c
Examining data/infernal-1.1.3/easel/esl_graph.h
Examining data/infernal-1.1.3/easel/esl_gumbel.c
Examining data/infernal-1.1.3/easel/esl_gumbel.h
Examining data/infernal-1.1.3/easel/esl_heap.c
Examining data/infernal-1.1.3/easel/esl_heap.h
Examining data/infernal-1.1.3/easel/esl_histogram.c
Examining data/infernal-1.1.3/easel/esl_histogram.h
Examining data/infernal-1.1.3/easel/esl_hmm.c
Examining data/infernal-1.1.3/easel/esl_hmm.h
Examining data/infernal-1.1.3/easel/esl_huffman.c
Examining data/infernal-1.1.3/easel/esl_huffman.h
Examining data/infernal-1.1.3/easel/esl_hyperexp.c
Examining data/infernal-1.1.3/easel/esl_hyperexp.h
Examining data/infernal-1.1.3/easel/esl_json.c
Examining data/infernal-1.1.3/easel/esl_json.h
Examining data/infernal-1.1.3/easel/esl_keyhash.c
Examining data/infernal-1.1.3/easel/esl_keyhash.h
Examining data/infernal-1.1.3/easel/esl_matrixops.c
Examining data/infernal-1.1.3/easel/esl_matrixops.h
Examining data/infernal-1.1.3/easel/esl_mem.c
Examining data/infernal-1.1.3/easel/esl_mem.h
Examining data/infernal-1.1.3/easel/esl_minimizer.c
Examining data/infernal-1.1.3/easel/esl_minimizer.h
Examining data/infernal-1.1.3/easel/esl_mixdchlet.c
Examining data/infernal-1.1.3/easel/esl_mixdchlet.h
Examining data/infernal-1.1.3/easel/esl_mixgev.c
Examining data/infernal-1.1.3/easel/esl_mixgev.h
Examining data/infernal-1.1.3/easel/esl_mpi.c
Examining data/infernal-1.1.3/easel/esl_mpi.h
Examining data/infernal-1.1.3/easel/esl_msa.c
Examining data/infernal-1.1.3/easel/esl_msa.h
Examining data/infernal-1.1.3/easel/esl_msacluster.c
Examining data/infernal-1.1.3/easel/esl_msacluster.h
Examining data/infernal-1.1.3/easel/esl_msafile.c
Examining data/infernal-1.1.3/easel/esl_msafile.h
Examining data/infernal-1.1.3/easel/esl_msafile2.c
Examining data/infernal-1.1.3/easel/esl_msafile2.h
Examining data/infernal-1.1.3/easel/esl_msafile_a2m.c
Examining data/infernal-1.1.3/easel/esl_msafile_a2m.h
Examining data/infernal-1.1.3/easel/esl_msafile_afa.c
Examining data/infernal-1.1.3/easel/esl_msafile_afa.h
Examining data/infernal-1.1.3/easel/esl_msafile_clustal.c
Examining data/infernal-1.1.3/easel/esl_msafile_clustal.h
Examining data/infernal-1.1.3/easel/esl_msafile_phylip.c
Examining data/infernal-1.1.3/easel/esl_msafile_phylip.h
Examining data/infernal-1.1.3/easel/esl_msafile_psiblast.c
Examining data/infernal-1.1.3/easel/esl_msafile_psiblast.h
Examining data/infernal-1.1.3/easel/esl_msafile_selex.c
Examining data/infernal-1.1.3/easel/esl_msafile_selex.h
Examining data/infernal-1.1.3/easel/esl_msafile_stockholm.c
Examining data/infernal-1.1.3/easel/esl_msafile_stockholm.h
Examining data/infernal-1.1.3/easel/esl_msashuffle.c
Examining data/infernal-1.1.3/easel/esl_msashuffle.h
Examining data/infernal-1.1.3/easel/esl_msaweight.c
Examining data/infernal-1.1.3/easel/esl_msaweight.h
Examining data/infernal-1.1.3/easel/esl_neon.c
Examining data/infernal-1.1.3/easel/esl_neon.h
Examining data/infernal-1.1.3/easel/esl_normal.c
Examining data/infernal-1.1.3/easel/esl_normal.h
Examining data/infernal-1.1.3/easel/esl_paml.c
Examining data/infernal-1.1.3/easel/esl_paml.h
Examining data/infernal-1.1.3/easel/esl_quicksort.c
Examining data/infernal-1.1.3/easel/esl_quicksort.h
Examining data/infernal-1.1.3/easel/esl_rand64.c
Examining data/infernal-1.1.3/easel/esl_rand64.h
Examining data/infernal-1.1.3/easel/esl_random.c
Examining data/infernal-1.1.3/easel/esl_random.h
Examining data/infernal-1.1.3/easel/esl_randomseq.c
Examining data/infernal-1.1.3/easel/esl_randomseq.h
Examining data/infernal-1.1.3/easel/esl_ratematrix.c
Examining data/infernal-1.1.3/easel/esl_ratematrix.h
Examining data/infernal-1.1.3/easel/esl_recorder.c
Examining data/infernal-1.1.3/easel/esl_recorder.h
Examining data/infernal-1.1.3/easel/esl_red_black.c
Examining data/infernal-1.1.3/easel/esl_red_black.h
Examining data/infernal-1.1.3/easel/esl_regexp.c
Examining data/infernal-1.1.3/easel/esl_regexp.h
Examining data/infernal-1.1.3/easel/esl_rootfinder.c
Examining data/infernal-1.1.3/easel/esl_rootfinder.h
Examining data/infernal-1.1.3/easel/esl_scorematrix.c
Examining data/infernal-1.1.3/easel/esl_scorematrix.h
Examining data/infernal-1.1.3/easel/esl_sq.c
Examining data/infernal-1.1.3/easel/esl_sq.h
Examining data/infernal-1.1.3/easel/esl_sqio.c
Examining data/infernal-1.1.3/easel/esl_sqio.h
Examining data/infernal-1.1.3/easel/esl_sqio_ascii.c
Examining data/infernal-1.1.3/easel/esl_sqio_ascii.h
Examining data/infernal-1.1.3/easel/esl_sqio_ncbi.c
Examining data/infernal-1.1.3/easel/esl_sqio_ncbi.h
Examining data/infernal-1.1.3/easel/esl_sse.c
Examining data/infernal-1.1.3/easel/esl_sse.h
Examining data/infernal-1.1.3/easel/esl_ssi.c
Examining data/infernal-1.1.3/easel/esl_ssi.h
Examining data/infernal-1.1.3/easel/esl_stack.c
Examining data/infernal-1.1.3/easel/esl_stack.h
Examining data/infernal-1.1.3/easel/esl_stats.c
Examining data/infernal-1.1.3/easel/esl_stats.h
Examining data/infernal-1.1.3/easel/esl_stopwatch.c
Examining data/infernal-1.1.3/easel/esl_stopwatch.h
Examining data/infernal-1.1.3/easel/esl_stretchexp.c
Examining data/infernal-1.1.3/easel/esl_stretchexp.h
Examining data/infernal-1.1.3/easel/esl_subcmd.c
Examining data/infernal-1.1.3/easel/esl_subcmd.h
Examining data/infernal-1.1.3/easel/esl_swat.c
Examining data/infernal-1.1.3/easel/esl_threads.c
Examining data/infernal-1.1.3/easel/esl_threads.h
Examining data/infernal-1.1.3/easel/esl_tree.c
Examining data/infernal-1.1.3/easel/esl_tree.h
Examining data/infernal-1.1.3/easel/esl_varint.c
Examining data/infernal-1.1.3/easel/esl_varint.h
Examining data/infernal-1.1.3/easel/esl_vectorops.c
Examining data/infernal-1.1.3/easel/esl_vectorops.h
Examining data/infernal-1.1.3/easel/esl_vmx.c
Examining data/infernal-1.1.3/easel/esl_vmx.h
Examining data/infernal-1.1.3/easel/esl_weibull.c
Examining data/infernal-1.1.3/easel/esl_weibull.h
Examining data/infernal-1.1.3/easel/esl_workqueue.c
Examining data/infernal-1.1.3/easel/esl_workqueue.h
Examining data/infernal-1.1.3/easel/esl_wuss.c
Examining data/infernal-1.1.3/easel/esl_wuss.h
Examining data/infernal-1.1.3/easel/interface_gsl.c
Examining data/infernal-1.1.3/easel/interface_gsl.h
Examining data/infernal-1.1.3/easel/interface_lapack.c
Examining data/infernal-1.1.3/easel/interface_lapack.h
Examining data/infernal-1.1.3/easel/miniapps/cmd_alistat.c
Examining data/infernal-1.1.3/easel/miniapps/cmd_downsample.c
Examining data/infernal-1.1.3/easel/miniapps/cmd_filter.c
Examining data/infernal-1.1.3/easel/miniapps/easel.c
Examining data/infernal-1.1.3/easel/miniapps/esl-afetch.c
Examining data/infernal-1.1.3/easel/miniapps/esl-alimanip.c
Examining data/infernal-1.1.3/easel/miniapps/esl-alimap.c
Examining data/infernal-1.1.3/easel/miniapps/esl-alimask.c
Examining data/infernal-1.1.3/easel/miniapps/esl-alimerge.c
Examining data/infernal-1.1.3/easel/miniapps/esl-alipid.c
Examining data/infernal-1.1.3/easel/miniapps/esl-alirev.c
Examining data/infernal-1.1.3/easel/miniapps/esl-alistat.c
Examining data/infernal-1.1.3/easel/miniapps/esl-compalign.c
Examining data/infernal-1.1.3/easel/miniapps/esl-compstruct.c
Examining data/infernal-1.1.3/easel/miniapps/esl-construct.c
Examining data/infernal-1.1.3/easel/miniapps/esl-histplot.c
Examining data/infernal-1.1.3/easel/miniapps/esl-mask.c
Examining data/infernal-1.1.3/easel/miniapps/esl-mixdchlet.c
Examining data/infernal-1.1.3/easel/miniapps/esl-reformat.c
Examining data/infernal-1.1.3/easel/miniapps/esl-selectn.c
Examining data/infernal-1.1.3/easel/miniapps/esl-seqrange.c
Examining data/infernal-1.1.3/easel/miniapps/esl-seqstat.c
Examining data/infernal-1.1.3/easel/miniapps/esl-sfetch.c
Examining data/infernal-1.1.3/easel/miniapps/esl-shuffle.c
Examining data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c
Examining data/infernal-1.1.3/easel/miniapps/esl-translate.c
Examining data/infernal-1.1.3/easel/miniapps/esl-weight.c
Examining data/infernal-1.1.3/easel/easel.c
Examining data/infernal-1.1.3/easel/easel.h
Examining data/infernal-1.1.3/easel/esl_alloc.c
Examining data/infernal-1.1.3/easel/esl_alloc.h
Examining data/infernal-1.1.3/easel/esl_alphabet.c
Examining data/infernal-1.1.3/easel/esl_alphabet.h
Examining data/infernal-1.1.3/easel/esl_arr2.c
Examining data/infernal-1.1.3/easel/esl_arr2.h
Examining data/infernal-1.1.3/easel/esl_arr3.c
Examining data/infernal-1.1.3/easel/esl_arr3.h
Examining data/infernal-1.1.3/easel/esl_avx.c
Examining data/infernal-1.1.3/easel/esl_avx.h
Examining data/infernal-1.1.3/easel/esl_avx512.c
Examining data/infernal-1.1.3/easel/esl_avx512.h
Examining data/infernal-1.1.3/hmmer/libdivsufsort/divsufsort.c
Examining data/infernal-1.1.3/hmmer/profmark/rocplot.c
Examining data/infernal-1.1.3/hmmer/profmark/create-profmark.c
Examining data/infernal-1.1.3/hmmer/src/generic_fwdback_rescaled.c
Examining data/infernal-1.1.3/hmmer/src/generic_msv.c
Examining data/infernal-1.1.3/hmmer/src/generic_null2.c
Examining data/infernal-1.1.3/hmmer/src/generic_optacc.c
Examining data/infernal-1.1.3/hmmer/src/generic_stotrace.c
Examining data/infernal-1.1.3/hmmer/src/generic_viterbi.c
Examining data/infernal-1.1.3/hmmer/src/generic_vtrace.c
Examining data/infernal-1.1.3/hmmer/src/h2_io.c
Examining data/infernal-1.1.3/hmmer/src/heatmap.c
Examining data/infernal-1.1.3/hmmer/src/hmmalign.c
Examining data/infernal-1.1.3/hmmer/src/hmmbuild.c
Examining data/infernal-1.1.3/hmmer/src/hmmc2.c
Examining data/infernal-1.1.3/hmmer/src/hmmconvert.c
Examining data/infernal-1.1.3/hmmer/src/hmmd_search_status.c
Examining data/infernal-1.1.3/hmmer/src/hmmdmstr.c
Examining data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c
Examining data/infernal-1.1.3/hmmer/src/hmmdutils.c
Examining data/infernal-1.1.3/hmmer/src/hmmdwrkr.c
Examining data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c
Examining data/infernal-1.1.3/hmmer/src/hmmemit.c
Examining data/infernal-1.1.3/hmmer/src/hmmer.c
Examining data/infernal-1.1.3/hmmer/src/hmmer.h
Examining data/infernal-1.1.3/hmmer/src/hmmerfm-exactmatch.c
Examining data/infernal-1.1.3/hmmer/src/hmmfetch.c
Examining data/infernal-1.1.3/hmmer/src/hmmlogo.c
Examining data/infernal-1.1.3/hmmer/src/hmmpgmd.c
Examining data/infernal-1.1.3/hmmer/src/hmmpgmd.h
Examining data/infernal-1.1.3/hmmer/src/hmmpgmd2msa.c
Examining data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.c
Examining data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.h
Examining data/infernal-1.1.3/hmmer/src/hmmpress.c
Examining data/infernal-1.1.3/hmmer/src/hmmscan.c
Examining data/infernal-1.1.3/hmmer/src/hmmsearch.c
Examining data/infernal-1.1.3/hmmer/src/hmmsim.c
Examining data/infernal-1.1.3/hmmer/src/hmmstat.c
Examining data/infernal-1.1.3/hmmer/src/itest_brute.c
Examining data/infernal-1.1.3/hmmer/src/jackhmmer.c
Examining data/infernal-1.1.3/hmmer/src/logsum.c
Examining data/infernal-1.1.3/hmmer/src/makehmmerdb.c
Examining data/infernal-1.1.3/hmmer/src/modelconfig.c
Examining data/infernal-1.1.3/hmmer/src/modelstats.c
Examining data/infernal-1.1.3/hmmer/src/mpisupport.c
Examining data/infernal-1.1.3/hmmer/src/nhmmer.c
Examining data/infernal-1.1.3/hmmer/src/nhmmscan.c
Examining data/infernal-1.1.3/hmmer/src/p7_alidisplay.c
Examining data/infernal-1.1.3/hmmer/src/p7_bg.c
Examining data/infernal-1.1.3/hmmer/src/p7_domain.c
Examining data/infernal-1.1.3/hmmer/src/p7_domaindef.c
Examining data/infernal-1.1.3/hmmer/src/p7_gbands.c
Examining data/infernal-1.1.3/hmmer/src/p7_gbands.h
Examining data/infernal-1.1.3/hmmer/src/p7_gmx.c
Examining data/infernal-1.1.3/hmmer/src/p7_gmxb.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/p7_omx.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/ssvfilter.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/stotrace.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/vitfilter.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/vitscore.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/decoding.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/fwdback.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/impl_sse.h
Examining data/infernal-1.1.3/hmmer/src/impl_sse/io.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/msvfilter.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/null2.c
Examining data/infernal-1.1.3/hmmer/src/impl_sse/optacc.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/decoding.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/fwdback.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/impl_vmx.h
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/io.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/msvfilter.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/null2.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/optacc.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/p7_omx.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/stotrace.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/vitfilter.c
Examining data/infernal-1.1.3/hmmer/src/impl_vmx/vitscore.c
Examining data/infernal-1.1.3/hmmer/src/p7_gmxb.h
Examining data/infernal-1.1.3/hmmer/src/p7_gmxchk.c
Examining data/infernal-1.1.3/hmmer/src/p7_gmxchk.h
Examining data/infernal-1.1.3/hmmer/src/p7_hit.c
Examining data/infernal-1.1.3/hmmer/src/p7_hmm.c
Examining data/infernal-1.1.3/hmmer/src/p7_hmmcache.c
Examining data/infernal-1.1.3/hmmer/src/p7_hmmcache.h
Examining data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c
Examining data/infernal-1.1.3/hmmer/src/p7_hmmfile.c
Examining data/infernal-1.1.3/hmmer/src/p7_hmmwindow.c
Examining data/infernal-1.1.3/hmmer/src/p7_null3.c
Examining data/infernal-1.1.3/hmmer/src/p7_pipeline.c
Examining data/infernal-1.1.3/hmmer/src/p7_prior.c
Examining data/infernal-1.1.3/hmmer/src/p7_profile.c
Examining data/infernal-1.1.3/hmmer/src/p7_scoredata.c
Examining data/infernal-1.1.3/hmmer/src/p7_spensemble.c
Examining data/infernal-1.1.3/hmmer/src/p7_trace.c
Examining data/infernal-1.1.3/hmmer/src/phmmer.c
Examining data/infernal-1.1.3/hmmer/src/seqmodel.c
Examining data/infernal-1.1.3/hmmer/src/tracealign.c
Examining data/infernal-1.1.3/hmmer/src/alimask.c
Examining data/infernal-1.1.3/hmmer/src/build.c
Examining data/infernal-1.1.3/hmmer/src/cachedb.c
Examining data/infernal-1.1.3/hmmer/src/cachedb.h
Examining data/infernal-1.1.3/hmmer/src/cachedb_shard.c
Examining data/infernal-1.1.3/hmmer/src/cachedb_shard.h
Examining data/infernal-1.1.3/hmmer/src/emit.c
Examining data/infernal-1.1.3/hmmer/src/errors.c
Examining data/infernal-1.1.3/hmmer/src/evalues.c
Examining data/infernal-1.1.3/hmmer/src/eweight.c
Examining data/infernal-1.1.3/hmmer/src/fm_alphabet.c
Examining data/infernal-1.1.3/hmmer/src/fm_general.c
Examining data/infernal-1.1.3/hmmer/src/fm_sse.c
Examining data/infernal-1.1.3/hmmer/src/fm_ssv.c
Examining data/infernal-1.1.3/hmmer/src/generic_decoding.c
Examining data/infernal-1.1.3/hmmer/src/generic_fwdback.c
Examining data/infernal-1.1.3/hmmer/src/generic_fwdback_banded.c
Examining data/infernal-1.1.3/hmmer/src/generic_fwdback_chk.c
Examining data/infernal-1.1.3/hmmer/src/p7_builder.c
Examining data/infernal-1.1.3/hmmer/src/p7_tophits.c
FINAL RESULTS:
data/infernal-1.1.3/easel/easel.c:2490:7: [5] (race) chmod:
This accepts filename arguments; if an attacker can move those files, a
race condition results. (CWE-362). Use fchmod( ) instead.
if (chmod(tmpfile, mode) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:76:16: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
if (errbuf) vsnprintf(errbuf, eslERRBUFSIZE, format, ap);
data/infernal-1.1.3/easel/easel.c:151:4: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/easel.c:303:7: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/easel.c:756:12: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
if ( vfprintf(fp, format, argp) < 0 ) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
data/infernal-1.1.3/easel/easel.c:796:12: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
if ( vprintf(format, argp) < 0 ) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
data/infernal-1.1.3/easel/easel.c:836:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new, s);
data/infernal-1.1.3/easel/easel.c:1235:13: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
if ((n2 = vsnprintf(s, n1+1, format, *ap)) >= n1)
data/infernal-1.1.3/easel/easel.c:1238:11: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
if (vsnprintf(s, n2+1, format, ap2) == -1) ESL_XEXCEPTION(eslESYS, "vsnprintf() failed");
data/infernal-1.1.3/easel/easel.c:1655:26: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (lastslash == NULL) strcpy(tail, path);
data/infernal-1.1.3/easel/easel.c:1656:26: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(tail, lastslash+1);
data/infernal-1.1.3/easel/easel.c:1750:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(path, file);
data/infernal-1.1.3/easel/easel.c:1752:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(path, file);
data/infernal-1.1.3/easel/easel.c:1754:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(path, "%s%s", dir, file);
data/infernal-1.1.3/easel/easel.c:1756:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(path, "%s%c%s", dir, eslDIRSLASH, file);
data/infernal-1.1.3/easel/easel.c:1812:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new+nf+1, sfx);
data/infernal-1.1.3/easel/easel.c:1888:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(path, "%s%c%s", s, eslDIRSLASH, fname); /* // won't hurt */
data/infernal-1.1.3/easel/easel.h:246:26: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define ESL_DPRINTF1(x) printf x
data/infernal-1.1.3/easel/easel.h:253:26: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define ESL_DPRINTF2(x) printf x
data/infernal-1.1.3/easel/easel.h:260:26: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define ESL_DPRINTF3(x) printf x
data/infernal-1.1.3/easel/esl_alphabet.c:136:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(a->sym, alphabet);
data/infernal-1.1.3/easel/esl_buffer.c:342:17: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((bf->fp = popen(cmd, "r")) == NULL)
data/infernal-1.1.3/easel/esl_buffer.c:2372:7: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (system(cmd) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_distance.c:1481:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(as[1], as[0]);
data/infernal-1.1.3/easel/esl_dsqdata.c:200:8: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ( sprintf(dd->basename, "%s.dsqi", basename) <= 0) ESL_XEXCEPTION_SYS(eslESYS, "sprintf() failure");
data/infernal-1.1.3/easel/esl_dsqdata.c:203:8: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ( sprintf(dd->basename, "%s.dsqm", basename) <= 0) ESL_XEXCEPTION_SYS(eslESYS, "sprintf() failure");
data/infernal-1.1.3/easel/esl_dsqdata.c:206:8: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ( sprintf(dd->basename, "%s.dsqs", basename) <= 0) ESL_XEXCEPTION_SYS(eslESYS, "sprintf() failure");
data/infernal-1.1.3/easel/esl_dsqdata.c:209:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dd->basename, basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:636:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outfile, "%s.dsqm", basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:638:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outfile, "%s.dsqs", basename);
data/infernal-1.1.3/easel/esl_gencode.c:292:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(gcode->desc, esl_transl_tables[t].desc);
data/infernal-1.1.3/easel/esl_getopts.c:746:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(cmdline, "%s ", g->argv[0]);
data/infernal-1.1.3/easel/esl_getopts.c:757:37: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (g->opt[i].type == eslARG_NONE) sprintf(cmdline + ntot, "%s ", g->opt[i].name);
data/infernal-1.1.3/easel/esl_getopts.c:758:37: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else sprintf(cmdline + ntot, "%s %s ", g->opt[i].name, g->val[i]);
data/infernal-1.1.3/easel/esl_getopts.c:768:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(cmdline + ntot, "%s ", g->argv[j]);
data/infernal-1.1.3/easel/esl_getopts.c:1231:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(g->val[opti], optarg);
data/infernal-1.1.3/easel/esl_histogram.c:956:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buffer, "<%5.1f %6llu %6s|", x+h->w, (unsigned long long) lowcount, "-");
data/infernal-1.1.3/easel/esl_histogram.c:967:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buffer, ">%5.1f %6llu %6s|", x, (unsigned long long) highcount, "-");
data/infernal-1.1.3/easel/esl_histogram.c:984:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buffer, "%6.1f %6llu %6s|", x, (unsigned long long) h->obs[i], "-");
data/infernal-1.1.3/easel/esl_histogram.c:991:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(buffer, "%6.1f %6.2e %6s|", x, (double) h->obs[i], "-");
data/infernal-1.1.3/easel/esl_json.c:1284:12: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ( sprintf(sj, "{ \"a\" : %s }", s) < 0) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:269:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new_msa->aseq[i], msa->aseq[i]);
data/infernal-1.1.3/easel/esl_msa.c:2315:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(new_msa->aseq[nidx], msa->aseq[oidx]);
data/infernal-1.1.3/easel/esl_msafile2.c:213:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(cmd, "gzip -dc %s", filename);
data/infernal-1.1.3/easel/esl_msafile2.c:214:21: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((afp->f = popen(cmd, "r")) == NULL) { status = eslENOTFOUND; goto ERROR; }
data/infernal-1.1.3/easel/esl_msafile_phylip.c:505:7: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
if (fprintf(fp, " %d %" PRId64, msa->nseq, msa->alen) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "interleaved phylip write failed");
data/infernal-1.1.3/easel/esl_msashuffle.c:60:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(shuf->aseq[i], msa->aseq[i]);
data/infernal-1.1.3/easel/esl_msashuffle.c:441:16: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (xs != x) strcpy(xs, x);
data/infernal-1.1.3/easel/esl_msashuffle.c:442:16: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (ys != y) strcpy(ys, y);
data/infernal-1.1.3/easel/esl_randomseq.c:226:22: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (shuffled != s) strcpy(shuffled, s);
data/infernal-1.1.3/easel/esl_randomseq.c:298:26: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (s != shuffled) strcpy(shuffled, s);
data/infernal-1.1.3/easel/esl_randomseq.c:498:22: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (shuffled != s) strcpy(shuffled, s);
data/infernal-1.1.3/easel/esl_randomseq.c:579:22: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (shuffled != s) strcpy(shuffled, s);
data/infernal-1.1.3/easel/esl_randomseq.c:698:26: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (s != markoved) strcpy(markoved, s);
data/infernal-1.1.3/easel/esl_randomseq.c:1584:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(s, s2);
data/infernal-1.1.3/easel/esl_randomseq.c:1600:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(s, s2);
data/infernal-1.1.3/easel/esl_randomseq.c:1616:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(s, s2);
data/infernal-1.1.3/easel/esl_randomseq.c:1632:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(s, s2);
data/infernal-1.1.3/easel/esl_randomseq.c:1712:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(s, s2);
data/infernal-1.1.3/easel/esl_randomseq.c:1739:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(s, s2);
data/infernal-1.1.3/easel/esl_recorder.c:999:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tmpfile, template);
data/infernal-1.1.3/easel/esl_regexp.c:1537:10: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
(void) strcat(buf, p);
data/infernal-1.1.3/easel/esl_sq.c:302:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dst->seq, src->seq);
data/infernal-1.1.3/easel/esl_sq.c:303:28: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (src->ss != NULL) strcpy(dst->ss, src->ss);
data/infernal-1.1.3/easel/esl_sq.c:305:26: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (src->xr[x] != NULL) strcpy(dst->xr[x], src->xr[x]);
data/infernal-1.1.3/easel/esl_sq.c:311:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dst->ss+1, src->ss);
data/infernal-1.1.3/easel/esl_sq.c:314:30: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (src->xr[x] != NULL) { strcpy(dst->xr[x]+1, src->xr[x]); dst->xr[x][0] = '\0'; }
data/infernal-1.1.3/easel/esl_sq.c:320:28: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (src->ss != NULL) strcpy(dst->ss, src->ss+1);
data/infernal-1.1.3/easel/esl_sq.c:322:26: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (src->xr[x] != NULL) strcpy(dst->xr[x], src->xr[x]+1);
data/infernal-1.1.3/easel/esl_sq.c:330:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dst->ss+1, src->ss+1);
data/infernal-1.1.3/easel/esl_sq.c:334:28: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (src->xr[x] != NULL) { strcpy(dst->xr[x]+1, src->xr[x]+1); dst->xr[x][0] = '\0'; }
data/infernal-1.1.3/easel/esl_sq.c:339:33: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (src->xr_tag[x] != NULL) strcpy(dst->xr_tag[x], src->xr_tag[x]);
data/infernal-1.1.3/easel/esl_sq.c:788:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->ss+1, ss);
data/infernal-1.1.3/easel/esl_sq.c:1061:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->name, name);
data/infernal-1.1.3/easel/esl_sq.c:1099:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->acc, acc);
data/infernal-1.1.3/easel/esl_sq.c:1139:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->desc, desc);
data/infernal-1.1.3/easel/esl_sq.c:1177:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->source, source);
data/infernal-1.1.3/easel/esl_sq.c:1215:12: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
if ((n = vsnprintf(sq->name, sq->nalloc, name, argp)) >= sq->nalloc)
data/infernal-1.1.3/easel/esl_sq.c:1219:7: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf(sq->name, sq->nalloc, name, argp2);
data/infernal-1.1.3/easel/esl_sq.c:1257:12: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
if ((n = vsnprintf(sq->acc, sq->aalloc, acc, argp)) >= sq->aalloc)
data/infernal-1.1.3/easel/esl_sq.c:1261:7: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf(sq->acc, sq->aalloc, acc, argp2);
data/infernal-1.1.3/easel/esl_sq.c:1301:12: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
if ((n = vsnprintf(sq->desc, sq->dalloc, desc, argp)) >= sq->dalloc)
data/infernal-1.1.3/easel/esl_sq.c:1305:7: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf(sq->desc, sq->dalloc, desc, argp2);
data/infernal-1.1.3/easel/esl_sq.c:1344:12: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
if ((n = vsnprintf(sq->source, sq->srcalloc, source, argp)) >= sq->srcalloc)
data/infernal-1.1.3/easel/esl_sq.c:1348:7: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf(sq->source, sq->srcalloc, source, argp2);
data/infernal-1.1.3/easel/esl_sq.c:1394:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->desc + dlen, desc);
data/infernal-1.1.3/easel/esl_sq.c:1797:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->seq, msa->aseq[which]);
data/infernal-1.1.3/easel/esl_sq.c:1800:22: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(sq->ss, ss);
data/infernal-1.1.3/easel/esl_sq.c:1817:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->ss+1, ss);
data/infernal-1.1.3/easel/esl_sq.c:1819:10: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else { strcpy(sq->ss+1, ss); sq->ss[0] = '\0'; }
data/infernal-1.1.3/easel/esl_sq.c:1825:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->xr[x]+1, xr[x]);
data/infernal-1.1.3/easel/esl_sq.c:1926:29: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(sq->xr[x], xr[x]);
data/infernal-1.1.3/easel/esl_sq.c:1931:33: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(sq->xr_tag[x], xr_tag[x]);
data/infernal-1.1.3/easel/esl_sq.c:1951:17: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->xr[x]+1, xr[x]);
data/infernal-1.1.3/easel/esl_sq.c:1955:17: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->xr[x]+1, xr[x]);
data/infernal-1.1.3/easel/esl_sq.c:1962:34: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(sq->xr_tag[x], xr_tag[x]);
data/infernal-1.1.3/easel/esl_sq.c:2233:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->name, name);
data/infernal-1.1.3/easel/esl_sq.c:2247:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->desc, desc);
data/infernal-1.1.3/easel/esl_sq.c:2261:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq->acc, acc);
data/infernal-1.1.3/easel/esl_sq.c:2314:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq2->seq, seq);
data/infernal-1.1.3/easel/esl_sq.c:2438:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq2->ss+1, ss); sq2->ss[0] = '\0';
data/infernal-1.1.3/easel/esl_sq.c:2709:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq2->seq, testseq);
data/infernal-1.1.3/easel/esl_sq.c:2772:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sq2->ss+1, ss);
data/infernal-1.1.3/easel/esl_sq.h:161:97: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
extern int esl_sq_FormatName (ESL_SQ *sq, const char *name, ...) ESL_ATTRIBUTE_FORMAT(printf, 2, 3);
data/infernal-1.1.3/easel/esl_sq.h:162:97: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
extern int esl_sq_FormatAccession(ESL_SQ *sq, const char *acc, ...) ESL_ATTRIBUTE_FORMAT(printf, 2, 3);
data/infernal-1.1.3/easel/esl_sq.h:163:97: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
extern int esl_sq_FormatDesc (ESL_SQ *sq, const char *desc, ...) ESL_ATTRIBUTE_FORMAT(printf, 2, 3);
data/infernal-1.1.3/easel/esl_sq.h:164:97: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
extern int esl_sq_FormatSource (ESL_SQ *sq, const char *source, ...) ESL_ATTRIBUTE_FORMAT(printf, 2, 3);
data/infernal-1.1.3/easel/esl_sqio.c:167:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sqfp->filename, filename);
data/infernal-1.1.3/easel/esl_sqio.c:191:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(list + 2, s1);
data/infernal-1.1.3/easel/esl_sqio.c:199:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(path, s1);
data/infernal-1.1.3/easel/esl_sqio.c:201:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(path+n+1, filename);
data/infernal-1.1.3/easel/esl_sqio.c:1180:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cache->filename, seqfile);
data/infernal-1.1.3/easel/esl_sqio.c:1209:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(c->name, sq->name);
data/infernal-1.1.3/easel/esl_sqio.c:1216:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(c->acc, sq->acc);
data/infernal-1.1.3/easel/esl_sqio.c:1223:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(c->desc, sq->desc);
data/infernal-1.1.3/easel/esl_sqio.c:1401:24: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(msa->aseq[0], sq->seq);
data/infernal-1.1.3/easel/esl_sqio.c:1851:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(ssifile, "%s.ssi", tmpfile);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:221:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(cmd, "gzip -dc %s", filename);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:222:21: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ascii->fp = popen(cmd, "r");
data/infernal-1.1.3/easel/esl_sqio_ascii.c:759:12: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ascii->errbuf, ascii->afp->errmsg); /* errbufs same size! */
data/infernal-1.1.3/easel/esl_sqio_ascii.c:854:11: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ascii->errbuf, ascii->afp->errmsg); /* errbufs same size! */
data/infernal-1.1.3/easel/esl_sqio_ascii.c:957:11: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ascii->errbuf, ascii->afp->errmsg); /* errbufs same size! */
data/infernal-1.1.3/easel/esl_sqio_ascii.c:1136:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ascii->errbuf, ascii->afp->errmsg); /* errbufs same size! */
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:268:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(name, filename);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:337:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(name, filename);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:350:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dbname, filename);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:426:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ncbi->vols[vol].name, dbptr);
data/infernal-1.1.3/easel/esl_ssi.c:1093:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", ns->ptmpfile, ns->ptmpfile);
data/infernal-1.1.3/easel/esl_ssi.c:1094:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (system(cmd) != 0) ESL_XFAIL(eslESYS, ns->errbuf, "external sort of primary keys failed");
data/infernal-1.1.3/easel/esl_ssi.c:1099:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", ns->stmpfile, ns->stmpfile);
data/infernal-1.1.3/easel/esl_ssi.c:1100:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (system(cmd) != 0) ESL_XFAIL(eslESYS, ns->errbuf, "external sort of secondary keys failed");
data/infernal-1.1.3/easel/miniapps/esl-afetch.c:30:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:265:4: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf("%-6d %-20s %10s %7d %7" PRId64 " %12" PRId64,
data/infernal-1.1.3/easel/miniapps/esl-mask.c:26:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/miniapps/esl-selectn.c:32:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/miniapps/esl-seqrange.c:28:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/miniapps/esl-seqstat.c:53:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/miniapps/esl-seqstat.c:173:6: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf("%-30s %6" PRId64, sq->name, sq->L);
data/infernal-1.1.3/easel/miniapps/esl-sfetch.c:31:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/miniapps/esl-shuffle.c:77:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:2889:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ps->modelname, curstr);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:3086:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(newstr, curstr);
data/infernal-1.1.3/easel/miniapps/esl-weight.c:43:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:126:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/hmmer/profmark/rocplot.c:121:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/hmmer/src/cachedb.c:121:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cache->id, ptr);
data/infernal-1.1.3/hmmer/src/cachedb.c:194:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(hdr_ptr, buffer);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:129:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cache->id, ptr);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:207:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(hdr_ptr, buffer);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:406:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cache->id, ptr);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:506:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(hdr_ptr, buffer);
data/infernal-1.1.3/hmmer/src/errors.c:32:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/hmmer/src/errors.c:50:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/hmmer/src/generic_fwdback_rescaled.c:308:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_RF) strcpy(gm->rf, hmm->rf);
data/infernal-1.1.3/hmmer/src/generic_fwdback_rescaled.c:309:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_MMASK) strcpy(gm->mm, hmm->mm);
data/infernal-1.1.3/hmmer/src/generic_fwdback_rescaled.c:310:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_CONS) strcpy(gm->consensus, hmm->consensus); /* must be present, actually, so the flag test is just for symmetry w/ other optional HMM fields */
data/infernal-1.1.3/hmmer/src/generic_fwdback_rescaled.c:311:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_CS) strcpy(gm->cs, hmm->cs);
data/infernal-1.1.3/hmmer/src/hmmalign.c:52:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stdout, format, argp);
data/infernal-1.1.3/hmmer/src/hmmbuild.c:361:44: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
apply_fixed_gap_params(P7_HMM *hmm, double popen, double pextend){
data/infernal-1.1.3/hmmer/src/hmmbuild.c:365:10: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (popen != -1) {
data/infernal-1.1.3/hmmer/src/hmmbuild.c:366:39: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[k][p7H_MM] = 1.0 - 2 * popen;
data/infernal-1.1.3/hmmer/src/hmmbuild.c:367:29: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[k][p7H_MI] = popen;
data/infernal-1.1.3/hmmer/src/hmmbuild.c:368:29: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[k][p7H_MD] = popen;
data/infernal-1.1.3/hmmer/src/hmmbuild.c:381:7: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (popen != -1) {
data/infernal-1.1.3/hmmer/src/hmmbuild.c:382:36: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[hmm->M][p7H_MM] = 1.0 - popen;
data/infernal-1.1.3/hmmer/src/hmmbuild.c:504:20: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
double popen;
data/infernal-1.1.3/hmmer/src/hmmbuild.c:595:133: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (esl_opt_IsOn(go, "--mxfile")) status = p7_builder_SetScoreSystem (info[i].bld, esl_opt_GetString(go, "--mxfile"), NULL, popen, pextend, info[i].bg);
data/infernal-1.1.3/hmmer/src/hmmbuild.c:596:133: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else status = p7_builder_LoadScoreSystem(info[i].bld, mx, popen, pextend, info[i].bg);
data/infernal-1.1.3/hmmer/src/hmmbuild.c:599:69: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (esl_opt_IsUsed(go, "--popen") ) info[i].bld->popen = popen;
data/infernal-1.1.3/hmmer/src/hmmbuild.c:891:7: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
if (vfprintf(stderr, format, argp) < 0) exit(eslEWRITE);
data/infernal-1.1.3/hmmer/src/hmmbuild.c:962:69: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if ((status = esl_sq_FetchFromMSA(msa, 0, &sq)) != eslOK) { strcpy(errmsg, bld->errbuf); goto ERROR; }
data/infernal-1.1.3/hmmer/src/hmmbuild.c:963:90: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if ((status = p7_SingleBuilder(bld, sq, bg, &hmm, NULL, NULL, NULL)) != eslOK) { strcpy(errmsg, bld->errbuf); goto ERROR; }
data/infernal-1.1.3/hmmer/src/hmmbuild.c:968:98: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if ((status = p7_Builder(bld, msa, bg, &hmm, NULL, NULL, NULL, postmsa_ptr)) != eslOK) { strcpy(errmsg, bld->errbuf); goto ERROR; }
data/infernal-1.1.3/hmmer/src/hmmbuild.c:1048:24: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (info->bld->popen != -1 || info->bld->pextend != -1) {
data/infernal-1.1.3/hmmer/src/hmmbuild.c:1049:50: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
apply_fixed_gap_params(hmm, info->bld->popen, info->bld->pextend);
data/infernal-1.1.3/hmmer/src/hmmbuild.c:1243:24: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (info->bld->popen != -1 || info->bld->pextend != -1) {
data/infernal-1.1.3/hmmer/src/hmmbuild.c:1244:56: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
apply_fixed_gap_params(item->hmm, info->bld->popen, info->bld->pextend);
data/infernal-1.1.3/hmmer/src/hmmc2.c:237:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(serv_ip, argv[i+1]);
data/infernal-1.1.3/hmmer/src/hmmc2.c:310:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(seq, buffer);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:140:16: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
s.msg_size = vsnprintf(ebuf, sizeof(ebuf), format, ap) +1; /* +1 because we send the \0 */
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1038:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(parms->ip_addr, data->ip_addr);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1323:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(parms->ip_addr, data->ip_addr);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1707:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p, parent->seq_db->name);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1719:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p, parent->hmm_db->name);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:160:16: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
s.msg_size = vsnprintf(ebuf, sizeof(ebuf), format, ap) +1; /* +1 because we send the \0 */
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1077:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(parms->ip_addr, data->ip_addr);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1362:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(parms->ip_addr, data->ip_addr);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1747:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p, parent->seq_db->name);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1761:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(p, parent->hmm_db->name);
data/infernal-1.1.3/hmmer/src/hmmdutils.c:177:3: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(format, ap);
data/infernal-1.1.3/hmmer/src/hmmemit.c:131:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stdout, format, argp);
data/infernal-1.1.3/hmmer/src/hmmer.h:1302:24: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
double popen; /* gap open probability */
data/infernal-1.1.3/hmmer/src/hmmer.h:1507:108: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
extern int p7_builder_LoadScoreSystem(P7_BUILDER *bld, const char *matrix, double popen, double pextend, P7_BG *bg);
data/infernal-1.1.3/hmmer/src/hmmer.h:1508:108: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
extern int p7_builder_SetScoreSystem (P7_BUILDER *bld, const char *mxfile, const char *env, double popen, double pextend, P7_BG *bg);
data/infernal-1.1.3/hmmer/src/hmmer.h:1770:43: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ESL_DMATRIX *P, float *f, double popen, double pextend,
data/infernal-1.1.3/hmmer/src/hmmfetch.c:30:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/hmmer/src/hmmscan.c:582:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/hmmer/src/hmmsearch.c:667:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/hmmer/src/hmmsim.c:452:61: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (status == eslEOD) { xstatus = status; sprintf(errbuf, "read failed, HMM file %s may be truncated?", cfg->hmmfile); }
data/infernal-1.1.3/hmmer/src/hmmsim.c:453:61: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (status == eslEFORMAT) { xstatus = status; sprintf(errbuf, "bad file format in HMM file %s", cfg->hmmfile); }
data/infernal-1.1.3/hmmer/src/hmmsim.c:454:61: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (status == eslEINCOMPAT) { xstatus = status; sprintf(errbuf, "HMM file %s contains different alphabets", cfg->hmmfile); }
data/infernal-1.1.3/hmmer/src/hmmsim.c:455:61: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (status != eslEOF) { xstatus = status; sprintf(errbuf, "Unexpected error in reading HMMs from %s", cfg->hmmfile); }
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:1038:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->rf, gm->rf);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:1039:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->mm, gm->mm);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:1040:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->cs, gm->cs);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:1041:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->consensus, gm->consensus);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:953:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->rf, gm->rf);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:954:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->mm, gm->mm);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:955:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->cs, gm->cs);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:956:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(om->consensus, gm->consensus);
data/infernal-1.1.3/hmmer/src/jackhmmer.c:844:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:652:17: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(meta->seq_data[numseqs].name, block->list[i].name );
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:654:17: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(meta->seq_data[numseqs].acc, block->list[i].acc );
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:656:17: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(meta->seq_data[numseqs].source, block->list[i].source );
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:658:17: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
else strcpy(meta->seq_data[numseqs].desc, block->list[i].desc );
data/infernal-1.1.3/hmmer/src/modelconfig.c:77:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_RF) strcpy(gm->rf, hmm->rf);
data/infernal-1.1.3/hmmer/src/modelconfig.c:78:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_MMASK) strcpy(gm->mm, hmm->mm);
data/infernal-1.1.3/hmmer/src/modelconfig.c:79:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_CONS) strcpy(gm->consensus, hmm->consensus); /* must be present, actually, so the flag test is just for symmetry w/ other optional HMM fields */
data/infernal-1.1.3/hmmer/src/modelconfig.c:80:31: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (hmm->flags & p7H_CS) strcpy(gm->cs, hmm->cs);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:169:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->hmmname, om->name);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:170:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (om->acc != NULL) strcpy(ad->hmmacc, om->acc); else ad->hmmacc[0] = 0;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:171:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (om->desc != NULL) strcpy(ad->hmmdesc, om->desc); else ad->hmmdesc[0] = 0;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:173:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqname, sq->name);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:174:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqacc, sq->acc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:175:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqdesc, sq->desc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:604:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->rfline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:610:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->mmline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:616:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->csline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:621:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->model);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:625:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->mline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:630:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->aseq);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:636:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->ntseq);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:642:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->ppline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:647:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->hmmname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:651:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->hmmacc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:655:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->hmmdesc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:659:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->sqname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:663:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->sqacc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:667:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->sqdesc);
data/infernal-1.1.3/hmmer/src/p7_builder.c:196:72: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
p7_builder_LoadScoreSystem(P7_BUILDER *bld, const char *matrix, double popen, double pextend, P7_BG *bg)
data/infernal-1.1.3/hmmer/src/p7_builder.c:228:18: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bld->popen = popen;
data/infernal-1.1.3/hmmer/src/p7_builder.c:283:88: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
p7_builder_SetScoreSystem(P7_BUILDER *bld, const char *mxfile, const char *env, double popen, double pextend, P7_BG *bg)
data/infernal-1.1.3/hmmer/src/p7_builder.c:327:18: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bld->popen = popen;
data/infernal-1.1.3/hmmer/src/p7_builder.c:506:85: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((status = p7_Seqmodel(bld->abc, sq->dsq, sq->n, sq->name, bld->Q, bg->f, bld->popen, bld->pextend, &hmm)) != eslOK) goto ERROR;
data/infernal-1.1.3/hmmer/src/p7_hit.c:326:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->name);
data/infernal-1.1.3/hmmer/src/p7_hit.c:331:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->acc);
data/infernal-1.1.3/hmmer/src/p7_hit.c:337:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy((char *) ptr, obj->desc);
data/infernal-1.1.3/hmmer/src/p7_hit.c:521:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ret_obj->name, (char *) ptr);
data/infernal-1.1.3/hmmer/src/p7_hit.c:534:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ret_obj->acc, (char *) ptr);
data/infernal-1.1.3/hmmer/src/p7_hit.c:551:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ret_obj->desc, (char *) ptr);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:416:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(hmm->name, name);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:454:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(hmm->acc, acc);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:487:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(hmm->desc, desc);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:532:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(hmm->comlog, argv[i]);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:535:3: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(hmm->comlog, argv[argc-1]);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:323:19: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((hfp->f = popen(cmd, "r")) == NULL) ESL_XFAIL(eslENOTFOUND, errbuf, "gzip -dc %s failed; gzip not installed or not in PATH?", filename);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:789:54: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (format == p7_HMMFILE_3f) { if ((offset = sprintf(ret_hmm, "HMMER3/f [%s | %s]\n", HMMER_VERSION, HMMER_DATE)) < 0) return eslEWRITE; }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:790:54: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (format == p7_HMMFILE_3e) { if ((offset = sprintf(ret_hmm, "HMMER3/e [%s | %s; reverse compatibility mode]\n", HMMER_VERSION, HMMER_DATE)) < 0) return eslEWRITE; }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:791:54: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (format == p7_HMMFILE_3d) { if ((offset = sprintf(ret_hmm, "HMMER3/d [%s | %s; reverse compatibility mode]\n", HMMER_VERSION, HMMER_DATE)) < 0) return eslEWRITE; }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:792:54: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (format == p7_HMMFILE_3c) { if ((offset = sprintf(ret_hmm, "HMMER3/c [%s | %s; reverse compatibility mode]\n", HMMER_VERSION, HMMER_DATE)) < 0) return eslEWRITE; }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:793:54: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (format == p7_HMMFILE_3b) { if ((offset = sprintf(ret_hmm, "HMMER3/b [%s | %s; reverse compatibility mode]\n", HMMER_VERSION, HMMER_DATE)) < 0) return eslEWRITE; }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:794:54: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
else if (format == p7_HMMFILE_3a) { if ((offset = sprintf(ret_hmm, "HMMER3/a [%s | %s; reverse compatibility mode]\n", HMMER_VERSION, HMMER_DATE)) < 0) return eslEWRITE; }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:798:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm + coffset, "NAME %s\n", hmm->name)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:802:18: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if((offset = sprintf(ret_hmm + coffset, "ACC %s\n", hmm->acc)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:807:19: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm + coffset, "DESC %s\n", hmm->desc)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:819:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm + coffset, "ALPH %s\n", esl_abc_DecodeType(hmm->abc->type))) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:822:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm+coffset, "RF %s\n", (hmm->flags & p7H_RF) ? "yes" : "no")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:826:19: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm+coffset, "MM %s\n", (hmm->flags & p7H_MMASK) ? "yes" : "no")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:831:18: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if((offset = sprintf(ret_hmm+coffset, "CONS %s\n", (hmm->flags & p7H_CONS) ? "yes" : "no")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:835:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm+coffset, "CS %s\n", (hmm->flags & p7H_CS) ? "yes" : "no")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:838:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm+coffset, "MAP %s\n", (hmm->flags & p7H_MAP) ? "yes" : "no")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:842:20: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if((offset = sprintf(ret_hmm + coffset, "DATE %s\n", hmm->ctime)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:915:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm + coffset, " %8s %8s %8s %8s %8s %8s %8s\n",
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:966:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(ret_hmm + coffset, " %6s", "-")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2116:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(*ret_str + *coffset, "%s [%d] ", pfx, nline++)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2124:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if ((offset = sprintf(*ret_str + *coffset, "%s [%d] %s\n", pfx, nline++, sptr)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2165:28: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if (p == 0.0) { if (sprintf(*str+offset, " %*s", fieldwidth, "*") < 0) return( eslEWRITE ); }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2383:33: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (format < p7_HMMFILE_3e) { strcpy(new->consensus, hmm->consensus); }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2397:33: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (format < p7_HMMFILE_3e) { strcpy(new->consensus, hmm->consensus); }
data/infernal-1.1.3/hmmer/src/p7_profile.c:176:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dst->rf, src->rf); /* RF is optional: if it's not set, *rf=0, and strcpy still works fine */
data/infernal-1.1.3/hmmer/src/p7_profile.c:177:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dst->mm, src->mm); /* MM is also optional annotation */
data/infernal-1.1.3/hmmer/src/p7_profile.c:178:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dst->cs, src->cs); /* CS is also optional annotation */
data/infernal-1.1.3/hmmer/src/p7_profile.c:179:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dst->consensus, src->consensus); /* consensus though is always present on a valid profile */
data/infernal-1.1.3/hmmer/src/phmmer.c:726:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/hmmer/src/seqmodel.c:49:39: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ESL_DMATRIX *Q, float *f, double popen, double pextend,
data/infernal-1.1.3/hmmer/src/seqmodel.c:67:37: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[k][p7H_MM] = 1.0 - 2 * popen;
data/infernal-1.1.3/hmmer/src/seqmodel.c:68:27: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[k][p7H_MI] = popen;
data/infernal-1.1.3/hmmer/src/seqmodel.c:69:27: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[k][p7H_MD] = popen;
data/infernal-1.1.3/hmmer/src/seqmodel.c:79:29: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
hmm->t[M][p7H_MM] = 1.0 - popen;
data/infernal-1.1.3/hmmer/src/seqmodel.c:205:63: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
p7_Seqmodel(abc, qsq->dsq, qsq->n, qsq->name, Q, bg->f, popen, pextend, &hmm);
data/infernal-1.1.3/hmmer/src/seqmodel.c:253:52: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ( p7_builder_LoadScoreSystem(bld, "BLOSUM62", popen, pextend, bg) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/seqmodel.c:254:63: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ( p7_Seqmodel(abc, dsq, L, "aatest", bld->Q, bg->f, bld->popen, bld->pextend, &hmm) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/rmark/rmark-create.c:148:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/rmark/rmark-rocplot.c:149:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/src/cm.c:2595:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cm->name, name);
data/infernal-1.1.3/src/cm.c:2633:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cm->acc, acc);
data/infernal-1.1.3/src/cm.c:2666:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cm->desc, desc);
data/infernal-1.1.3/src/cm.c:2793:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(cm->comlog, argv[i]);
data/infernal-1.1.3/src/cm.c:2796:3: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(cm->comlog, argv[argc-1]);
data/infernal-1.1.3/src/cm.c:2801:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(cm->comlog, seedstr);
data/infernal-1.1.3/src/cm_alidisplay.c:289:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->cmname, cm->name);
data/infernal-1.1.3/src/cm_alidisplay.c:290:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (cm->acc != NULL) strcpy(ad->cmacc, cm->acc); else ad->cmacc[0] = 0;
data/infernal-1.1.3/src/cm_alidisplay.c:291:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (cm->desc != NULL) strcpy(ad->cmdesc, cm->desc); else ad->cmdesc[0] = 0;
data/infernal-1.1.3/src/cm_alidisplay.c:292:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqname, sq->name);
data/infernal-1.1.3/src/cm_alidisplay.c:293:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqacc, sq->acc);
data/infernal-1.1.3/src/cm_alidisplay.c:294:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqdesc, sq->desc);
data/infernal-1.1.3/src/cm_alidisplay.c:297:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->aseq_el, tmpmsa->aseq[0]);
data/infernal-1.1.3/src/cm_alidisplay.c:298:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->rfline_el, tmpmsa->rf);
data/infernal-1.1.3/src/cm_alidisplay.c:299:20: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if(adata->ppstr) strcpy(ad->ppline_el, tmpmsa->pp[0]);
data/infernal-1.1.3/src/cm_alidisplay.c:328:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(ad->aseq+pos, "<[%*s]*", wtrunc_R-4, "0");
data/infernal-1.1.3/src/cm_alidisplay.c:585:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(ad->aseq+pos, "*[%*s]>", wtrunc_L-4, "0");
data/infernal-1.1.3/src/cm_alidisplay.c:740:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->cmname, cm->name);
data/infernal-1.1.3/src/cm_alidisplay.c:741:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (cm->acc != NULL) strcpy(ad->cmacc, cm->acc); else ad->cmacc[0] = 0;
data/infernal-1.1.3/src/cm_alidisplay.c:742:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if (cm->desc != NULL) strcpy(ad->cmdesc, cm->desc); else ad->cmdesc[0] = 0;
data/infernal-1.1.3/src/cm_alidisplay.c:743:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqname, sq->name);
data/infernal-1.1.3/src/cm_alidisplay.c:744:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqacc, sq->acc);
data/infernal-1.1.3/src/cm_alidisplay.c:745:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->sqdesc, sq->desc);
data/infernal-1.1.3/src/cm_alidisplay.c:748:20: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if(p7ad->rfline) strcpy(ad->rfline, p7ad->rfline);
data/infernal-1.1.3/src/cm_alidisplay.c:749:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->csline, p7ad->csline);
data/infernal-1.1.3/src/cm_alidisplay.c:750:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->model, p7ad->model);
data/infernal-1.1.3/src/cm_alidisplay.c:751:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->mline, p7ad->mline);
data/infernal-1.1.3/src/cm_alidisplay.c:752:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ad->aseq, p7ad->aseq);
data/infernal-1.1.3/src/cm_alidisplay.c:753:20: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if(p7ad->ppline) strcpy(ad->ppline, p7ad->ppline);
data/infernal-1.1.3/src/cm_file.c:304:22: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if ((cmfp->f = popen(cmd, "r")) == NULL) ESL_XFAIL(eslENOTFOUND, errbuf, "gzip -dc %s failed; gzip not installed or not in PATH?", filename);
data/infernal-1.1.3/src/cm_p7_modelmaker.c:190:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cm->mlp7->rf, cm->rf);
data/infernal-1.1.3/src/cm_parsetree.c:1172:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(msa->au, "Infernal %s", INFERNAL_VERSION);
data/infernal-1.1.3/src/cm_tophits.c:2468:9: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(any_oidxstr, "%" PRId64, ao);
data/infernal-1.1.3/src/cm_tophits.c:2487:9: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(win_oidxstr, "%" PRId64, wo);
data/infernal-1.1.3/src/cmalign.c:1332:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/src/cmbuild.c:2090:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
{ strcpy(errbuf, cfg->fp7_bld->errbuf); return status; }
data/infernal-1.1.3/src/cmbuild.c:2100:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(fhmm->rf, cm->rf);
data/infernal-1.1.3/src/cmbuild.c:2106:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(fhmm->cs+1, cm->cmcons->cstr); /* careful: off-by-one */
data/infernal-1.1.3/src/cmcalibrate.c:1321:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/src/cmcalibrate.c:1496:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(cfg->tmpfile, cfg->cmfile);
data/infernal-1.1.3/src/cmemit.c:365:28: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if(cm->name != NULL) sprintf(name, "%s-sample%d", cm->name, i+offset);
data/infernal-1.1.3/src/cmemit.c:515:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if(cm->name != NULL) sprintf(name, "%s-sample%d", cm->name, i+offset);
data/infernal-1.1.3/src/cmemit.c:539:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if(cm->name != NULL) sprintf(name, "%s-sample%d", cm->name, i+offset);
data/infernal-1.1.3/src/cmfetch.c:33:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/src/cmscan.c:2711:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest_sq->name, src_sq->name);
data/infernal-1.1.3/src/cmscan.c:2719:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest_sq->desc, src_sq->desc);
data/infernal-1.1.3/src/cmscan.c:2727:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest_sq->acc, src_sq->acc);
data/infernal-1.1.3/src/cmscan.c:2906:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/src/cmsearch.c:2240:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tmp_filename, (*dbfp_ptr)->filename);
data/infernal-1.1.3/src/cmsearch.c:2262:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tmp_filename, (*dbfp_ptr)->filename);
data/infernal-1.1.3/src/cmsearch.c:2503:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf(str, sizeof(str), format, argp);
data/infernal-1.1.3/src/cp9_trace.c:1269:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(msa->au, "Infernal %s", INFERNAL_VERSION);
data/infernal-1.1.3/src/errors.c:43:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/src/errors.c:62:3: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, argp);
data/infernal-1.1.3/easel/easel.c:1878:12: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if ((s = getenv(env)) == NULL) return eslENOTFOUND;
data/infernal-1.1.3/easel/easel.c:1986:16: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
tmpdir = getenv("TMPDIR");
data/infernal-1.1.3/easel/easel.c:1987:36: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if (tmpdir == NULL) tmpdir = getenv("TMP");
data/infernal-1.1.3/easel/esl_getopts.c:477:12: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
(optarg = getenv(g->opt[i].envvar)) != NULL)
data/infernal-1.1.3/easel/esl_sqio.c:189:17: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if ((s1 = getenv(env)) == NULL) { status = eslENOTFOUND; goto ERROR; }
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:518:3: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand(time(0)); // reseed randomness
data/infernal-1.1.3/hmmer/src/p7_tophits.c:2004:7: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if (getenv("SOURCE_DATE_EPOCH") != NULL) {
data/infernal-1.1.3/src/cm.c:2852:21: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char *sde = getenv("SOURCE_DATE_EPOCH");
data/infernal-1.1.3/src/cm_tophits.c:2783:7: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if (getenv("SOURCE_DATE_EPOCH") != NULL) {
data/infernal-1.1.3/easel/easel.c:898:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((*dest)+len1, src, len2);
data/infernal-1.1.3/easel/easel.c:1609:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename, "r"))) { fclose(fp); return TRUE; }
data/infernal-1.1.3/easel/easel.c:1889:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(path, "r")) != NULL) break;
data/infernal-1.1.3/easel/easel.c:1993:13: [2] (tmpfile) mkstemp:
Potential for temporary file vulnerability in some circumstances. Some
older Unix-like systems create temp files with permission to write by all
by default, so be sure to set the umask to override this. Also, some older
Unix systems might fail to use O_EXCL when opening the file, so make sure
that O_EXCL is used by the library (CWE-377).
if ((fd = mkstemp(path)) < 0) ESL_XEXCEPTION(eslESYS, "mkstemp() failed.");
data/infernal-1.1.3/easel/easel.c:2070:13: [2] (tmpfile) mkstemp:
Potential for temporary file vulnerability in some circumstances. Some
older Unix-like systems create temp files with permission to write by all
by default, so be sure to set the umask to override this. Also, some older
Unix systems might fail to use O_EXCL when opening the file, so make sure
that O_EXCL is used by the library (CWE-377).
if ((fd = mkstemp(basename6X)) < 0) return eslFAIL;
data/infernal-1.1.3/easel/easel.c:2472:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/easel.c:2472:9: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/easel.c:2480:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2484:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (! esl_FileExists(tmpfile)) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2488:12: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (stat(tmpfile, &st) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2490:13: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (chmod(tmpfile, mode) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2491:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_FileExists(tmpfile)) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2494:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/easel.c:2495:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_FileExists(tmpfile)) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2502:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/easel.c:2502:9: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/easel.c:2504:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/infernal-1.1.3/easel/easel.c:2506:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2509:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2509:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/easel.c:2513:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/easel.c:2604:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX"; /* a transient, secure tmpfile: 6 X's are important */
data/infernal-1.1.3/easel/easel.c:2605:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX"; /* a named tmpfile */
data/infernal-1.1.3/easel/easel.c:2607:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/infernal-1.1.3/easel/easel.c:2624:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(tmpfile2, "r");
data/infernal-1.1.3/easel/esl_alphabet.c:792:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dcopy, dsq, sizeof(ESL_DSQ) * (L+2));
data/infernal-1.1.3/easel/esl_alphabet.c:833:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new, dsq, sizeof(ESL_DSQ) * (L+2));
data/infernal-1.1.3/easel/esl_buffer.c:205:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((bf->fp = fopen(filename, "rb")) == NULL)
data/infernal-1.1.3/easel/esl_buffer.c:1080:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(p, bf->mem+bf->pos, nc);
data/infernal-1.1.3/easel/esl_buffer.c:1146:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(s, bf->mem+bf->pos, nc);
data/infernal-1.1.3/easel/esl_buffer.c:1343:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(tok, bf->mem+bf->pos, nc);
data/infernal-1.1.3/easel/esl_buffer.c:1426:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(tok, bf->mem+bf->pos, nc);
data/infernal-1.1.3/easel/esl_buffer.c:1502:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(p, bf->mem+bf->pos, nbytes);
data/infernal-1.1.3/easel/esl_buffer.c:1955:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/infernal-1.1.3/easel/esl_buffer.c:1976:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/infernal-1.1.3/easel/esl_buffer.c:1995:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/infernal-1.1.3/easel/esl_buffer.c:2023:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fd = open(filename, O_RDONLY);
data/infernal-1.1.3/easel/esl_buffer.c:2043:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fd = open(filename, O_RDONLY);
data/infernal-1.1.3/easel/esl_buffer.c:2057:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/infernal-1.1.3/easel/esl_buffer.c:2074:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/infernal-1.1.3/easel/esl_buffer.c:2091:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/infernal-1.1.3/easel/esl_buffer.c:2116:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/infernal-1.1.3/easel/esl_buffer.c:2199:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((bf->fp = fopen(filename, "rb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2230:48: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
create_testfile_lines(ESL_RANDOMNESS *r, char *tmpfile, int nlines)
data/infernal-1.1.3/easel/esl_buffer.c:2244:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2311:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_SetOffset(const char *tmpfile, int nlines_expected)
data/infernal-1.1.3/easel/esl_buffer.c:2325:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char gzipfile[32];
data/infernal-1.1.3/easel/esl_buffer.c:2326:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cmd[256];
data/infernal-1.1.3/easel/esl_buffer.c:2331:23: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_buffer_Open(tmpfile, NULL, &bf) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2354:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_buffer_Open(tmpfile, NULL, &bf) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2370:37: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
snprintf(gzipfile, 32, "%s.gz", tmpfile);
data/infernal-1.1.3/easel/esl_buffer.c:2371:59: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
snprintf(cmd, 256, "gzip -c %s 2>/dev/null > %s", tmpfile, gzipfile);
data/infernal-1.1.3/easel/esl_buffer.c:2376:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2376:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( (fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2406:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (buffer_OpenFileAs(tmpfile, eslBUFFER_FILE, &bf) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2430:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[8192];
data/infernal-1.1.3/easel/esl_buffer.c:2677:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_buffer.c:2677:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_buffer.c:2685:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2690:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_buffer_OpenFile (tmpfile, &bf) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2700:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_buffer.c:2705:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_OpenFile(const char *tmpfile, int nlines)
data/infernal-1.1.3/easel/esl_buffer.c:2715:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_OpenStream(const char *tmpfile, int nlines)
data/infernal-1.1.3/easel/esl_buffer.c:2727:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_OpenPipe(const char *tmpfile, int nlines)
data/infernal-1.1.3/easel/esl_buffer.c:2736:27: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_buffer_OpenPipe(tmpfile, badcmd, &bf) != eslFAIL || bf == NULL) esl_fatal(msg); else esl_buffer_Close(bf);
data/infernal-1.1.3/easel/esl_buffer.c:2817:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_buffer.c:2817:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_buffer.c:2823:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
create_testfile_lines(r, tmpfile, nlines);
data/infernal-1.1.3/easel/esl_buffer.c:2824:69: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (be_verbose) printf("created file %s; rng seed %" PRIu32 "\n", tmpfile, esl_randomness_GetSeed(r));
data/infernal-1.1.3/easel/esl_buffer.c:2826:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_OpenFile (tmpfile, nlines);
data/infernal-1.1.3/easel/esl_buffer.c:2827:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_OpenStream(tmpfile, nlines);
data/infernal-1.1.3/easel/esl_buffer.c:2828:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_OpenPipe (tmpfile, nlines);
data/infernal-1.1.3/easel/esl_buffer.c:2830:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_SetOffset (tmpfile, nlines);
data/infernal-1.1.3/easel/esl_buffer.c:2841:37: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
case 0: if (esl_buffer_OpenFile (tmpfile, &bf) != eslOK) esl_fatal(msg); break;
data/infernal-1.1.3/easel/esl_buffer.c:2842:37: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
case 1: if ( buffer_OpenFileAs(tmpfile, eslBUFFER_ALLFILE, &bf) != eslOK) esl_fatal(msg); break;
data/infernal-1.1.3/easel/esl_buffer.c:2843:37: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
case 2: if ( buffer_OpenFileAs(tmpfile, eslBUFFER_MMAP, &bf) != eslOK) esl_fatal(msg); break;
data/infernal-1.1.3/easel/esl_buffer.c:2844:37: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
case 3: if ( buffer_OpenFileAs(tmpfile, eslBUFFER_FILE, &bf) != eslOK) esl_fatal(msg); break;
data/infernal-1.1.3/easel/esl_buffer.c:2846:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "rb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2846:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "rb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2850:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_buffer_OpenPipe(tmpfile, cmdfmt, &bf) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2853:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_buffer_OpenFile(tmpfile, &bftmp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2884:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_buffer.c:3035:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_buffer.c:3035:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_buffer.c:3038:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/infernal-1.1.3/easel/esl_buffer.c:3044:21: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
esl_tmpfile_named(tmpfile, &fp);
data/infernal-1.1.3/easel/esl_buffer.c:3049:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
status = esl_buffer_Open(tmpfile, NULL, &bf);
data/infernal-1.1.3/easel/esl_buffer.h:38:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errmsg[eslERRBUFSIZE]; /* error message storage */
data/infernal-1.1.3/easel/esl_dmatrix.c:180:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest->mx[0], src->mx[0], src->ncells * sizeof(double));
data/infernal-1.1.3/easel/esl_dsqdata.c:164:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[4096];
data/infernal-1.1.3/easel/esl_dsqdata.c:201:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( dd->ifp = fopen(dd->basename, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open index file %s\n", dd->basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:204:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( dd->mfp = fopen(dd->basename, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open metadata file %s\n", dd->basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:207:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( dd->sfp = fopen(dd->basename, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open sequence file %s\n", dd->basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:210:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( dd->stubfp = fopen(dd->basename, "r")) == NULL) ESL_XFAIL(eslENOTFOUND, dd->errbuf, "Failed to find or open stub file %s\n", dd->basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:635:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( ifp = fopen(outfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata index file %s for writing", outfile);
data/infernal-1.1.3/easel/esl_dsqdata.c:637:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( mfp = fopen(outfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata metadata file %s for writing", outfile);
data/infernal-1.1.3/easel/esl_dsqdata.c:639:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( sfp = fopen(outfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata sequence file %s for writing", outfile);
data/infernal-1.1.3/easel/esl_dsqdata.c:640:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( stubfp = fopen(basename, "w")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "failed to open dsqdata stub file %s for writing", basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:1544:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_dsqdata.c:1544:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_dsqdata.c:1545:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char basename[32];
data/infernal-1.1.3/easel/esl_dsqdata.c:1561:36: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (( status = esl_tmpfile_named(tmpfile, &tmpfp)) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_dsqdata.c:1574:46: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (( status = esl_sqfile_OpenDigital(abc, tmpfile, eslSQFILE_FASTA, NULL, &sqfp)) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_dsqdata.c:1575:50: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (( snprintf(basename, 32, "%s-db", tmpfile)) <= 0) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_dsqdata.c:1598:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_dsqdata.c:1600:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
snprintf(basename, 32, "%s-db.dsqi", tmpfile); remove(basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:1601:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
snprintf(basename, 32, "%s-db.dsqm", tmpfile); remove(basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:1602:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
snprintf(basename, 32, "%s-db.dsqs", tmpfile); remove(basename);
data/infernal-1.1.3/easel/esl_dsqdata.c:1692:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_dsqdata.h:129:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; // User-directed error message in case of a failed open or read.
data/infernal-1.1.3/easel/esl_exponential.c:564:63: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (strcmp(argv[opti], "-n") == 0) n = atoi(argv[++opti]);
data/infernal-1.1.3/easel/esl_exponential.c:586:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(plotfile, "w")) == NULL) esl_fatal("Failed to open plotfile");
data/infernal-1.1.3/easel/esl_fileparser.c:67:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
else if ((efp->fp = fopen(filename, "r")) != NULL) {
data/infernal-1.1.3/easel/esl_fileparser.c:236:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
{ sprintf(efp->errbuf, "esl_strtok() failed"); return tokcode;}
data/infernal-1.1.3/easel/esl_fileparser.c:355:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(efp->buf, prefix, plen);
data/infernal-1.1.3/easel/esl_fileparser.c:546:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(efp->buf, efp->mem_buffer + efp->mem_pos, len);
data/infernal-1.1.3/easel/esl_fileparser.c:553:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
{ sprintf(efp->errbuf, "esl_fgets() failed"); return status;}
data/infernal-1.1.3/easel/esl_fileparser.c:583:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename, "r")) == NULL) esl_fatal("File open failed");
data/infernal-1.1.3/easel/esl_fileparser.c:613:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char expect[32];
data/infernal-1.1.3/easel/esl_fileparser.c:624:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(expect, "token%d", ntok);
data/infernal-1.1.3/easel/esl_fileparser.c:686:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_fileparser.c:686:9: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_fileparser.c:699:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal("File open failed");
data/infernal-1.1.3/easel/esl_fileparser.c:706:18: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_GetToken(tmpfile);
data/infernal-1.1.3/easel/esl_fileparser.c:707:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_GetTokenOnLine(tmpfile);
data/infernal-1.1.3/easel/esl_fileparser.c:710:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_fileparser.h:19:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for holding error diagnostics */
data/infernal-1.1.3/easel/esl_gamma.c:704:63: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (strcmp(argv[opti], "-n") == 0) n = atoi(argv[++opti]);
data/infernal-1.1.3/easel/esl_gamma.c:727:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(plotfile, "w")) == NULL) esl_fatal("Failed to open plotfile");
data/infernal-1.1.3/easel/esl_gencode.c:417:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char aas[65];
data/infernal-1.1.3/easel/esl_gencode.c:418:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char mline[65];
data/infernal-1.1.3/easel/esl_gencode.c:419:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char base1[65];
data/infernal-1.1.3/easel/esl_gencode.c:420:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char base2[65];
data/infernal-1.1.3/easel/esl_gencode.c:421:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char base3[65];
data/infernal-1.1.3/easel/esl_gencode.c:1038:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_gencode.c:1038:8: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_gencode.c:1050:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_gencode.c:1050:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_gencode.c:1054:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_gencode.c:1058:32: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_fileparser_Open(tmpfile, /*envvar=*/NULL, &efp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_gencode.c:1065:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_gencode.c:1119:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char codon[4];
data/infernal-1.1.3/easel/esl_gencode.h:16:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char desc[128]; // Description, or "". ... ditto
data/infernal-1.1.3/easel/esl_getopts.c:920:10: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return atoi(g->val[opti]);
data/infernal-1.1.3/easel/esl_getopts.c:1678:7: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
n = atoi(arg);
data/infernal-1.1.3/easel/esl_getopts.c:1683:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
lower = atoi(lp);
data/infernal-1.1.3/easel/esl_getopts.c:1688:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
upper = atoi(up);
data/infernal-1.1.3/easel/esl_getopts.c:1934:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char file1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_getopts.c:1935:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char file2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_getopts.c:1972:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((f1 = fopen(file1, "r")) == NULL) esl_fatal("getopts fopen() 1 failed");
data/infernal-1.1.3/easel/esl_getopts.c:1973:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((f2 = fopen(file2, "r")) == NULL) esl_fatal("getopts fopen() 2 failed");
data/infernal-1.1.3/easel/esl_getopts.h:70:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* buffer for reporting user error */
data/infernal-1.1.3/easel/esl_gev.c:660:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
do_test[atoi(argv[i])] = 1;
data/infernal-1.1.3/easel/esl_gev.c:664:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.1", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:679:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.2", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:700:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.3", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:715:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.4", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:736:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.5", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:751:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.6", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:773:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.7", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:781:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.8", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:789:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.9", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_gev.c:797:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen("stats.10", "w")) == NULL) abort();
data/infernal-1.1.3/easel/esl_heap.c:268:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_histogram.c:883:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[81]; /* output line buffer */
data/infernal-1.1.3/easel/esl_histogram.c:982:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%6.1f %6llu %6d|", x, (unsigned long long) h->obs[i], (int) h->expect[i]);
data/infernal-1.1.3/easel/esl_histogram.c:989:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%6.1f %6.2e %6.2e|", x, (double) h->obs[i], h->expect[i]);
data/infernal-1.1.3/easel/esl_histogram.c:1731:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfp = fopen(ascfile, "w");
data/infernal-1.1.3/easel/esl_histogram.c:1737:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfp = fopen(plotfile, "w");
data/infernal-1.1.3/easel/esl_histogram.c:1743:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfp = fopen(survfile, "w");
data/infernal-1.1.3/easel/esl_histogram.c:1749:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfp = fopen(qqfile, "w");
data/infernal-1.1.3/easel/esl_hmm.c:87:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dup->t[k], hmm->t[k], sizeof(float) * (hmm->M+1));
data/infernal-1.1.3/easel/esl_hmm.c:88:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dup->e[k], hmm->e[k], sizeof(float) * (hmm->abc->K));
data/infernal-1.1.3/easel/esl_hmm.c:92:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dup->eo[x], hmm->eo[x], sizeof(float) * (hmm->M));
data/infernal-1.1.3/easel/esl_hmm.c:94:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dup->pi, hmm->pi, sizeof(float) * (hmm->M+1));
data/infernal-1.1.3/easel/esl_huffman.c:1041:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(argv[1], "r");
data/infernal-1.1.3/easel/esl_hyperexp.c:572:8: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nc = atoi(tok);
data/infernal-1.1.3/easel/esl_hyperexp.c:574:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(e->errbuf, "Expected # of components K >= 1 as first token");
data/infernal-1.1.3/easel/esl_hyperexp.c:592:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(e->errbuf, "Expected a mixture coefficient q[k], 0<=q[k]<=1");
data/infernal-1.1.3/easel/esl_hyperexp.c:596:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(e->errbuf, "Expected a lambda parameter, lambda>0");
data/infernal-1.1.3/easel/esl_hyperexp.c:602:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(e->errbuf, "Expected mixture coefficients to sum to 1");
data/infernal-1.1.3/easel/esl_hyperexp.c:641:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename, "r")) == NULL)
data/infernal-1.1.3/easel/esl_hyperexp.c:1174:63: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
else if (strcmp(argv[opti], "-n") == 0) n = atoi(argv[++opti]);
data/infernal-1.1.3/easel/esl_hyperexp.c:1211:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(plotfile, "w")) == NULL)
data/infernal-1.1.3/easel/esl_json.c:1145:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_json.c:1219:79: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
struct tests_s { char *json; float trueval; float rtol; float atol; int status; }
data/infernal-1.1.3/easel/esl_json.c:1254:81: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
} else if (esl_FCompareNew(tests[i].trueval, val, tests[i].rtol, tests[i].atol) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_json.c:1269:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char s[32]; // randomly generated decimal string rep of a float
data/infernal-1.1.3/easel/esl_json.c:1270:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char sj[64]; // JSON string constructed from <s>, e.g. { "a" = 42.0 }
data/infernal-1.1.3/easel/esl_keyhash.c:104:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(nw->smem, kh->smem, sizeof(char) * kh->sn);
data/infernal-1.1.3/easel/esl_keyhash.c:542:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/infernal-1.1.3/easel/esl_keyhash.c:550:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(file1, "r")) == NULL)
data/infernal-1.1.3/easel/esl_keyhash.c:565:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(file2, "r")) == NULL)
data/infernal-1.1.3/easel/esl_keyhash.c:905:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/infernal-1.1.3/easel/esl_keyhash.c:911:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(argv[1], "r")) == NULL) esl_fatal("couldn't open %s\n", argv[1]);
data/infernal-1.1.3/easel/esl_keyhash.c:924:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(argv[2], "r")) == NULL) esl_fatal("couldn't open %s\n", argv[1]);
data/infernal-1.1.3/easel/esl_mem.c:714:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(s, p, n);
data/infernal-1.1.3/easel/esl_mem.c:737:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest, p, n);
data/infernal-1.1.3/easel/esl_mem.c:759:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char fixedbuf[128];
data/infernal-1.1.3/easel/esl_mem.c:765:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fixedbuf, p, sizeof(char) * n);
data/infernal-1.1.3/easel/esl_mem.c:773:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(bigbuf, p, sizeof(char) * n);
data/infernal-1.1.3/easel/esl_mem.c:800:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char fixedbuf[128];
data/infernal-1.1.3/easel/esl_mem.c:806:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fixedbuf, p, sizeof(char) * n);
data/infernal-1.1.3/easel/esl_mem.c:814:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(bigbuf, p, sizeof(char) * n);
data/infernal-1.1.3/easel/esl_mem.c:1122:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char s[32]; // random generated string representation of a float. Max len of slen+'.'+flen+'e'+"-xx" = 18.
data/infernal-1.1.3/easel/esl_mixdchlet.c:472:7: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
K = atoi(tok);
data/infernal-1.1.3/easel/esl_mixdchlet.c:476:7: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
Q = atoi(tok);
data/infernal-1.1.3/easel/esl_mixdchlet.c:719:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_mixdchlet.c:719:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_mixdchlet.c:736:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_mixdchlet.c:741:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_mixdchlet.c:741:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_mixdchlet.c:751:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_mixgev.c:746:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen("data.out", "w");
data/infernal-1.1.3/easel/esl_msa.c:273:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new_msa->ax[i], msa->ax[i], (msa->alen+2) * sizeof(ESL_DSQ));
data/infernal-1.1.3/easel/esl_msa.c:877:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf2[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_msa.c:1700:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(msa->gs[tagidx][sqidx]+n1+1, value, n2);
data/infernal-1.1.3/easel/esl_msa.c:2312:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new_msa->ax[nidx], msa->ax[oidx], sizeof(ESL_DSQ) * (msa->alen+2));
data/infernal-1.1.3/easel/esl_msa.c:3628:23: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_MinimGaps(char *tmpfile)
data/infernal-1.1.3/easel/esl_msa.c:3635:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(NULL, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3645:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(&abc, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3659:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_NoGaps(char *tmpfile)
data/infernal-1.1.3/easel/esl_msa.c:3666:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(NULL, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3677:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(&abc, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3741:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_SymConvert(char *tmpfile)
data/infernal-1.1.3/easel/esl_msa.c:3748:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(NULL, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3770:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(&abc, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3790:33: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_ZeroLengthMSA(const char *tmpfile)
data/infernal-1.1.3/easel/esl_msa.c:3801:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_msa.c:3804:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(NULL, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3828:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(&abc, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msa.c:3912:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX"; /* tmpfile template */
data/infernal-1.1.3/easel/esl_msa.c:3912:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX"; /* tmpfile template */
data/infernal-1.1.3/easel/esl_msa.c:3924:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal("failed to create tmpfile");
data/infernal-1.1.3/easel/esl_msa.c:3930:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(NULL, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal("Failed to open MSA tmp file");
data/infernal-1.1.3/easel/esl_msa.c:3941:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_MinimGaps(tmpfile);
data/infernal-1.1.3/easel/esl_msa.c:3942:16: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_NoGaps(tmpfile);
data/infernal-1.1.3/easel/esl_msa.c:3944:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_SymConvert(tmpfile);
data/infernal-1.1.3/easel/esl_msa.c:3945:23: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_ZeroLengthMSA(tmpfile);
data/infernal-1.1.3/easel/esl_msa.c:3951:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(&abc, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &mfp) != eslOK) esl_fatal("MSA digital open failed");
data/infernal-1.1.3/easel/esl_msa.c:3956:23: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_Digitize(abc, tmpfile);
data/infernal-1.1.3/easel/esl_msa.c:3957:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_Textize(abc, tmpfile);
data/infernal-1.1.3/easel/esl_msa.c:3965:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile.c:1281:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile.c:1282:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile.c:1283:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile3[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile.h:70:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errmsg[eslERRBUFSIZE]; /* user-directed message for normal errors */
data/infernal-1.1.3/easel/esl_msafile2.c:225:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((afp->f = fopen(filename, "r")) != NULL)
data/infernal-1.1.3/easel/esl_msafile2.c:1372:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile2.c:1372:17: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile2.c:1379:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile2.c:1401:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(NULL, tmpfile, NULL, eslMSAFILE_PFAM, NULL, &afp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile2.c:1409:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile2.c:1445:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile2.c:1445:16: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile2.c:1447:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal("failed to create tmpfile");
data/infernal-1.1.3/easel/esl_msafile2.c:1451:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_ReadInfoPfam(tmpfile);
data/infernal-1.1.3/easel/esl_msafile2.c:1452:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_RegurgitatePfam(tmpfile);
data/infernal-1.1.3/easel/esl_msafile2.c:1454:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile2.h:34:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* buffer for holding parse error info */
data/infernal-1.1.3/easel/esl_msafile_a2m.c:695:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:696:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:786:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char a2mfile2[32] = "esltmpa2m2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:787:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:835:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char a2mfile2[32] = "esltmpa2m2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:836:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:876:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char a2mfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:944:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char a2mfile[32] = "esltmpa2mXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:945:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile[32] = "esltmpstkXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_a2m.c:949:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_a2m.c:949:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_a2m.c:970:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_a2m.c:970:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_a2m.c:971:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_a2m.c:977:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_goodfile(tmpfile, testnumber, expected_alphatype, expected_nseq, expected_alen);
data/infernal-1.1.3/easel/esl_msafile_a2m.c:978:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_afa.c:280:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[61];
data/infernal-1.1.3/easel/esl_msafile_afa.c:351:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:352:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:442:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char afafile2[32] = "esltmpafa2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:443:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:491:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char afafile2[32] = "esltmpafa2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:492:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:562:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char afafile[32] = "esltmpafaXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:563:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile[32] = "esltmpstkXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_afa.c:567:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_afa.c:567:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_afa.c:586:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_afa.c:586:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_afa.c:587:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_afa.c:592:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_goodfile(tmpfile, testnumber, expected_alphatype, expected_nseq, expected_alen);
data/infernal-1.1.3/easel/esl_msafile_afa.c:593:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_clustal.c:684:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:685:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:775:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char alnfile2[32] = "esltmpaln2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:776:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:824:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char alnfile2[32] = "esltmpaln2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:825:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:895:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char alnfile[32] = "esltmpalnXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:896:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile[32] = "esltmpstkXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_clustal.c:900:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_clustal.c:900:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_clustal.c:919:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_clustal.c:919:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_clustal.c:920:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_clustal.c:927:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_goodfile(tmpfile, testnumber, expected_format, expected_alphatype, expected_nseq, expected_alen);
data/infernal-1.1.3/easel/esl_msafile_clustal.c:928:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1323:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "alignment length disagrees");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1336:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "first field isn't an integer");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1349:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "second field isn't an integer");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1362:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "only one field found");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1374:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "no alignment data");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1387:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "line too short");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1400:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "invalid character(s) in sequence name");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1413:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "one or more invalid sequence characters");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1426:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "number of residues on line differs from previous seqs");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1442:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected number of sequences in block");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1459:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "alignment length disagrees with header");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1496:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1497:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1603:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1603:9: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1617:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1617:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1618:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1624:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_msafile_Open(&abc, tmpfile, /*env=*/NULL, eslMSAFILE_UNKNOWN, /*fmtd=*/NULL, &afp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1637:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1683:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1683:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1690:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char expected_errmsg[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1695:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1695:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1696:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1707:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_goodfile(tmpfile, testnumber, expected_format, expected_alphatype, expected_nseq, expected_alen);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1708:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1714:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1714:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1715:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1732:21: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_badfile(tmpfile, testnumber, expected_alphatype, expected_errstatus, expected_linenumber, expected_errmsg);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1733:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1739:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1739:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1740:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1747:23: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_ambigfile(tmpfile, testnumber);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:1748:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:444:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:445:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:530:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char pbfile2[32] = "esltmppb2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:531:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:579:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char pbfile2[32] = "esltmppb2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:580:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:650:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char pbfile[32] = "esltmppbXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:651:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile[32] = "esltmpstkXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:655:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:655:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:673:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:673:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:674:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:680:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_goodfile(tmpfile, testnumber, expected_alphatype, expected_nseq, expected_alen);
data/infernal-1.1.3/easel/esl_msafile_psiblast.c:681:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_selex.c:721:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ntext) memcpy(p+msa->alen+nleft, b->line[idx]+b->lpos[idx], sizeof(char)*ntext);
data/infernal-1.1.3/easel/esl_msafile_selex.c:869:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:870:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:957:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char slxfile2[32] = "esltmpslx2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:958:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:1006:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char slxfile2[32] = "esltmpslx2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:1007:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile2[32] = "esltmpstk2XXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:1077:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char slxfile[32] = "esltmpslxXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:1078:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char stkfile[32] = "esltmpstkXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_selex.c:1082:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_selex.c:1082:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_selex.c:1100:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_selex.c:1100:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_selex.c:1101:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_selex.c:1109:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_goodfile(tmpfile, testnumber, expected_alphatype, expected_nseq, expected_alen);
data/infernal-1.1.3/easel/esl_msafile_selex.c:1110:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1416:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "missing Stockholm header");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1431:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "number of seqs in block did not match number in earlier block(s)");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1446:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "number of seqs in block did not match number annotated by #=GS lines");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1458:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "missing // terminator after MSA");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1470:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "no alignment data followed Stockholm header");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1485:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GF line is missing <tag>, annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1497:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "faux #=GF line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1509:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "No name found on #=GF ID line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1521:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GF ID line should have only one name (no whitespace allowed)");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1533:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "No accession found on #=GF AC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1545:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GF AC line should have only one accession (no whitespace allowed)");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1557:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "Expected a real number for GA1 value on #=GF GA line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1569:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "Expected a real number for GA2 value on #=GF GA line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1581:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "No GA threshold value found on #=GF GA line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1593:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "Expected a real number for NC1 value on #=GF NC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1605:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "Expected a real number for NC2 value on #=GF NC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1617:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "No NC threshold value found on #=GF NC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1629:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "Expected a real number for TC1 value on #=GF TC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1641:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "Expected a real number for TC2 value on #=GF TC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1653:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "No TC threshold value found on #=GF TC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1665:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GS line missing <seqname>, <tag>, annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1677:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GS line missing <tag>, annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1689:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "faux #=GS line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1701:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "no weight value found on #=GS <seqname> WT line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1714:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "sequence has more than one #=GS <seqname> WT line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1726:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GS <seqname> WT line should have only one field, the weight");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1738:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "value on #=GS <seqname> WT line isn't a real number");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1750:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "no accession found on #=GS <seqname> AC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1763:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "sequence has more than one #=GS <seqname> AC accession line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1775:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GS <seqname> AC line should have only one field, the accession");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1788:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "sequence has more than one #=GS <seqname> DE accession line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1800:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GC line missing <tag>, annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1812:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "faux #=GC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1824:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GC line missing annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1841:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GC SS_cons");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1858:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GC SA_cons");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1875:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GC PP_cons");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1892:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GC RF");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1909:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GC line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1923:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GC SS_cons line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1937:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GC SA_cons line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1951:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GC PP_cons line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1965:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GC RF line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1979:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GC XX line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1992:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected # of aligned annotation in #=GC XX line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2005:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GR line missing <seqname>, <tag>, annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2018:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GR line missing <tag>, annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2031:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "faux #=GR line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2044:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "#=GR line missing annotation");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2061:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GR <seqname> SS");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2078:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GR <seqname> SA");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2095:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GR <seqname> PP");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2112:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected #=GR line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2129:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected seqname seq2; expected seq1 from prev blocks");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2143:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GR seq1 SS line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2157:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GR seq1 PP line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2171:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GR seq1 SA line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2185:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more than one #=GR seq1 XX line in block");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2198:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected # of aligned annotation in #=GR seq2 XX line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2210:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "sequence line with no sequence");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2226:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "more lines than expected; earlier blocks had fewer");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2243:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected seq line; earlier block(s) in different order");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2260:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected seq name seq3; expected seq2 from prev block order");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2272:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "invalid sequence character(s) on line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2284:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(errmsg, "unexpected number of aligned residues parsed on line");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2295:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2296:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2384:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile1[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2385:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile2[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2478:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2478:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2485:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char expected_errmsg[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2499:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2499:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2500:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2505:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_goodfile(tmpfile, testnumber, expected_alphatype, expected_nseq, expected_alen);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2506:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2512:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2512:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2513:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2584:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_bad_format(tmpfile, testnumber, expected_linenumber, expected_errmsg);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2585:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_msashuffle.c:84:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(shuf->ax[i], msa->ax[i], (msa->alen + 2) * sizeof(ESL_DSQ));
data/infernal-1.1.3/easel/esl_paml.c:147:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename, "r")) == NULL) esl_fatal("open failed");
data/infernal-1.1.3/easel/esl_rand64.c:773:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( fp = fopen(bitfile, "w")) == NULL)
data/infernal-1.1.3/easel/esl_random.c:1027:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
i += sprintf(s+i, "%d", exponent);
data/infernal-1.1.3/easel/esl_random.c:1362:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(bitfile, "w")) == NULL)
data/infernal-1.1.3/easel/esl_randomseq.c:106:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c[127];
data/infernal-1.1.3/easel/esl_randomseq.c:285:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Z[26]; /* connectivity in last edge graph Z */
data/infernal-1.1.3/easel/esl_randomseq.c:967:28: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (dsq != shuffled) memcpy(shuffled, dsq, sizeof(ESL_DSQ) * (L+2));
data/infernal-1.1.3/easel/esl_randomseq.c:1296:28: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (dsq != markoved) memcpy(markoved, dsq, sizeof(ESL_DSQ) * (L+2));
data/infernal-1.1.3/easel/esl_ratematrix.c:634:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_ratematrix.c:687:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_recorder.c:648:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename, "r")) == NULL) esl_fatal("no such file %s\n", filename);
data/infernal-1.1.3/easel/esl_recorder.c:658:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename, "r")) == NULL) esl_fatal("no such file %s\n", filename);
data/infernal-1.1.3/easel/esl_recorder.c:683:46: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
generate_testfile(ESL_RANDOMNESS *rng, char *tmpfile, int *is_data, int nlines)
data/infernal-1.1.3/easel/esl_recorder.c:691:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:705:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_basic(char *tmpfile, int N)
data/infernal-1.1.3/easel/esl_recorder.c:713:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:713:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:718:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:728:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:738:18: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_grow(char *tmpfile, int N)
data/infernal-1.1.3/easel/esl_recorder.c:746:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:746:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:751:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:763:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:772:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_grow2(char *tmpfile, int N)
data/infernal-1.1.3/easel/esl_recorder.c:782:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:782:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:787:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:795:7: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != 4) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:803:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:812:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_shrink(char *tmpfile, int N)
data/infernal-1.1.3/easel/esl_recorder.c:820:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:820:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:825:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:836:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:845:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_block(ESL_RANDOMNESS *rng, char *tmpfile, int *is_data, int N)
data/infernal-1.1.3/easel/esl_recorder.c:863:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:863:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "r")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:877:6: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != linenumber) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:888:6: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(buf+1) != linenumber) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:901:8: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(block[i]+1) != from+i) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_recorder.c:985:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char template[13]= "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_recorder.c:986:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[13];
data/infernal-1.1.3/easel/esl_recorder.c:986:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[13];
data/infernal-1.1.3/easel/esl_recorder.c:999:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, template);
data/infernal-1.1.3/easel/esl_recorder.c:1000:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
generate_testfile(rng, tmpfile, is_data, N);
data/infernal-1.1.3/easel/esl_recorder.c:1002:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_basic (tmpfile, N);
data/infernal-1.1.3/easel/esl_recorder.c:1003:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_grow (tmpfile, N);
data/infernal-1.1.3/easel/esl_recorder.c:1004:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_grow2 (tmpfile, N);
data/infernal-1.1.3/easel/esl_recorder.c:1005:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_shrink(tmpfile, N);
data/infernal-1.1.3/easel/esl_recorder.c:1006:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_block (rng, tmpfile, is_data, N);
data/infernal-1.1.3/easel/esl_recorder.c:1008:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_recorder.c:1085:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(argv[1], "r");
data/infernal-1.1.3/easel/esl_regexp.c:370:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tok1[32];
data/infernal-1.1.3/easel/esl_regexp.c:371:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tok2[32];
data/infernal-1.1.3/easel/esl_regexp.c:378:16: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
*ret_start = atol(tok1);
data/infernal-1.1.3/easel/esl_regexp.c:379:40: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
*ret_end = (tok2[0] == '\0') ? 0 : atol(tok2);
data/infernal-1.1.3/easel/esl_regexp.c:538:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char regdummy[3]; /* NOTHING, 0 next ptr */
data/infernal-1.1.3/easel/esl_regexp.c:1467:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char buf[50];
data/infernal-1.1.3/easel/esl_regexp.c:1511:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf+strlen(buf), "OPEN%d", OP(op)-OPEN);
data/infernal-1.1.3/easel/esl_regexp.c:1523:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf+strlen(buf), "CLOSE%d", OP(op)-CLOSE);
data/infernal-1.1.3/easel/esl_regexp.c:1759:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/infernal-1.1.3/easel/esl_regexp.c:1812:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ntok = atoi(argv[3]);
data/infernal-1.1.3/easel/esl_regexp.c:1847:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[64];
data/infernal-1.1.3/easel/esl_regexp.h:27:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *startp[ESL_REGEXP_NSUB]; /* ptrs to starts of submatches on target string */
data/infernal-1.1.3/easel/esl_regexp.h:28:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *endp[ESL_REGEXP_NSUB]; /* ptrs to 1 char after ends of submatches */
data/infernal-1.1.3/easel/esl_regexp.h:33:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char program[1]; /* Unwarranted chumminess with compiler. */
data/infernal-1.1.3/easel/esl_scorematrix.c:827:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(S->outorder, "ARNDCQEGHILKMFPSTWYVBZX*");
data/infernal-1.1.3/easel/esl_scorematrix.c:847:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(S->outorder, "ACGTRYMKSWHBVDN");
data/infernal-1.1.3/easel/esl_scorematrix.c:1112:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
S->s[map[row]][map[col]] = atoi(tok);
data/infernal-1.1.3/easel/esl_scorematrix.c:1835:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (ofp = fopen(mfile, "w")) == NULL) esl_fatal("failed to open %s for writing scorematrix", mfile);
data/infernal-1.1.3/easel/esl_scorematrix.c:1837:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(S0->outorder, "ARNDCQEGHILKMFPSTWYV");
data/infernal-1.1.3/easel/esl_scorematrix.c:1853:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (ofp = fopen(yfile, "w")) == NULL) esl_fatal("failed to open XY file %s for writing\n", yfile);
data/infernal-1.1.3/easel/esl_scorematrix.c:1987:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_scorematrix.c:1987:8: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_scorematrix.c:1992:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal("failed to open tmp file");
data/infernal-1.1.3/easel/esl_scorematrix.c:1996:27: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_fileparser_Open(tmpfile, NULL, &efp) != eslOK) esl_fatal("failed to open tmpfile containing BLOSUM62 matrix");
data/infernal-1.1.3/easel/esl_scorematrix.c:2000:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_sq.c:2494:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_sq.c:2494:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_sq.c:2505:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_sq.c:2505:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_sq.c:2506:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &ofp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_sq.c:2511:26: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
esl_msafile_Open(&abc, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp1);
data/infernal-1.1.3/easel/esl_sq.c:2534:26: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
esl_msafile_Open(NULL, tmpfile, NULL, eslMSAFILE_STOCKHOLM, NULL, &afp2);
data/infernal-1.1.3/easel/esl_sq.c:2557:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_sqio.c:1235:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(res_ptr + 1, sq->dsq + 1, sq->n + 1);
data/infernal-1.1.3/easel/esl_sqio.c:1597:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(filename, O_RDONLY);
data/infernal-1.1.3/easel/esl_sqio.c:1619:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "r");
data/infernal-1.1.3/easel/esl_sqio.c:1643:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "r");
data/infernal-1.1.3/easel/esl_sqio.c:1670:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(filename, O_RDONLY);
data/infernal-1.1.3/easel/esl_sqio.c:1712:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ascii[128];
data/infernal-1.1.3/easel/esl_sqio.c:1788:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[61];
data/infernal-1.1.3/easel/esl_sqio.c:1817:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[64];
data/infernal-1.1.3/easel/esl_sqio.c:1839:47: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
make_ssi_index(ESL_ALPHABET *abc, const char *tmpfile, int format, char *ssifile, int mode)
data/infernal-1.1.3/easel/esl_sqio.c:1851:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
sprintf(ssifile, "%s.ssi", tmpfile);
data/infernal-1.1.3/easel/esl_sqio.c:1853:30: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_newssi_AddFile(ns, tmpfile, format, &fh) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_sqio.c:1854:35: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_sqfile_OpenDigital(abc, tmpfile, format, NULL, &sqfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_sqio.c:2095:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_sqio.c:2095:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_sqio.c:2105:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_sqio.c:2111:35: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_sqfile_OpenDigital(abc, tmpfile, format, NULL, &sqfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_sqio.c:2127:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_sqio.c:2149:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_sqio.c:2149:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_sqio.c:2157:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_sqio.c:2157:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_sqio.c:2158:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_sqio.c:2162:27: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_sqfile_Open(tmpfile, eslSQFILE_FASTA, NULL, &sqfp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_sqio.c:2169:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_sqio.c:2221:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32];
data/infernal-1.1.3/easel/esl_sqio.c:2221:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32];
data/infernal-1.1.3/easel/esl_sqio.c:2222:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ssifile[32];
data/infernal-1.1.3/easel/esl_sqio.c:2235:7: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_sqio.c:2235:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(tmpfile, "esltmpXXXXXX");
data/infernal-1.1.3/easel/esl_sqio.c:2236:29: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal("failed to make tmpfile");
data/infernal-1.1.3/easel/esl_sqio.c:2250:27: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
make_ssi_index(abc, tmpfile, eslSQFILE_FASTA, ssifile, mode);
data/infernal-1.1.3/easel/esl_sqio.c:2252:41: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_read (abc, sqarr, N, tmpfile, eslSQFILE_FASTA, mode);
data/infernal-1.1.3/easel/esl_sqio.c:2253:41: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_read_info (abc, sqarr, N, tmpfile, eslSQFILE_FASTA, mode);
data/infernal-1.1.3/easel/esl_sqio.c:2254:41: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_read_window (abc, sqarr, N, tmpfile, eslSQFILE_FASTA, mode);
data/infernal-1.1.3/easel/esl_sqio.c:2255:44: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_fetch_subseq(r, abc, sqarr, N, tmpfile, ssifile, eslSQFILE_FASTA);
data/infernal-1.1.3/easel/esl_sqio.c:2257:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:202:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ascii->fp = fopen(filename, "r")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ascii.c:1192:8: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sq->seq, tmpsq->seq + sq->start - 1, sizeof(char) * sq->n);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:1195:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sq->ss, tmpsq->ss + sq->start - 1, sizeof(char) * sq->n);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:1201:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sq->dsq + 1, tmpsq->dsq + sq->start, sizeof(ESL_DSQ) * sq->n);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:1204:8: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sq->ss + 1, tmpsq->ss + sq->start, sizeof(char) * sq->n);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:2136:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ascii->buf + ascii->nc, ascii->mem + ascii->mpos, n);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:2150:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ascii->buf + ascii->nc, ascii->mem + ascii->mpos, n);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:3136:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[61];
data/infernal-1.1.3/easel/esl_sqio_ascii.h:29:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];/* parse error mesg. Size must match msa.h */
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:239:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&ncbi->total_res, info+1, sizeof(uint64_t));
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:271:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(name+len, ".Xin");
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:273:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ncbi->fppin = fopen(name, "rb")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:277:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(name+len, ".Xhr");
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:279:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ncbi->fpphr = fopen(name, "rb")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:283:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(name+len, ".Xsq");
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:285:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ncbi->fppsq = fopen(name, "rb")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:326:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[80];
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:340:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(name+len, ".Xal");
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:342:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(name, "r")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1422:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(name+len, ".Xin");
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1424:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ncbi->fppin = fopen(name, "rb")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1428:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(name+len, ".Xhr");
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1430:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ncbi->fpphr = fopen(name, "rb")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1434:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(name+len, ".Xsq");
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1436:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ncbi->fppsq = fopen(name, "rb")) == NULL) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2565:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char id[32];
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2566:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(id, "%d", ncbi->int_id);
data/infernal-1.1.3/easel/esl_sqio_ncbi.h:44:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];/* parse error mesg. Size must match msa.h */
data/infernal-1.1.3/easel/esl_ssi.c:72:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ssi->fp = fopen(filename, "rb")) == NULL) goto ERROR;
data/infernal-1.1.3/easel/esl_ssi.c:670:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ns->ssifp = fopen(ssifile, "w")) == NULL) { status = eslENOTFOUND; goto ERROR; }
data/infernal-1.1.3/easel/esl_ssi.c:1080:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cmd[1024];
data/infernal-1.1.3/easel/esl_ssi.c:1095:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ns->ptmp = fopen(ns->ptmpfile, "r")) == NULL) ESL_XFAIL(eslESYS, ns->errbuf, "failed to reopen primary key tmp file after sort");
data/infernal-1.1.3/easel/esl_ssi.c:1101:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ns->stmp = fopen(ns->stmpfile, "r")) == NULL) ESL_XFAIL(eslESYS, ns->errbuf, "failed to reopen secondary key tmp file after sort");
data/infernal-1.1.3/easel/esl_ssi.c:1347:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ns->ptmp = fopen(ns->ptmpfile, "w")) == NULL) ESL_XFAIL(eslENOTFOUND, ns->errbuf, "Failed to open primary key tmpfile for external sort");
data/infernal-1.1.3/easel/esl_ssi.c:1348:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ns->stmp = fopen(ns->stmpfile, "w")) == NULL) ESL_XFAIL(eslENOTFOUND, ns->errbuf, "Failed to open secondary key tmpfile for external sort");
data/infernal-1.1.3/easel/esl_ssi.c:1419:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pkey->fnum = (uint16_t) atoi(tok);
data/infernal-1.1.3/easel/esl_ssi.c:1842:9: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(td->seqname[i], "DUP"); // Allocated space is guaranteed to be enough,
data/infernal-1.1.3/easel/esl_ssi.c:1843:9: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(td->seqname[j], "DUP"); // because the original name was "seq%d-file%d"
data/infernal-1.1.3/easel/esl_ssi.c:1845:9: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(td->seqdesc[i], "DUP");
data/infernal-1.1.3/easel/esl_ssi.c:1846:9: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(td->seqdesc[j], "DUP");
data/infernal-1.1.3/easel/esl_ssi.c:1891:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char query[32]; // name of sequence to retrieve
data/infernal-1.1.3/easel/esl_ssi.c:1942:42: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if (esl_rnd_Roll(rng, 2) == 0) sprintf(query, "seq%d-file%d", i, j); // by primary key
data/infernal-1.1.3/easel/esl_ssi.c:1943:42: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else sprintf(query, "desc%d-file%d", i, j); // by secondary key
data/infernal-1.1.3/easel/esl_ssi.c:2065:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(fafile, "r")) == NULL) esl_fatal("failed to open %s", fafile);
data/infernal-1.1.3/easel/esl_ssi.c:2125:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(fafile, "r")) == NULL) esl_fatal("failed to open %s", fafile);
data/infernal-1.1.3/easel/esl_ssi.h:102:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_stopwatch.c:162:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%02d:%02d:%02d.%02d", h,m,s,hs);
data/infernal-1.1.3/easel/esl_stopwatch.c:164:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%02d:%02d:%02d", h,m,s);
data/infernal-1.1.3/easel/esl_stopwatch.c:193:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[128]; /* (safely holds up to 10^14 years; I'll be dead by then) */
data/infernal-1.1.3/easel/esl_stretchexp.c:565:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(plotfile, "w")) == NULL)
data/infernal-1.1.3/easel/esl_tree.c:144:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_tree.c:144:13: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_tree.c:148:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile(tmpfile, &fp) != eslOK) goto ERROR;
data/infernal-1.1.3/easel/esl_tree.c:1179:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[4096]; /* 4K input buffer */
data/infernal-1.1.3/easel/esl_tree.c:2025:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_tree.c:2025:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/esl_tree.c:2029:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_tree.c:2031:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_tree.c:2176:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/esl_tree.c:2179:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(argv[1], "r")) == NULL) esl_fatal("Failed to open %s", argv[1]);
data/infernal-1.1.3/easel/esl_weibull.c:612:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (plotfile && (pfp = fopen(plotfile, "w")) == NULL) ESL_EXCEPTION(eslFAIL, "Failed to open plotfile");
data/infernal-1.1.3/easel/miniapps/cmd_alistat.c:73:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( fp = fopen(msafile, "r")) == NULL) esl_fatal("Failed to open %s as a file\n", msafile);
data/infernal-1.1.3/easel/miniapps/cmd_filter.c:93:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
ofp = (esl_opt_GetString (go, "-o") == NULL ? stdout : fopen(esl_opt_GetString(go, "-o"), "w"));
data/infernal-1.1.3/easel/miniapps/esl-afetch.c:127:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-afetch.c:132:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:149:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:335:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:361:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((treefp = fopen(esl_opt_GetString(go, "--tree"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:365:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((mxfp = fopen(esl_opt_GetString(go, "--c-mx"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimap.c:71:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE*4];
data/infernal-1.1.3/easel/miniapps/esl-alimap.c:139:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((subfp = fopen(esl_opt_GetString(go, "--submap"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimap.c:586:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(esl_opt_GetString(go, "--mask-a2a"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimap.c:607:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(esl_opt_GetString(go, "--mask-a2rf"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimap.c:633:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(esl_opt_GetString(go, "--mask-rf2a"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimap.c:657:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(esl_opt_GetString(go, "--mask-rf2rf"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimask.c:95:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* buffer for error messages */
data/infernal-1.1.3/easel/miniapps/esl-alimask.c:282:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alimask.c:1152:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(filename, "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open output file %s\n", filename);
data/infernal-1.1.3/easel/miniapps/esl-alimask.c:1185:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tok1[32];
data/infernal-1.1.3/easel/miniapps/esl-alimask.c:1186:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tok2[32];
data/infernal-1.1.3/easel/miniapps/esl-alimask.c:1194:11: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
start = atol(tok1);
data/infernal-1.1.3/easel/miniapps/esl-alimask.c:1200:11: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
end = atol(tok2);
data/infernal-1.1.3/easel/miniapps/esl-alimerge.c:123:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* buffer for error messages */
data/infernal-1.1.3/easel/miniapps/esl-alimerge.c:194:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:89:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:186:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((listfp = fopen(esl_opt_GetString(go, "--list"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:190:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((icinfofp = fopen(esl_opt_GetString(go, "--icinfo"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:194:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((rinfofp = fopen(esl_opt_GetString(go, "--rinfo"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:198:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pcinfofp = fopen(esl_opt_GetString(go, "--pcinfo"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:202:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((psinfofp = fopen(esl_opt_GetString(go, "--psinfo"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:206:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((iinfofp = fopen(esl_opt_GetString(go, "--iinfo"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:210:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cinfofp = fopen(esl_opt_GetString(go, "--cinfo"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:214:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((bpinfofp = fopen(esl_opt_GetString(go, "--bpinfo"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:730:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ppstring[12] = "0123456789*.";
data/infernal-1.1.3/easel/miniapps/esl-alistat.c:802:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ppstring[12] = "0123456789*.";
data/infernal-1.1.3/easel/miniapps/esl-compalign.c:105:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ppchars[11] = "0123456789*";
data/infernal-1.1.3/easel/miniapps/esl-compalign.c:109:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/easel/miniapps/esl-compalign.c:167:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((dfp = fopen(esl_opt_GetString(go, "--c2dfile"), "w")) == NULL) esl_fatal("Failed to open --c2dfile output file %s\n", esl_opt_GetString(go, "--c2dfile"));
data/infernal-1.1.3/easel/miniapps/esl-compalign.c:197:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ks, ka->ax[i], (ka->alen+2) * sizeof(ESL_DSQ));
data/infernal-1.1.3/easel/miniapps/esl-compalign.c:201:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ts, ta->ax[i], (ta->alen+2) * sizeof(ESL_DSQ));
data/infernal-1.1.3/easel/miniapps/esl-construct.c:185:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-construct.c:189:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((lfp = fopen(esl_opt_GetString(go, "-l"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-histplot.c:138:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
ifp = fopen(datafile, "rb");
data/infernal-1.1.3/easel/miniapps/esl-histplot.c:144:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
ofp = fopen(outfile, "w");
data/infernal-1.1.3/easel/miniapps/esl-mask.c:132:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-mixdchlet.c:139:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( ofp = fopen(outfile, "w")) == NULL) esl_fatal("failed to open %s for writing", outfile);
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:106:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for error messages */
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:177:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
else if ((ofp = fopen(outfile, "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:323:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:338:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((mapfp = fopen(mapfile, "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:520:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ac_tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:529:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char de_tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:541:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char aseqbuf[61];
data/infernal-1.1.3/easel/miniapps/esl-selectn.c:71:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
m = atoi(esl_opt_GetArg(go, 1));
data/infernal-1.1.3/easel/miniapps/esl-selectn.c:80:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(filename, "r")) == NULL) esl_fatal("Failed to open file %s\n", filename);
data/infernal-1.1.3/easel/miniapps/esl-seqrange.c:79:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
procidx = atoi(esl_opt_GetArg(go, 2));
data/infernal-1.1.3/easel/miniapps/esl-seqrange.c:80:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nproc = atoi(esl_opt_GetArg(go, 3));
data/infernal-1.1.3/easel/miniapps/esl-sfetch.c:129:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-sfetch.c:134:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-sfetch.c:439:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
start = atoi(s);
data/infernal-1.1.3/easel/miniapps/esl-sfetch.c:445:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
end = atoi(s);
data/infernal-1.1.3/easel/miniapps/esl-shuffle.c:359:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:591:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[ERRBUFSIZE]; /* for printing error messages */
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:997:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((tabfp = fopen(esl_opt_GetString(go, "--tabfile"), "w")) == NULL) esl_fatal("Failed to open output file %s\n", esl_opt_GetString(go, "--tabfile"));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1116:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(outfile, "w")) == NULL)
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1677:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(text[1], "as the least ambiguous nt that represents >= %0.2f", esl_opt_GetReal(go, "--athresh"));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1689:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(text[2], "Capitalized nts occur in >= %0.2f fraction of sequences", esl_opt_GetReal(go, "--cthresh"));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:2934:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ps->leg_posn = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:2940:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ps->leg_cellsize = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6562:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(rflen != atoi(tok)) {
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6563:118: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
esl_fatal("Error reading insert file, read consensus length of %d on line %d of file %s, but expected length %d\n", atoi(tok), efp->linenumber, ifile, rflen);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6578:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
seqlen = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6581:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
spos = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6585:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
epos = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6593:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
rfpos = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6598:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
uapos = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6603:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nins = atoi(tok);
data/infernal-1.1.3/easel/miniapps/esl-weight.c:87:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
ofp = (esl_opt_GetString (go, "-o") == NULL ? stdout : fopen(esl_opt_GetString(go, "-o"), "w"));
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:158:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfile[256]; /* name of an output file */
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:200:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.out_msafp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open MSA output file %s\n", outfile);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:202:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.out_seqfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open FASTA output file %s\n", outfile);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:204:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.possummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open pos test set summary file %s\n", outfile);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:206:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.negsummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open neg test set summary file %s\n", outfile);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:208:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.tblfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open benchmark table file %s\n", outfile);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:211:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.pidfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open %%id table file %s\n", outfile);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:531:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sq->dsq+i+1, domain1->dsq+1, sizeof(ESL_DSQ) * d1n);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:536:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sq->dsq+j+d1n+1, domain2->dsq+1, sizeof(ESL_DSQ) * d2n);
data/infernal-1.1.3/hmmer/profmark/create-profmark.c:672:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dsq, sq->dsq+1, sizeof(ESL_DSQ) * L);
data/infernal-1.1.3/hmmer/src/alimask.c:343:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
postmsafp = fopen(postmsafile, "w");
data/infernal-1.1.3/hmmer/src/alimask.c:349:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
ofp = fopen(esl_opt_GetString(go, "-o"), "w");
data/infernal-1.1.3/hmmer/src/build.c:266:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/build.c:413:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char msafile[16] = "p7tmpXXXXXX"; /* tmpfile name template */
data/infernal-1.1.3/hmmer/src/build.c:455:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char msafile[16] = "p7tmpXXXXXX"; /* tmpfile name template */
data/infernal-1.1.3/hmmer/src/cachedb.c:55:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[512];
data/infernal-1.1.3/hmmer/src/cachedb.c:151:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(buffer, "000000001");
data/infernal-1.1.3/hmmer/src/cachedb.c:189:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(res_ptr, sq->dsq, sq->n + 1);
data/infernal-1.1.3/hmmer/src/cachedb.c:371:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[10];
data/infernal-1.1.3/hmmer/src/cachedb.c:405:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) {
data/infernal-1.1.3/hmmer/src/cachedb.c:459:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(info->dsq, sq->dsq, sq->n+2);
data/infernal-1.1.3/hmmer/src/cachedb.c:495:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(buffer, "000000001");
data/infernal-1.1.3/hmmer/src/cachedb.c:501:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[80];
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:62:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[512];
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:161:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(buffer, "000000001");
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:333:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[512];
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:436:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(buffer, "000000001");
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:495:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(res_ptr, sq->dsq, sq->n + 1);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:715:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[10];
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:749:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) {
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:803:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(info->dsq, sq->dsq, sq->n+2);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:839:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(buffer, "000000001");
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:845:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[80];
data/infernal-1.1.3/hmmer/src/emit.c:556:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/fm_sse.c:40:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[144];
data/infernal-1.1.3/hmmer/src/fm_sse.c:50:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[144];
data/infernal-1.1.3/hmmer/src/generic_fwdback.c:551:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_fwdback.c:665:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_fwdback_chk.c:662:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_msv.c:441:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_optacc.c:545:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_stotrace.c:307:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_stotrace.c:459:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_viterbi.c:506:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_viterbi.c:584:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_viterbi.c:654:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/generic_vtrace.c:209:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmalign.c:100:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmalign.c:133:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(outfile, "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmbuild.c:526:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->hmmfp = fopen(cfg->hmmfile, "w");
data/infernal-1.1.3/hmmer/src/hmmbuild.c:531:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->ofp = fopen(esl_opt_GetString(go, "-o"), "w");
data/infernal-1.1.3/hmmer/src/hmmbuild.c:538:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->postmsafp = fopen(cfg->postmsafile, "w");
data/infernal-1.1.3/hmmer/src/hmmbuild.c:697:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errmsg[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmbuild.c:723:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->hmmfp = fopen(cfg->hmmfile, "w");
data/infernal-1.1.3/hmmer/src/hmmbuild.c:728:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->ofp = fopen(esl_opt_GetString(go, "-o"), "w");
data/infernal-1.1.3/hmmer/src/hmmbuild.c:735:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->postmsafp = fopen(cfg->postmsafile, "w");
data/infernal-1.1.3/hmmer/src/hmmbuild.c:916:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errmsg[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmbuild.c:1023:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errmsg[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmbuild.c:1078:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errmsg[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmc2.c:184:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char opts[MAX_READ_LEN];
data/infernal-1.1.3/hmmer/src/hmmc2.c:190:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[MAX_READ_LEN];
data/infernal-1.1.3/hmmer/src/hmmc2.c:205:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char serv_ip[64];
data/infernal-1.1.3/hmmer/src/hmmc2.c:214:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(serv_ip, "127.0.0.1");
data/infernal-1.1.3/hmmer/src/hmmc2.c:229:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
serv_port = atoi(argv[i+1]);
data/infernal-1.1.3/hmmer/src/hmmconvert.c:42:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmd_search_status.c:79:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/hmmd_search_status.c:84:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/hmmd_search_status.c:122:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/hmmd_search_status.c:127:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:60:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ip_addr[64];
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:94:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ip_addr[64];
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:133:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ebuf[512];
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:523:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1002:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1059:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char opt_str[MAX_BUFFER];
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1080:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1262:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, opt_str, cmd->srch.opts_length);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1270:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, seq->name, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1274:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, seq->desc, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1278:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, seq->dsq, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1285:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, hmm, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1289:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, *hmm->t, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1293:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, *hmm->mat, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1295:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, *hmm->ins, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1298:50: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->name) { n = strlen(hmm->name) + 1; memcpy(ptr, hmm->name, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1299:50: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->acc) { n = strlen(hmm->acc) + 1; memcpy(ptr, hmm->acc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1300:50: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->desc) { n = strlen(hmm->desc) + 1; memcpy(ptr, hmm->desc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1303:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_RF) { memcpy(ptr, hmm->rf, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1304:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_MMASK) { memcpy(ptr, hmm->mm, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1305:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CONS) { memcpy(ptr, hmm->consensus, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1306:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CS) { memcpy(ptr, hmm->cs, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1307:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CA) { memcpy(ptr, hmm->ca, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1311:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, hmm->map, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1539:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&cmd, worker->cmd, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:63:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ip_addr[64];
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:100:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ip_addr[64];
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:153:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ebuf[512];
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:556:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1041:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1098:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char opt_str[MAX_BUFFER];
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1119:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1301:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, opt_str, cmd->srch.opts_length);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1309:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, seq->name, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1313:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, seq->desc, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1317:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, seq->dsq, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1324:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, hmm, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1328:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, *hmm->t, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1332:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, *hmm->mat, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1334:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, *hmm->ins, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1337:50: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->name) { n = strlen(hmm->name) + 1; memcpy(ptr, hmm->name, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1338:50: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->acc) { n = strlen(hmm->acc) + 1; memcpy(ptr, hmm->acc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1339:50: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->desc) { n = strlen(hmm->desc) + 1; memcpy(ptr, hmm->desc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1342:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_RF) { memcpy(ptr, hmm->rf, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1343:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_MMASK) { memcpy(ptr, hmm->mm, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1344:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CONS) { memcpy(ptr, hmm->consensus, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1345:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CS) { memcpy(ptr, hmm->cs, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1346:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CA) { memcpy(ptr, hmm->ca, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1350:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, hmm->map, n);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1579:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&cmd, worker->cmd, n);
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:99:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf1[16];
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:106:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf1, "%02d:%02d.%02d", m,s,hs);
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:210:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:400:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&thmm, p, sizeof(P7_HMM));
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:420:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*hmm->t, p, n); p += n;
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:423:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*hmm->mat, p, n); p += n;
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:424:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*hmm->ins, p, n); p += n;
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:431:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_RF) { memcpy(hmm->rf, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:432:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_MMASK) { memcpy(hmm->mm, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:433:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CONS) { memcpy(hmm->consensus, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:434:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CS) { memcpy(hmm->cs, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:435:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CA) { memcpy(hmm->ca, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:438:34: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_MAP) { memcpy(hmm->map, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:116:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf1[16];
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:123:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf1, "%02d:%02d.%02d", m,s,hs);
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:228:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:427:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&thmm, p, sizeof(P7_HMM));
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:447:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*hmm->t, p, n); p += n;
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:450:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*hmm->mat, p, n); p += n;
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:451:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*hmm->ins, p, n); p += n;
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:458:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_RF) { memcpy(hmm->rf, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:459:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_MMASK) { memcpy(hmm->mm, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:460:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CONS) { memcpy(hmm->consensus, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:461:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CS) { memcpy(hmm->cs, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:462:35: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_CA) { memcpy(hmm->ca, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:465:34: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (hmm->flags & p7H_MAP) { memcpy(hmm->map, p, n); p += n; }
data/infernal-1.1.3/hmmer/src/hmmemit.c:74:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmemit.c:85:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s", esl_opt_GetString(go, "-o"));
data/infernal-1.1.3/hmmer/src/hmmer.h:434:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmer.h:1250:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmer.h:1309:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* informative message on model construction failure */
data/infernal-1.1.3/hmmer/src/hmmer.h:1521:74: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
extern int p7_domain_Compare(P7_DOMAIN *first, P7_DOMAIN *second, double atol, double rtol);
data/infernal-1.1.3/hmmer/src/hmmer.h:1553:65: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
extern int p7_hit_Compare(P7_HIT *first, P7_HIT *second, double atol, double rtol);
data/infernal-1.1.3/hmmer/src/hmmerfm-exactmatch.c:75:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char retbuf[30];
data/infernal-1.1.3/hmmer/src/hmmerfm-exactmatch.c:261:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
out = fopen(outname,"w");
data/infernal-1.1.3/hmmer/src/hmmerfm-exactmatch.c:269:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((fp_fm = fopen(fname_fm, "rb")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmerfm-exactmatch.c:313:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(fname_queries,"r");
data/infernal-1.1.3/hmmer/src/hmmfetch.c:75:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmfetch.c:129:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(keyname, "w")) == NULL) p7_Fail("Failed to open output file %s\n", keyname);
data/infernal-1.1.3/hmmer/src/hmmfetch.c:133:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmlogo.c:188:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmpgmd.c:84:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(pid_file, "w");
data/infernal-1.1.3/hmmer/src/hmmpgmd.c:104:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(CONF_FILE, "r")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmpgmd.h:59:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char data[1]; /* search data */
data/infernal-1.1.3/hmmer/src/hmmpgmd.h:64:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char sid[MAX_INIT_DESC]; /* unique id for sequence database */
data/infernal-1.1.3/hmmer/src/hmmpgmd.h:65:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hid[MAX_INIT_DESC]; /* unique id for hmm database */
data/infernal-1.1.3/hmmer/src/hmmpgmd.h:72:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char data[1]; /* string data */
data/infernal-1.1.3/hmmer/src/hmmpgmd.h:77:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ip_addr[1]; /* ip address */
data/infernal-1.1.3/hmmer/src/hmmpgmd.h:114:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ip_addr[64];
data/infernal-1.1.3/hmmer/src/hmmpgmd2msa.c:330:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy( th.unsrt, hits, sizeof(P7_HIT) * stats->nhits);
data/infernal-1.1.3/hmmer/src/hmmpgmd2msa.c:398:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad2->mem, p, ad->memsize);
data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.c:85:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(pid_file, "w");
data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.c:105:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(CONF_FILE, "r")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.h:9:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char sid[MAX_INIT_DESC]; /* unique id for sequence database */
data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.h:10:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hid[MAX_INIT_DESC]; /* unique id for hmm database */
data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.h:19:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char data[1]; /* string data */
data/infernal-1.1.3/hmmer/src/hmmpgmd_shard.h:41:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ip_addr[64];
data/infernal-1.1.3/hmmer/src/hmmpress.c:58:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmpress.c:153:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmpress.c:181:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((dbf->mfp = fopen(dbf->mfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "Failed to open binary HMM file %s for writing", dbf->mfile);
data/infernal-1.1.3/hmmer/src/hmmpress.c:182:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((dbf->ffp = fopen(dbf->ffile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "Failed to open binary MSV filter file %s for writing", dbf->ffile);
data/infernal-1.1.3/hmmer/src/hmmpress.c:183:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((dbf->pfp = fopen(dbf->pfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "Failed to open binary profile file %s for writing", dbf->pfile);
data/infernal-1.1.3/hmmer/src/hmmscan.c:347:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmscan.c:384:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
data/infernal-1.1.3/hmmer/src/hmmscan.c:385:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblout")); }
data/infernal-1.1.3/hmmer/src/hmmscan.c:386:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout")) { if ((domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-dom output file %s for writing\n", esl_opt_GetString(go, "--domtblout")); }
data/infernal-1.1.3/hmmer/src/hmmscan.c:387:59: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--pfamtblout")){ if ((pfamtblfp = fopen(esl_opt_GetString(go, "--pfamtblout"), "w")) == NULL) esl_fatal("Failed to open pfam-style tabular output file %s for writing\n", esl_opt_GetString(go, "--pfamtblout")); }
data/infernal-1.1.3/hmmer/src/hmmscan.c:576:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/hmmer/src/hmmscan.c:746:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmscan.c:782:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o") && (ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmscan.c:784:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout") && (tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmscan.c:786:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout") && (domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmscan.c:788:56: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--pfamtblout") && (pfamtblfp = fopen(esl_opt_GetString(go, "--pfamtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmscan.c:1012:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmsearch.c:379:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmsearch.c:415:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) p7_Fail("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
data/infernal-1.1.3/hmmer/src/hmmsearch.c:416:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A")) { if ((afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL) p7_Fail("Failed to open alignment file %s for writing\n", esl_opt_GetString(go, "-A")); }
data/infernal-1.1.3/hmmer/src/hmmsearch.c:417:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblout")); }
data/infernal-1.1.3/hmmer/src/hmmsearch.c:418:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout")) { if ((domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-dom output file %s for writing\n", esl_opt_GetString(go, "--domtblout")); }
data/infernal-1.1.3/hmmer/src/hmmsearch.c:419:59: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--pfamtblout")){ if ((pfamtblfp = fopen(esl_opt_GetString(go, "--pfamtblout"), "w")) == NULL) esl_fatal("Failed to open pfam-style tabular output file %s for writing\n", esl_opt_GetString(go, "--pfamtblout")); }
data/infernal-1.1.3/hmmer/src/hmmsearch.c:661:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/hmmer/src/hmmsearch.c:834:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmsearch.c:870:40: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o") && (ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsearch.c:873:40: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A") && (afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsearch.c:876:48: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout") && (tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsearch.c:879:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout") && (domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsearch.c:882:56: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--pfamtblout") && (pfamtblfp = fopen(esl_opt_GetString(go, "--pfamtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsearch.c:1152:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmsim.c:308:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->ofp = fopen(filename, "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsim.c:316:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->survfp = fopen(filename, "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsim.c:323:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->efp = fopen(filename, "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsim.c:330:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->ffp = fopen(filename, "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsim.c:337:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->xfp = fopen(filename, "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsim.c:344:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->alfp = fopen(filename, "w")) == NULL)
data/infernal-1.1.3/hmmer/src/hmmsim.c:361:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmsim.c:427:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmsim.c:545:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/hmmsim.c:729:26: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if (status == eslEMEM) sprintf(errbuf, "allocation failure");
data/infernal-1.1.3/hmmer/src/hmmstat.c:37:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:749:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((msvfp = fopen(msvfile, "r")) == NULL) p7_Fail("Failed to open MSV file %s for reading.\n", msvfile);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:788:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:788:16: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:801:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:806:26: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:807:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&mfile, "%s.h3m", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:808:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&ffile, "%s.h3f", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:809:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&pfile, "%s.h3p", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:810:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&ssifile, "%s.h3i", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:813:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( mfp = fopen(mfile, "wb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:814:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( ffp = fopen(ffile, "wb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:815:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( pfp = fopen(pfile, "wb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:829:33: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_newssi_AddFile(nssi, tmpfile, 0, &fh) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:840:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( p7_hmmfile_OpenE(tmpfile, NULL, &hfp, NULL) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:854:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:972:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:981:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ffp = fopen(fname, "wb")) == NULL) p7_Fail("failed to open %s\n", fname);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:982:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(pname, "wb")) == NULL) p7_Fail("failed to open %s\n", pname);
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:684:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_sse/null2.c:60:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pp->dpf[0], pp->dpf[1], sizeof(__m128) * 3 * Q);
data/infernal-1.1.3/hmmer/src/impl_sse/optacc.c:875:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:311:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rbv[0], om1->rbv[0], sizeof(__m128i) * nqb * abc->Kp);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:312:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->sbv[0], om1->sbv[0], sizeof(__m128i) * nqs * abc->Kp);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:313:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rwv[0], om1->rwv[0], sizeof(__m128i) * nqw * abc->Kp);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:314:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rfv[0], om1->rfv[0], sizeof(__m128i) * nqf * abc->Kp);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:369:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rf, om1->rf, size);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:370:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->mm, om1->mm, size);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:371:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->cs, om1->cs, size);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:372:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->consensus, om1->consensus, size);
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:409:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2, om1, sizeof(P7_OPROFILE));
data/infernal-1.1.3/hmmer/src/impl_sse/p7_oprofile.c:2121:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_sse/stotrace.c:418:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_sse/stotrace.c:586:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:744:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((msvfp = fopen(msvfile, "r")) == NULL) p7_Fail("Failed to open MSV file %s for reading.\n", msvfile);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:783:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:783:16: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[16] = "esltmpXXXXXX";
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:796:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:801:26: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:802:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&mfile, "%s.h3m", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:803:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&ffile, "%s.h3f", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:804:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&pfile, "%s.h3p", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:805:40: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_sprintf(&ssifile, "%s.h3i", tmpfile) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:808:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( mfp = fopen(mfile, "wb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:809:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( ffp = fopen(ffile, "wb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:810:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (( pfp = fopen(pfile, "wb")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:824:33: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( esl_newssi_AddFile(nssi, tmpfile, 0, &fh) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:835:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( p7_hmmfile_OpenE(tmpfile, NULL, &hfp, NULL) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:849:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:967:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:976:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ffp = fopen(fname, "wb")) == NULL) p7_Fail("failed to open %s\n", fname);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:977:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(pname, "wb")) == NULL) p7_Fail("failed to open %s\n", pname);
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:685:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_vmx/null2.c:65:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pp->dpf[0], pp->dpf[1], sizeof(vector float) * 3 * Q);
data/infernal-1.1.3/hmmer/src/impl_vmx/optacc.c:884:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:291:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rbv[0], om1->rbv[0], sizeof(vector unsigned char) * nqb * abc->Kp);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:292:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rwv[0], om1->rwv[0], sizeof(vector signed short) * nqw * abc->Kp);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:293:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rfv[0], om1->rfv[0], sizeof(vector float) * nqf * abc->Kp);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:347:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->rf, om1->rf, size);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:348:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->mm, om1->mm, size);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:349:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->cs, om1->cs, size);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:350:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2->consensus, om1->consensus, size);
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:387:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(om2, om1, sizeof(P7_OPROFILE));
data/infernal-1.1.3/hmmer/src/impl_vmx/p7_oprofile.c:2050:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_vmx/stotrace.c:426:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/impl_vmx/stotrace.c:587:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/itest_brute.c:134:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *ofp = fopen(hmmfile, "w");
data/infernal-1.1.3/hmmer/src/jackhmmer.c:499:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o") && (ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:501:55: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A") && (afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:503:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout") && (tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:505:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout") && (domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:838:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1050:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o") && (ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1052:55: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A") && (afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1054:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout") && (tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1056:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout") && (domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1567:32: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (nquery == 1) { if ((fp = fopen(filename, "w")) == NULL) p7_Fail("Failed to open HMM checkpoint file %s for writing\n", filename); }
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1568:32: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
else { if ((fp = fopen(filename, "a")) == NULL) p7_Fail("Failed to open HMM checkpoint file %s for append\n", filename); }
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1590:32: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (nquery == 1) { if ((fp = fopen(filename, "w")) == NULL) p7_Fail("Failed to open MSA checkpoint file %s for writing\n", filename); }
data/infernal-1.1.3/hmmer/src/jackhmmer.c:1591:32: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
else { if ((fp = fopen(filename, "a")) == NULL) p7_Fail("Failed to open MSA checkpoint file %s for append\n", filename); }
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:362:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp_filename[16] = "fmtmpXXXXXX";
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:725:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((fp = fopen(fname_out, "wb")) == NULL)
data/infernal-1.1.3/hmmer/src/modelconfig.c:448:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/modelconfig.c:574:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(kpsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", kpsfile);
data/infernal-1.1.3/hmmer/src/modelconfig.c:579:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(ipsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", ipsfile);
data/infernal-1.1.3/hmmer/src/mpisupport.c:1620:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errmsg[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/mpisupport.c:1666:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/nhmmer.c:516:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/nhmmer.c:720:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((fm_meta->fp = fopen(cfg->dbfile, "rb")) == NULL)
data/infernal-1.1.3/hmmer/src/nhmmer.c:746:62: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) p7_Fail("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
data/infernal-1.1.3/hmmer/src/nhmmer.c:747:62: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A")) { if ((afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL) p7_Fail("Failed to open alignment file %s for writing\n", esl_opt_GetString(go, "-A")); }
data/infernal-1.1.3/hmmer/src/nhmmer.c:748:62: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular output file %s for writing\n", esl_opt_GetString(go, "--tblout")); }
data/infernal-1.1.3/hmmer/src/nhmmer.c:749:66: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--dfamtblout")) { if ((dfamtblfp = fopen(esl_opt_GetString(go, "--dfamtblout"),"w")) == NULL) esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
data/infernal-1.1.3/hmmer/src/nhmmer.c:750:66: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--aliscoresout")) { if ((aliscoresfp = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL) esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
data/infernal-1.1.3/hmmer/src/nhmmer.c:755:30: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((hmmoutfp = fopen(hmmfile,"w")) == NULL) esl_fatal("Failed to open hmm output file %s for writing\n", hmmfile);
data/infernal-1.1.3/hmmer/src/nhmmscan.c:333:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/nhmmscan.c:381:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
data/infernal-1.1.3/hmmer/src/nhmmscan.c:382:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
data/infernal-1.1.3/hmmer/src/nhmmscan.c:383:66: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--dfamtblout")) { if ((dfamtblfp = fopen(esl_opt_GetString(go, "--dfamtblout"),"w")) == NULL) esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
data/infernal-1.1.3/hmmer/src/nhmmscan.c:384:66: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--aliscoresout")) { if ((aliscoresfp = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL) esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:340:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad2->mem, ad->mem, ad->memsize);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:557:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(uint32_t)); // Write size of the serialized object into the buffer
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:562:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:567:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:572:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:577:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:582:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:587:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:592:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:596:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &presence_flags, sizeof(uint8_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:720:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:735:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:740:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:745:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:750:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:755:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:760:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:765:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:774:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ret_obj->mem, ptr, (obj_size - SER_BASE_SIZE));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:927:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->rfline) { memcpy(ad->mem+pos, ad->rfline, ad->N+1); free(ad->rfline); ad->rfline = ad->mem+pos; pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:928:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->mmline) { memcpy(ad->mem+pos, ad->mmline, ad->N+1); free(ad->mmline); ad->mmline = ad->mem+pos; pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:929:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->csline) { memcpy(ad->mem+pos, ad->csline, ad->N+1); free(ad->csline); ad->csline = ad->mem+pos; pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:930:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad->mem+pos, ad->model, ad->N+1); free(ad->model); ad->model = ad->mem+pos; pos += ad->N+1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:931:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad->mem+pos, ad->mline, ad->N+1); free(ad->mline); ad->mline = ad->mem+pos; pos += ad->N+1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:932:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad->mem+pos, ad->aseq, ad->N+1); free(ad->aseq); ad->aseq = ad->mem+pos; pos += ad->N+1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:933:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->ntseq) { memcpy(ad->mem+pos, ad->ntseq, (3*ad->N)+1); free(ad->ntseq); ad->ntseq = ad->mem+pos; pos += (3*ad->N)+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:934:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->ppline) { memcpy(ad->mem+pos, ad->ppline, ad->N+1); free(ad->ppline); ad->ppline = ad->mem+pos; pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:935:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->hmmname); memcpy(ad->mem + pos, ad->hmmname, n); free(ad->hmmname); ad->hmmname = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:936:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->hmmacc); memcpy(ad->mem + pos, ad->hmmacc, n); free(ad->hmmacc); ad->hmmacc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:937:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->hmmdesc); memcpy(ad->mem + pos, ad->hmmdesc, n); free(ad->hmmdesc); ad->hmmdesc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:938:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->sqname); memcpy(ad->mem + pos, ad->sqname, n); free(ad->sqname); ad->sqname = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:939:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->sqacc); memcpy(ad->mem + pos, ad->sqacc, n); free(ad->sqacc); ad->sqacc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:940:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->sqdesc); memcpy(ad->mem + pos, ad->sqdesc, n); free(ad->sqdesc); ad->sqdesc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:976:68: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->rfline) { ESL_ALLOC(ad->rfline, sizeof(char) * ad->N+1); memcpy(ad->rfline, ad->mem+pos, ad->N+1); pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:977:68: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->mmline) { ESL_ALLOC(ad->mmline, sizeof(char) * ad->N+1); memcpy(ad->mmline, ad->mem+pos, ad->N+1); pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:978:68: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->csline) { ESL_ALLOC(ad->csline, sizeof(char) * ad->N+1); memcpy(ad->csline, ad->mem+pos, ad->N+1); pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:979:49: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
ESL_ALLOC(ad->model, sizeof(char) * ad->N+1); memcpy(ad->model, ad->mem+pos, ad->N+1); pos += ad->N+1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:980:49: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
ESL_ALLOC(ad->mline, sizeof(char) * ad->N+1); memcpy(ad->mline, ad->mem+pos, ad->N+1); pos += ad->N+1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:981:49: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
ESL_ALLOC(ad->aseq, sizeof(char) * ad->N+1); memcpy(ad->aseq, ad->mem+pos, ad->N+1); pos += ad->N+1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:982:72: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->ntseq) { ESL_ALLOC(ad->ntseq, sizeof(char) * (3*ad->N)+1); memcpy(ad->ntseq, ad->mem+pos, (3*ad->N)+1); pos += (3*ad->N)+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:983:68: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (ad->ppline) { ESL_ALLOC(ad->ppline, sizeof(char) * ad->N+1); memcpy(ad->ppline, ad->mem+pos, ad->N+1); pos += ad->N+1; }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:984:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->hmmname, sizeof(char) * n); memcpy(ad->hmmname, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:985:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->hmmacc, sizeof(char) * n); memcpy(ad->hmmacc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:986:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->hmmdesc, sizeof(char) * n); memcpy(ad->hmmdesc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:987:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->sqname, sizeof(char) * n); memcpy(ad->sqname, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:988:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->sqacc, sizeof(char) * n); memcpy(ad->sqacc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:989:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->sqdesc, sizeof(char) * n); memcpy(ad->sqdesc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_bg.c:135:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dup->f, bg->f, sizeof(float) * bg->abc->K);
data/infernal-1.1.3/hmmer/src/p7_bg.c:563:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/hmmer/src/p7_bg.c:563:17: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX";
data/infernal-1.1.3/hmmer/src/p7_bg.c:577:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_tmpfile_named(tmpfile, &fp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_bg.c:582:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( p7_bg_Read(tmpfile, bg, NULL) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_bg.c:588:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/hmmer/src/p7_bg.c:739:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/p7_domain.c:156:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:161:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:166:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:171:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:176:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:181:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:186:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:193:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->envsc));
data/infernal-1.1.3/hmmer/src/p7_domain.c:198:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->domcorrection));
data/infernal-1.1.3/hmmer/src/p7_domain.c:203:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->dombias));
data/infernal-1.1.3/hmmer/src/p7_domain.c:208:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->oasc));
data/infernal-1.1.3/hmmer/src/p7_domain.c:213:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->bitscore));
data/infernal-1.1.3/hmmer/src/p7_domain.c:218:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->lnP));
data/infernal-1.1.3/hmmer/src/p7_domain.c:223:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:228:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:234:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:241:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:246:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:304:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:309:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:314:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:319:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:324:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:329:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:334:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:339:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:345:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:351:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:357:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:363:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:369:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:375:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:380:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:385:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t));
data/infernal-1.1.3/hmmer/src/p7_domain.c:396:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_domain.c:506:74: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
extern int p7_domain_Compare(P7_DOMAIN *first, P7_DOMAIN *second, double atol, double rtol){
data/infernal-1.1.3/hmmer/src/p7_domain.c:526:59: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->envsc, second->envsc, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_domain.c:529:74: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->domcorrection, second->domcorrection, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_domain.c:532:62: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->dombias, second->dombias, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_domain.c:535:57: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->oasc, second->oasc, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_domain.c:538:65: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->bitscore, second->bitscore, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_domain.c:541:46: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_DCompareNew(first->lnP, second->lnP, atol, rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_domain.c:567:85: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->scores_per_pos[i], second->scores_per_pos[i], (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_domaindef.c:672:20: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (d != d2) memcpy(ddef->sp->sigc + d, ddef->sp->sigc + d2, sizeof(struct p7_spcoord_s));
data/infernal-1.1.3/hmmer/src/p7_domaindef.c:1099:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(ofile, "w")) == NULL) p7_Fail("Failed to open output file %s\n", ofile);
data/infernal-1.1.3/hmmer/src/p7_hit.c:217:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:222:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:227:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->sortkey));
data/infernal-1.1.3/hmmer/src/p7_hit.c:232:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->score));
data/infernal-1.1.3/hmmer/src/p7_hit.c:237:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->pre_score));
data/infernal-1.1.3/hmmer/src/p7_hit.c:242:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->sum_score));
data/infernal-1.1.3/hmmer/src/p7_hit.c:247:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->lnP));
data/infernal-1.1.3/hmmer/src/p7_hit.c:252:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->pre_lnP));
data/infernal-1.1.3/hmmer/src/p7_hit.c:257:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->sum_lnP));
data/infernal-1.1.3/hmmer/src/p7_hit.c:262:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_32bit, sizeof(obj->nexpected));
data/infernal-1.1.3/hmmer/src/p7_hit.c:267:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:272:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:277:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:282:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:287:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:292:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:297:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:302:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:307:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_32bit, sizeof(int32_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:312:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:317:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &network_64bit, sizeof(int64_t));
data/infernal-1.1.3/hmmer/src/p7_hit.c:321:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptr, &presence_flags, 1);
data/infernal-1.1.3/hmmer/src/p7_hit.c:397:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:402:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:407:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(double)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:413:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(float)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:419:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(float)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:425:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(float)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:431:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(double)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:437:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(double)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:443:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(double)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:449:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(float)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:455:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:460:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:465:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:470:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:475:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:480:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:485:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:490:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:495:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_32bit, ptr, sizeof(uint32_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:500:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:505:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:510:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&presence_flags, ptr, 1); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hit.c:709:65: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
extern int p7_hit_Compare(P7_HIT *first, P7_HIT *second, double atol, double rtol){
data/infernal-1.1.3/hmmer/src/p7_hit.c:738:55: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_DCompareNew(first->sortkey, second->sortkey, atol, rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hit.c:742:59: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->score, second->score, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hit.c:746:67: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->pre_score, second->pre_score, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hit.c:750:67: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_FCompareNew(first->sum_score, second->sum_score, (float) atol, (float) rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hit.c:754:47: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_DCompareNew(first->lnP, second->lnP, atol, rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hit.c:758:54: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_DCompareNew(first->pre_lnP, second->pre_lnP, atol, rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hit.c:762:54: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(esl_DCompareNew(first->sum_lnP, second->sum_lnP, atol, rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hit.c:815:63: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if(p7_domain_Compare(&(first->dcl[i]), &(second->dcl[i]), atol, rtol) != eslOK){
data/infernal-1.1.3/hmmer/src/p7_hmmcache.c:197:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:92:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->elapsed)); //Use memcpy here because it does the right thing with unaligned copies
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:98:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->user));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:104:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->sys));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:110:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->Z));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:116:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->domZ));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:157:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->nmodels));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:162:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->nseqs));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:167:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->n_past_msv));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:172:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->n_past_bias));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:177:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->n_past_vit));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:182:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->n_past_fwd));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:187:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->nhits));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:192:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->nreported));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:197:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(obj->nincluded));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:202:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:208:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void *) ptr, (void *) &network_64bit, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:256:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:262:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:268:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:274:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:280:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:319:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:324:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:329:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:334:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:339:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:344:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:349:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:354:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:359:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t)); // Grab the bytes out of the buffer
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:364:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_hmmd_search_stats.c:382:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&network_64bit, ptr, sizeof(uint64_t));
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:285:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
union { char c[4]; uint32_t n; } magic;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:339:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((hfp->f = fopen(filename, "r")) != NULL) {
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:367:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((tmpfp = fopen(dbfile, "rb")) != NULL)
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:403:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((hfp->ffp = fopen(dbfile, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, errbuf, "Opened %s, a pressed HMM file; but no .h3f file found", hfp->fname);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:406:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((hfp->pfp = fopen(dbfile, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, errbuf, "Opened %s, a pressed HMM file; but no .h3p file found", hfp->fname);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:710:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buff[100];
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:726:15: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += 7 + sprintf(buff, "%d", hmm->M); /*LENG tag, we determine size of field later */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:727:65: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((format >= p7_HMMFILE_3c && hmm->max_length) ? 7 + sprintf(buff, "%d", hmm->max_length) : 0); /*MAXL line, later formats only, optional */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:745:15: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((sprintf(buff, "%d", n) + 8) * n); /*length of all the COM tags*/
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:749:34: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += (hmm->nseq > 0 ? 7 + sprintf(buff, "%d", hmm->nseq) : 0); /* NSEQ line */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:750:39: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += (hmm->eff_nseq >= 0 ? 7 + sprintf(buff, "%f", hmm->eff_nseq) : 0); /* EFFN line */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:751:42: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += (hmm->flags & p7H_CHKSUM ? 7 + sprintf(buff, "%u", hmm->checksum) : 0); /*CKSUM line */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:754:40: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((hmm->flags & p7H_GA) ? 8 + sprintf(buff, "%.2f", hmm->cutoff[p7_GA1])+sprintf(buff, "%.2f", hmm->cutoff[p7_GA2]) : 0);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:754:83: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((hmm->flags & p7H_GA) ? 8 + sprintf(buff, "%.2f", hmm->cutoff[p7_GA1])+sprintf(buff, "%.2f", hmm->cutoff[p7_GA2]) : 0);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:755:40: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((hmm->flags & p7H_TC) ? 8 + sprintf(buff, "%.2f", hmm->cutoff[p7_TC1])+sprintf(buff, "%.2f", hmm->cutoff[p7_TC2]) : 0);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:755:83: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((hmm->flags & p7H_TC) ? 8 + sprintf(buff, "%.2f", hmm->cutoff[p7_TC1])+sprintf(buff, "%.2f", hmm->cutoff[p7_TC2]) : 0);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:756:40: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((hmm->flags & p7H_NC) ? 8 + sprintf(buff, "%.2f", hmm->cutoff[p7_NC1])+sprintf(buff, "%.2f", hmm->cutoff[p7_NC2]) : 0);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:756:83: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
size += ((hmm->flags & p7H_NC) ? 8 + sprintf(buff, "%.2f", hmm->cutoff[p7_NC1])+sprintf(buff, "%.2f", hmm->cutoff[p7_NC2]) : 0);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:760:50: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
((format == p7_HMMFILE_3a) ? ( 75 + sprintf(buff, "%f", hmm->evparam[p7_MLAMBDA]) +
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:761:50: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buff, "%f", hmm->evparam[p7_MMU]) +
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:762:50: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buff, "%f", hmm->evparam[p7_FTAU])) :
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:763:50: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
( 75 + sprintf(buff, "%8.4f", hmm->evparam[p7_MMU]) + sprintf(buff, "%8.5f", hmm->evparam[p7_MLAMBDA]) +
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:763:98: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
( 75 + sprintf(buff, "%8.4f", hmm->evparam[p7_MMU]) + sprintf(buff, "%8.5f", hmm->evparam[p7_MLAMBDA]) +
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:764:50: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buff, "%8.4f", hmm->evparam[p7_VMU]) + sprintf(buff, "%8.5f", hmm->evparam[p7_VLAMBDA]) +
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:764:98: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buff, "%8.4f", hmm->evparam[p7_VMU]) + sprintf(buff, "%8.5f", hmm->evparam[p7_VLAMBDA]) +
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:765:50: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buff, "%8.4f", hmm->evparam[p7_FTAU]) + sprintf(buff, "%8.5f", hmm->evparam[p7_FLAMBDA])))
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:765:98: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buff, "%8.4f", hmm->evparam[p7_FTAU]) + sprintf(buff, "%8.5f", hmm->evparam[p7_FLAMBDA])))
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:811:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, "LENG %d\n", hmm->M)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:815:18: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if((offset = sprintf(ret_hmm + coffset, "MAXL %d\n", hmm->max_length)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:851:18: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if((offset = sprintf(ret_hmm + coffset, "NSEQ %d\n", hmm->nseq)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:856:18: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if((offset = sprintf(ret_hmm + coffset, "EFFN %f\n", hmm->eff_nseq)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:861:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf (ret_hmm + coffset, "CKSUM %u\n", hmm->checksum)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:868:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if(( offset = sprintf(ret_hmm + coffset , "GA %.2f %.2f\n", hmm->cutoff[p7_GA1], hmm->cutoff[p7_GA2])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:873:20: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if(( offset = sprintf(ret_hmm + coffset , "TC %.2f %.2f\n", hmm->cutoff[p7_TC1], hmm->cutoff[p7_TC2])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:878:20: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if(( offset = sprintf(ret_hmm + coffset , "NC %.2f %.2f\n", hmm->cutoff[p7_NC1], hmm->cutoff[p7_NC2])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:886:20: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset =sprintf(ret_hmm + coffset, "STATS LOCAL VLAMBDA %f\n", hmm->evparam[p7_MLAMBDA])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:888:20: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset =sprintf(ret_hmm + coffset, "STATS LOCAL VMU %f\n", hmm->evparam[p7_MMU])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:890:20: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset =sprintf(ret_hmm + coffset, "STATS LOCAL FTAU %f\n", hmm->evparam[p7_FTAU])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:893:20: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset =sprintf(ret_hmm + coffset, "STATS LOCAL MSV %8.4f %8.5f\n", hmm->evparam[p7_MMU], hmm->evparam[p7_MLAMBDA])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:895:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, "STATS LOCAL VITERBI %8.4f %8.5f\n", hmm->evparam[p7_VMU], hmm->evparam[p7_VLAMBDA])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:897:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, "STATS LOCAL FORWARD %8.4f %8.5f\n", hmm->evparam[p7_FTAU], hmm->evparam[p7_FLAMBDA])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:905:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, "HMM ")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:909:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " %c ", hmm->abc->sym[x])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:920:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " COMPO ")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:931:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " ")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:941:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " ")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:954:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " %6d ", k)) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:963:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " %6d", hmm->map[k])) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:971:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " %c", (hmm->flags & p7H_CONS) ? hmm->consensus[k] : '-')) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:975:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " %c", (hmm->flags & p7H_RF) ? hmm->rf[k] : '-')) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:979:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " %c", (hmm->flags & p7H_MMASK) ? hmm->mm[k] : '-')) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:983:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " %c\n", (hmm->flags & p7H_CS) ? hmm->cs[k] : '-')) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:987:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, " ")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:996:19: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if ((offset = sprintf(ret_hmm + coffset, "\n ")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1007:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if (sprintf(ret_hmm + coffset, "//\n") < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1358:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->M = atoi(tok1)) == 0) ESL_XFAIL(status, hfp->errbuf, "Invalid model length %s on LENG line", tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1363:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->max_length = atoi(tok1)) == 0) ESL_XFAIL(status, hfp->errbuf, "Invalid max length %s on MAXL line", tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1432:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->nseq = atoi(tok1)) == 0) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "Invalid nseq on NSEQ line: should be integer, not %s", tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1559:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(tok1) != k) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "Expected match line to start with %d (of %d); saw %s", k, hmm->M, tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1567:47: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (hmm->flags & p7H_MAP) hmm->map[k] = atoi(tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1817:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->M = atoi(tok1)) == 0) ESL_XFAIL(status, hfp->errbuf, "Invalid model length %s on LENG line", tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1876:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->nseq = atoi(tok1)) == 0 && strcmp(tok1, "0") != 0) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "Invalid nseq on NSEQ line: should be integer, not %s", tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1941:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(tok1) != k) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "Expected match line to start with %d (of %d); saw %s", k, hmm->M, tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1950:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
hmm->map[k] = atoi(tok1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2166:28: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else if (p == 1.0) { if (sprintf(*str+offset, " %*.5f", fieldwidth, 0.0) < 0) return( eslEWRITE ); }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2167:28: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else { if (sprintf(*str+offset, " %*.5f", fieldwidth, -logf(p)) < 0) return( eslEWRITE ); }
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2243:42: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return ((*s == '*') ? 0. : null * exp( atoi(s) * 0.00069314718));
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2293:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2361:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_30(char *tmpfile, int format, P7_HMM *hmm)
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2370:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "w")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2370:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "w")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2375:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (p7_hmmfile_OpenE(tmpfile, NULL, &hfp, NULL) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2392:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(tmpfile, "w")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2392:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((fp = fopen(tmpfile, "w")) == NULL) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2395:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (p7_hmmfile_OpenE(tmpfile, NULL, &hfp, NULL) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2413:24: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_current(char *tmpfile, P7_HMM *hmm)
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2419:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_30(tmpfile, -1, hmm);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2426:19: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_3a(char *tmpfile, P7_HMM *hmm)
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2442:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_30(tmpfile, p7_HMMFILE_3a, hmm);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2478:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "tmp-hmmerXXXXXX";
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2478:8: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "tmp-hmmerXXXXXX";
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2484:26: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((esl_tmpfile_named(tmpfile, &fp)) != eslOK) esl_fatal("failed to create tmp file");
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2489:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_current(tmpfile, hmm);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2490:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_3a (tmpfile, hmm);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2495:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_current(tmpfile, hmm);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2496:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
utest_io_3a (tmpfile, hmm);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2502:10: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2543:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:241:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->ssv_scores, src->ssv_scores, (src->M + 1) * Kp * sizeof(uint8_t) );
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:244:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->ssv_scores_f, src->ssv_scores_f, (src->M + 1) * Kp * sizeof(float) );
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:250:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->prefix_lengths, src->prefix_lengths, (src->M+1) * sizeof(float));
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:254:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->suffix_lengths, src->suffix_lengths, (src->M+1) * sizeof(float));
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:258:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->fwd_scores, src->fwd_scores, (src->M+1) * sizeof(float));
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:266:8: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->opt_ext_fwd[i], src->opt_ext_fwd[i], 10 * sizeof(float));
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:273:8: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->opt_ext_rev[i], src->opt_ext_rev[i], 10 * sizeof(float));
data/infernal-1.1.3/hmmer/src/p7_scoredata.c:280:8: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new->fwd_transitions[i], src->fwd_transitions[i], (src->M+1) * sizeof(float));
data/infernal-1.1.3/hmmer/src/p7_tophits.c:447:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new2, h2->unsrt, sizeof(P7_HIT) * h2->N);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:502:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer [13];
data/infernal-1.1.3/hmmer/src/p7_tophits.c:506:11: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
n = sprintf (buffer, "%" PRId64 "", h->unsrt[i].dcl[0].iali);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:508:11: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
n = sprintf (buffer, "%" PRId64 "", h->unsrt[i].dcl[0].jali);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1982:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1983:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char modestamp[16];
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1991:26: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
case p7_SEARCH_SEQS: strcpy(modestamp, "SEARCH"); break;
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1992:26: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
case p7_SCAN_MODELS: strcpy(modestamp, "SCAN"); break;
data/infernal-1.1.3/hmmer/src/phmmer.c:451:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) p7_Fail("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
data/infernal-1.1.3/hmmer/src/phmmer.c:452:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A")) { if ((afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL) p7_Fail("Failed to open alignment output file %s for writing\n", esl_opt_GetString(go, "-A")); }
data/infernal-1.1.3/hmmer/src/phmmer.c:453:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) p7_Fail("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
data/infernal-1.1.3/hmmer/src/phmmer.c:454:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout")) { if ((domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL) p7_Fail("Failed to open tabular per-dom output file %s for writing\n", esl_opt_GetString(go, "--domtblfp")); }
data/infernal-1.1.3/hmmer/src/phmmer.c:455:59: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--pfamtblout")){ if ((pfamtblfp = fopen(esl_opt_GetString(go, "--pfamtblout"), "w")) == NULL) esl_fatal("Failed to open pfam-style tabular output file %s for writing\n", esl_opt_GetString(go, "--pfamtblout")); }
data/infernal-1.1.3/hmmer/src/phmmer.c:720:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/hmmer/src/phmmer.c:943:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o") && (ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/phmmer.c:945:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A") && (afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/phmmer.c:947:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout") && (tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/phmmer.c:949:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--domtblout") && (domtblfp = fopen(esl_opt_GetString(go, "--domtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/phmmer.c:951:56: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--pfamtblout") && (pfamtblfp = fopen(esl_opt_GetString(go, "--pfamtblout"), "w")) == NULL)
data/infernal-1.1.3/hmmer/src/seqmodel.c:158:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/seqmodel.c:199:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((hmmfp = fopen(hmmfile, "w")) == NULL) esl_fatal("Failed to open output HMM file %s", hmmfile);
data/infernal-1.1.3/hmmer/src/seqmodel.c:249:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/tracealign.c:1151:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/hmmer/src/tracealign.c:1203:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(outfile, "w")) == NULL)
data/infernal-1.1.3/rmark/rmark-create.c:184:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfile[256]; /* name of an output file */
data/infernal-1.1.3/rmark/rmark-create.c:251:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.out_msafp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open MSA output file %s\n", outfile);
data/infernal-1.1.3/rmark/rmark-create.c:253:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.out_bmkfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open FASTA output file %s\n", outfile);
data/infernal-1.1.3/rmark/rmark-create.c:255:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.out_posfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open positive FASTA output file %s\n", outfile);
data/infernal-1.1.3/rmark/rmark-create.c:257:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.possummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open pos test set summary file %s\n", outfile);
data/infernal-1.1.3/rmark/rmark-create.c:259:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.ppossummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open pos-only test set summary file %s\n", outfile);
data/infernal-1.1.3/rmark/rmark-create.c:261:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.tblfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open benchmark table file %s\n", outfile);
data/infernal-1.1.3/rmark/rmark-create.c:264:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg.negsummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open neg test set summary file %s\n", outfile);
data/infernal-1.1.3/rmark/rmark-create.c:268:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((cfg.nseqfp = fopen(esl_opt_GetString(go, "--nfile"), "w")) == NULL) esl_fatal("Failed to open negative sequence file %s\n", esl_opt_GetString(go, "--nfile"));
data/infernal-1.1.3/rmark/rmark-create.c:272:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((cfg.tfp = fopen(esl_opt_GetString(go, "--tfile"), "w")) == NULL) esl_fatal("Failed to open alignment file %s\n", esl_opt_GetString(go, "--tfile"));
data/infernal-1.1.3/rmark/rmark-create.c:1140:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(negsq->dsq + negsq->n + 1, tmpdsq+1, sizeof(ESL_DSQ) * chunkL);
data/infernal-1.1.3/rmark/rmark-create.c:1158:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(bmksq->dsq+bmk_p, negsq->dsq+neg_p, sizeof(ESL_DSQ) * (negseqs_p[i][q] - neg_p + 1));
data/infernal-1.1.3/rmark/rmark-create.c:1171:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(bmksq->dsq+bmk_p, posseqs[j]->dsq+1, sizeof(ESL_DSQ) * posseqs[j]->n);
data/infernal-1.1.3/rmark/rmark-create.c:1185:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(bmksq->dsq+bmk_p, negsq->dsq+neg_p, sizeof(ESL_DSQ) * (negsq->n - neg_p + 1));
data/infernal-1.1.3/rmark/rmark-create.c:1300:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sq->dsq+1, dbsq->dsq+start, sizeof(ESL_DSQ) * L);
data/infernal-1.1.3/rmark/rmark-create.c:1324:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dsq, sq->dsq+1, sizeof(ESL_DSQ) * L);
data/infernal-1.1.3/rmark/rmark-create.c:1374:10: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
type = atoi(tok);
data/infernal-1.1.3/rmark/rmark-create.c:1381:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nstates = atoi(tok);
data/infernal-1.1.3/src/bandcyk-montecarlo-test.c:68:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for error messages */
data/infernal-1.1.3/src/bandcyk-truncation-test.c:64:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int Z1 = atoi(esl_opt_GetArg(go, 2));
data/infernal-1.1.3/src/bandcyk-truncation-test.c:65:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int Z2 = atoi(esl_opt_GetArg(go, 3));
data/infernal-1.1.3/src/bandcyk-truncation-test.c:79:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for error messages */
data/infernal-1.1.3/src/cm.c:594:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen(nullfile, "r")) == NULL)
data/infernal-1.1.3/src/cm.c:2800:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(seedstr, " --seed %" PRIu32 " ", seed);
data/infernal-1.1.3/src/cm_alidisplay.c:327:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ad->model+pos, "<[%*d]*", wtrunc_R-4, ntrunc_R);
data/infernal-1.1.3/src/cm_alidisplay.c:371:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ad->model+pos, "*[%*d]*", numwidth, qinset);
data/infernal-1.1.3/src/cm_alidisplay.c:372:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ad->aseq+pos, "*[%*d]*", numwidth, tinset);
data/infernal-1.1.3/src/cm_alidisplay.c:584:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ad->model+pos, "*[%*d]>", wtrunc_L-4, ntrunc_L);
data/infernal-1.1.3/src/cm_alidisplay.c:762:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad->aseq_el + n5p_skipped, p7ad->aseq, ad->N);
data/infernal-1.1.3/src/cm_alidisplay.c:768:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad->rfline_el + n5p_skipped, p7ad->model, ad->N);
data/infernal-1.1.3/src/cm_alidisplay.c:774:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad->ppline_el + n5p_skipped, p7ad->ppline, ad->N);
data/infernal-1.1.3/src/cm_alidisplay.c:822:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ad2->mem, ad->mem, ad->memsize);
data/infernal-1.1.3/src/cm_alidisplay.c:1372:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(msa->aseq[0], ad->aseq_el, ad->N_el);
data/infernal-1.1.3/src/cm_dpalign.c:5879:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_dpalign_trunc.c:9948:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_dpsearch.c:4329:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_dpsearch_trunc.c:3666:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_dpsmall.c:2889:19: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
yoffset = ((char **) shadow[v])[j][d];
data/infernal-1.1.3/src/cm_dpsmall.c:3416:57: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
else free_vjd_yshadow_deck((char **) shadow[v], i, j);
data/infernal-1.1.3/src/cm_dpsmall.c:6322:20: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
yoffset = ((char **) shadow[v])[j][vdp];
data/infernal-1.1.3/src/cm_dpsmall.c:7074:19: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
yoffset = ((char **) shadow[v])[j][dp];
data/infernal-1.1.3/src/cm_file.c:264:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
union { char c[4]; uint32_t n; } magic;
data/infernal-1.1.3/src/cm_file.c:321:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cmfp->f = fopen(filename, "r")) != NULL)
data/infernal-1.1.3/src/cm_file.c:354:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((tmpfp = fopen(dbfile, "rb")) != NULL)
data/infernal-1.1.3/src/cm_file.c:388:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cmfp->hfp->f = fopen(cmfp->fname, "r")) == NULL) goto ERROR;
data/infernal-1.1.3/src/cm_file.c:429:29: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cmfp->ffp = fopen(dbfile, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, errbuf, "Opened %s, a pressed CM file; but no .i1f file found", cmfp->fname);
data/infernal-1.1.3/src/cm_file.c:430:29: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cmfp->hfp->ffp = fopen(dbfile, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, errbuf, "Opened %s, a pressed CM file; but no .i1f file found", cmfp->fname);
data/infernal-1.1.3/src/cm_file.c:433:29: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cmfp->hfp->pfp = fopen(dbfile, "rb")) == NULL) ESL_XFAIL(eslENOTFOUND, errbuf, "Opened %s, a pressed CM file; but no .i1p file found", cmfp->fname);
data/infernal-1.1.3/src/cm_file.c:1615:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((cm->M = atoi(tok1)) == 0) ESL_XFAIL(status, cmfp->errbuf, "Invalid number of states %s on STATES line", tok1);
data/infernal-1.1.3/src/cm_file.c:1620:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((cm->nodes = atoi(tok1)) == 0) ESL_XFAIL(status, cmfp->errbuf, "Invalid number of nodes %s on NODES line", tok1);
data/infernal-1.1.3/src/cm_file.c:1625:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((cm->clen = atoi(tok1)) == 0) ESL_XFAIL(status, cmfp->errbuf, "Invalid consensus length %s on CLEN line", tok1);
data/infernal-1.1.3/src/cm_file.c:1630:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((cm->W = atoi(tok1)) == 0) ESL_XFAIL(status, cmfp->errbuf, "Invalid consensus length %s on W line", tok1);
data/infernal-1.1.3/src/cm_file.c:1722:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((cm->nseq = atoi(tok1)) == 0) ESL_XFAIL(eslEFORMAT, cmfp->errbuf, "Invalid nseq on NSEQ line: should be integer, not %s", tok1);
data/infernal-1.1.3/src/cm_file.c:1792:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->expA[exp_mode]->nrandhits = atoi(tok5);
data/infernal-1.1.3/src/cm_file.c:1864:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nd = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1884:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
tmp_map_left[nd] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1885:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
tmp_map_right[nd] = atoi(tok2);
data/infernal-1.1.3/src/cm_file.c:1890:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
tmp_map_left[nd] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1897:26: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
tmp_map_right[nd] = atoi(tok2);
data/infernal-1.1.3/src/cm_file.c:1967:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(tok1) != v) ESL_XFAIL(status, cmfp->errbuf, "Invalid state index on state line: should be %d, not %s", v, tok1);
data/infernal-1.1.3/src/cm_file.c:1972:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->plast[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1977:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->pnum[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1982:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->cfirst[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1987:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->cnum[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1992:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->qdbinfo->dmin2[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:1997:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->qdbinfo->dmin1[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:2002:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->qdbinfo->dmax1[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:2007:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->qdbinfo->dmax2[v] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:2408:8: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
M = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2414:8: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
N = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2420:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
alphabet_type = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2443:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->nseq = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2453:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
clen = atoi(tok); /* we'll compare this to what we calculate at end of func */
data/infernal-1.1.3/src/cm_file.c:2519:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
npartitions = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2555:8: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
p = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2576:36: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->expA[exp_mode]->nrandhits = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2641:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nd = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2658:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(tok) != v) ESL_XFAIL(eslEFORMAT, cmfp->errbuf, "Invalid state line for cm: %s state: %d", cm->name, v);
data/infernal-1.1.3/src/cm_file.c:2661:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->plast[v] = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2664:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->pnum[v] = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2667:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->cfirst[v] = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2670:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
cm->cnum[v] = atoi(tok);
data/infernal-1.1.3/src/cm_file.c:2859:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->M = atoi(tok1)) == 0) ESL_XFAIL(status, hfp->errbuf, "Invalid model length %s on LENG line", tok1);
data/infernal-1.1.3/src/cm_file.c:2864:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->max_length = atoi(tok1)) == 0) ESL_XFAIL(status, hfp->errbuf, "Invalid max length %s on MAXL line", tok1);
data/infernal-1.1.3/src/cm_file.c:2933:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if ((hmm->nseq = atoi(tok1)) == 0) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "Invalid nseq on NSEQ line: should be integer, not %s", tok1);
data/infernal-1.1.3/src/cm_file.c:3060:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(tok1) != k) ESL_XFAIL(eslEFORMAT, hfp->errbuf, "Expected match line to start with %d (of %d); saw %s", k, hmm->M, tok1);
data/infernal-1.1.3/src/cm_file.c:3068:47: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (hmm->flags & p7H_MAP) hmm->map[k] = atoi(tok1);
data/infernal-1.1.3/src/cm_file.c:3313:10: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char buffer[32];
data/infernal-1.1.3/src/cm_file.c:3316:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%.3f", sreLOG2(p/null));
data/infernal-1.1.3/src/cm_file.c:3644:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_file.c:3731:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_p7_domaindef.c:427:20: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (d != d2) memcpy(ddef->sp->sigc + d, ddef->sp->sigc + d2, sizeof(struct p7_spcoord_s));
data/infernal-1.1.3/src/cm_pipeline.c:3018:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void*)(seq->dsq), subdsq, (wlen+1) * sizeof(uint8_t));
data/infernal-1.1.3/src/cm_pipeline.c:3865:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void*)(seq->dsq), subdsq, (wlen+1) * sizeof(uint8_t));
data/infernal-1.1.3/src/cm_pipeline.c:4417:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void*)(dest_sq->dsq+1), src_sq->dsq+i, L * sizeof(ESL_DSQ));
data/infernal-1.1.3/src/cm_qdband.c:591:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_qdband.c:626:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(name, "seq%d", i+1);
data/infernal-1.1.3/src/cm_submodel.c:791:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
ofp = fopen("sub.cm", "w");
data/infernal-1.1.3/src/cm_tophits.c:550:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new2, h2->unsrt, sizeof(CM_HIT) * h2->N);
data/infernal-1.1.3/src/cm_tophits.c:1510:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(cur_rankstr, "(%d)", nprinted+1);
data/infernal-1.1.3/src/cm_tophits.c:1756:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(cur_rankstr, "(%d)", nprinted+1);
data/infernal-1.1.3/src/cm_tophits.c:2483:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(any_ofctstr1, "%6.3f", (float) nres / (float) len1);
data/infernal-1.1.3/src/cm_tophits.c:2484:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(any_ofctstr2, "%6.3f", (float) nres / (float) len2);
data/infernal-1.1.3/src/cm_tophits.c:2502:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(win_ofctstr1, "%6.3f", (float) nres / (float) len1);
data/infernal-1.1.3/src/cm_tophits.c:2503:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(win_ofctstr2, "%6.3f", (float) nres / (float) len2);
data/infernal-1.1.3/src/cm_tophits.c:2505:63: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
if (th->hit[h]->flags & CM_HIT_IS_MARKED_OVERLAP) { sprintf(olp_str, " = "); maybe_skip = TRUE; }
data/infernal-1.1.3/src/cm_tophits.c:2506:63: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else if(has_overlapA[th->hit[h]->hit_idx] == TRUE) { sprintf(olp_str, " ^ "); maybe_skip = FALSE; }
data/infernal-1.1.3/src/cm_tophits.c:2507:63: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else { sprintf(olp_str, " * "); maybe_skip = FALSE; }
data/infernal-1.1.3/src/cm_tophits.c:2762:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char timestamp[32];
data/infernal-1.1.3/src/cm_tophits.c:2763:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char modestamp[16];
data/infernal-1.1.3/src/cm_tophits.c:2770:24: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
case CM_SEARCH_SEQS: strcpy(modestamp, "SEARCH"); break;
data/infernal-1.1.3/src/cm_tophits.c:2771:24: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
case CM_SCAN_MODELS: strcpy(modestamp, "SCAN"); break;
data/infernal-1.1.3/src/cm_tophits.c:3056:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cm_tophits.c:3241:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmalign.c:205:129: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
static int create_and_output_final_msa(const ESL_GETOPTS *go, const struct cfg_s *cfg, char *errbuf, CM_t *cm, int nali, char *tmpfile);
data/infernal-1.1.3/src/cmalign.c:345:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for printing error messages */
data/infernal-1.1.3/src/cmalign.c:357:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX"; /* name of the tmpfile */
data/infernal-1.1.3/src/cmalign.c:357:8: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX"; /* name of the tmpfile */
data/infernal-1.1.3/src/cmalign.c:563:39: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((status = esl_tmpfile_named(tmpfile, &(cfg->tmpfp))) != eslOK) cm_Fail("Failed to open temporary output file (status %d)", status);
data/infernal-1.1.3/src/cmalign.c:604:73: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = create_and_output_final_msa(go, cfg, errbuf, cm, nali, tmpfile)) != eslOK) cm_Fail(errbuf);
data/infernal-1.1.3/src/cmalign.c:605:12: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/src/cmalign.c:784:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmalign.c:905:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for printing error messages */
data/infernal-1.1.3/src/cmalign.c:917:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpfile[32] = "esltmpXXXXXX"; /* name of the tmpfile */
data/infernal-1.1.3/src/cmalign.c:917:8: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char tmpfile[32] = "esltmpXXXXXX"; /* name of the tmpfile */
data/infernal-1.1.3/src/cmalign.c:1112:39: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((status = esl_tmpfile_named(tmpfile, &(cfg->tmpfp))) != eslOK) mpi_failure("Failed to open temporary output file (status %d)", status);
data/infernal-1.1.3/src/cmalign.c:1159:73: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = create_and_output_final_msa(go, cfg, errbuf, cm, nali, tmpfile)) != eslOK) mpi_failure(errbuf);
data/infernal-1.1.3/src/cmalign.c:1160:12: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
remove(tmpfile);
data/infernal-1.1.3/src/cmalign.c:1188:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for printing error messages */
data/infernal-1.1.3/src/cmalign.c:1326:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/src/cmalign.c:1542:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open -o output file %s\n", esl_opt_GetString(go, "-o"));
data/infernal-1.1.3/src/cmalign.c:1545:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->tfp = fopen(esl_opt_GetString(go, "--tfile"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open --tfile output file %s\n", esl_opt_GetString(go, "--tfile"));
data/infernal-1.1.3/src/cmalign.c:1548:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->ifp = fopen(esl_opt_GetString(go, "--ifile"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open --ifile output file %s\n", esl_opt_GetString(go, "--ifile"));
data/infernal-1.1.3/src/cmalign.c:1552:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->efp = fopen(esl_opt_GetString(go, "--elfile"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open --elfile output file %s\n", esl_opt_GetString(go, "--elfile"));
data/infernal-1.1.3/src/cmalign.c:1556:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->sfp = fopen(esl_opt_GetString(go, "--sfile"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open --sfile output file %s\n", esl_opt_GetString(go, "--sfile"));
data/infernal-1.1.3/src/cmalign.c:1559:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->rfp = fopen(esl_opt_GetString(go, "--regress"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open --regress output file %s\n", esl_opt_GetString(go, "--regress"));
data/infernal-1.1.3/src/cmalign.c:2068:117: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
create_and_output_final_msa(const ESL_GETOPTS *go, const struct cfg_s *cfg, char *errbuf, CM_t *cm, int nali, char *tmpfile)
data/infernal-1.1.3/src/cmalign.c:2109:34: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = esl_msafile2_Open(tmpfile, NULL, &afp)) != eslOK) cm_Fail("unable to open temp file %s for reading", tmpfile);
data/infernal-1.1.3/src/cmalign.c:2109:117: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = esl_msafile2_Open(tmpfile, NULL, &afp)) != eslOK) cm_Fail("unable to open temp file %s for reading", tmpfile);
data/infernal-1.1.3/src/cmalign.c:2174:36: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = esl_msafile2_Open(tmpfile, NULL, &afp)) != eslOK) cm_Fail("unable to open temp file %s for reading on second pass", tmpfile);
data/infernal-1.1.3/src/cmalign.c:2174:134: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = esl_msafile2_Open(tmpfile, NULL, &afp)) != eslOK) cm_Fail("unable to open temp file %s for reading on second pass", tmpfile);
data/infernal-1.1.3/src/cmalign.c:2204:34: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = esl_msafile2_Open(tmpfile, NULL, &afp)) != eslOK) cm_Fail("unable to open temp file %s for reading on second (or third) pass", tmpfile);
data/infernal-1.1.3/src/cmalign.c:2204:143: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if((status = esl_msafile2_Open(tmpfile, NULL, &afp)) != eslOK) cm_Fail("unable to open temp file %s for reading on second (or third) pass", tmpfile);
data/infernal-1.1.3/src/cmbuild.c:445:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmbuild.c:794:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->cmoutfp = fopen(cfg->cmfile, "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open CM file %s for writing", cfg->cmfile);
data/infernal-1.1.3/src/cmbuild.c:797:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->ofp = fopen(esl_opt_GetString(go, "-o"), "w");
data/infernal-1.1.3/src/cmbuild.c:803:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cfg->postmsafp = fopen(cfg->postmsafile, "w");
data/infernal-1.1.3/src/cmbuild.c:811:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(esl_opt_GetString(go, "--prior"), "r")) == NULL) cm_Fail("Failed to open prior file %s\n", esl_opt_GetString(go, "--prior"));
data/infernal-1.1.3/src/cmbuild.c:871:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((pfp = fopen(esl_opt_GetString(go, "--p7prior"), "r")) == NULL) cm_Fail("Failed to open p7 prior file %s\n", esl_opt_GetString(go, "--p7prior"));
data/infernal-1.1.3/src/cmbuild.c:887:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->cfp = fopen(esl_opt_GetString(go, "--cfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:892:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->escfp = fopen(esl_opt_GetString(go, "--efile"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:897:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->tblfp = fopen(esl_opt_GetString(go, "--cmtbl"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:902:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->efp = fopen(esl_opt_GetString(go, "--emap"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:907:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->gfp = fopen(esl_opt_GetString(go, "--gtree"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:912:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->gtblfp = fopen(esl_opt_GetString(go, "--gtbl"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:917:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->tfp = fopen(esl_opt_GetString(go, "--tfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:923:29: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->refinefp = fopen(esl_opt_GetString(go, "--refine"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:928:23: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->rdfp = fopen(esl_opt_GetString(go, "--rdump"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:937:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->cdfp = fopen(esl_opt_GetString(go, "--cdump"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:942:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->occfp = fopen(esl_opt_GetString(go, "--occfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:947:27: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->cp9occfp = fopen(esl_opt_GetString(go, "--cp9occfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:952:27: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->fp7occfp = fopen(esl_opt_GetString(go, "--fp7occfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmbuild.c:2654:16: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
ndigits += sprintf(buffer, ".%d", (m+1));
data/infernal-1.1.3/src/cmcalibrate.c:122:22: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
char *tmpfile; /* tmp file we're writing to */
data/infernal-1.1.3/src/cmcalibrate.c:213:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmcalibrate.c:320:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_FileExists(cfg.tmpfile)) cm_Fail("Ouch. Temporary file %s appeared during the run.", cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:320:121: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_FileExists(cfg.tmpfile)) cm_Fail("Ouch. Temporary file %s appeared during the run.", cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:321:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((outfp = fopen(cfg.tmpfile, cfg.mode)) == NULL) cm_Fail("Ouch. Temporary file %s couldn't be opened for writing.", cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:321:28: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((outfp = fopen(cfg.tmpfile, cfg.mode)) == NULL) cm_Fail("Ouch. Temporary file %s couldn't be opened for writing.", cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:321:128: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ((outfp = fopen(cfg.tmpfile, cfg.mode)) == NULL) cm_Fail("Ouch. Temporary file %s couldn't be opened for writing.", cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:356:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (rename(cfg.tmpfile, cfg.cmfile) != 0) cm_Fail("system error during rewrite of CM file.");
data/infernal-1.1.3/src/cmcalibrate.c:358:14: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
free(cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:399:11: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (cfg.tmpfile != NULL) free(cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:399:37: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (cfg.tmpfile != NULL) free(cfg.tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:437:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for printing error messages */
data/infernal-1.1.3/src/cmcalibrate.c:442:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char time_buf[128]; /* string for printing elapsed time (safely holds up to 10^14 years) */
data/infernal-1.1.3/src/cmcalibrate.c:799:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmcalibrate.c:882:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for printing error messages */
data/infernal-1.1.3/src/cmcalibrate.c:887:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char time_buf[128]; /* string for printing elapsed time (safely holds up to 10^14 years) */
data/infernal-1.1.3/src/cmcalibrate.c:1150:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for printing error messages */
data/infernal-1.1.3/src/cmcalibrate.c:1315:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/src/cmcalibrate.c:1461:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->hfp = fopen(esl_opt_GetString(go, "--hfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmcalibrate.c:1465:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->sfp = fopen(esl_opt_GetString(go, "--sfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmcalibrate.c:1469:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->qfp = fopen(esl_opt_GetString(go, "--qqfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmcalibrate.c:1473:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->ffp = fopen(esl_opt_GetString(go, "--ffile"), "w")) == NULL)
data/infernal-1.1.3/src/cmcalibrate.c:1477:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->xfp = fopen(esl_opt_GetString(go, "--xfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmcalibrate.c:1495:18: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
ESL_ALLOC(cfg->tmpfile, (sizeof(char) * (strlen(cfg->cmfile) + 5)));
data/infernal-1.1.3/src/cmcalibrate.c:1496:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcpy(cfg->tmpfile, cfg->cmfile);
data/infernal-1.1.3/src/cmcalibrate.c:1497:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(cfg->tmpfile, ".xxx"); /* could be more inventive here... */
data/infernal-1.1.3/src/cmcalibrate.c:1497:15: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
strcat(cfg->tmpfile, ".xxx"); /* could be more inventive here... */
data/infernal-1.1.3/src/cmcalibrate.c:1498:27: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_FileExists(cfg->tmpfile)) ESL_FAIL(eslFAIL, errbuf, "temporary file %s already exists; please delete it first", cfg->tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:1498:128: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if (esl_FileExists(cfg->tmpfile)) ESL_FAIL(eslFAIL, errbuf, "temporary file %s already exists; please delete it first", cfg->tmpfile);
data/infernal-1.1.3/src/cmcalibrate.c:1838:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char time_buf[128]; /* for printing run time */
data/infernal-1.1.3/src/cmcalibrate.c:1857:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char time_buf[128];
data/infernal-1.1.3/src/cmcalibrate.c:1990:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(sq->name, "irrelevant");
data/infernal-1.1.3/src/cmconvert.c:52:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmconvert.c:68:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open output file %s", esl_opt_GetString(go, "-o"));
data/infernal-1.1.3/src/cmemit.c:192:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open output file %s", esl_opt_GetString(go, "-o"));
data/infernal-1.1.3/src/cmemit.c:202:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->tfp = fopen(esl_opt_GetString(go, "--tfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmemit.c:225:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmemit.c:366:28: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else sprintf(name, "%d-sample%d", cfg->ncm, i+offset);
data/infernal-1.1.3/src/cmemit.c:516:23: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else sprintf(name, "%d-sample%d", cfg->ncm, i+offset);
data/infernal-1.1.3/src/cmemit.c:540:23: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
else sprintf(name, "%d-sample%d", cfg->ncm, i+offset);
data/infernal-1.1.3/src/cmfetch.c:78:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmfetch.c:140:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
data/infernal-1.1.3/src/cmfetch.c:145:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/src/cmpress.c:66:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmpress.c:164:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmpress.c:192:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((dbf->mfp = fopen(dbf->mfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "Failed to open binary CM file %s for writing", dbf->mfile);
data/infernal-1.1.3/src/cmpress.c:193:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((dbf->ffp = fopen(dbf->ffile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "Failed to open binary MSV filter file %s for writing", dbf->ffile);
data/infernal-1.1.3/src/cmpress.c:194:19: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((dbf->pfp = fopen(dbf->pfile, "wb")) == NULL) ESL_XFAIL(eslEWRITE, errbuf, "Failed to open binary profile file %s for writing", dbf->pfile);
data/infernal-1.1.3/src/cmscan.c:451:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmscan.c:511:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
data/infernal-1.1.3/src/cmscan.c:512:58: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
data/infernal-1.1.3/src/cmscan.c:1290:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmscan.c:1346:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o") && (ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/src/cmscan.c:1348:54: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout") && (tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL)
data/infernal-1.1.3/src/cmscan.c:1685:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmscan.c:2900:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/src/cmsearch.c:472:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmsearch.c:488:60: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) cm_Fail("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
data/infernal-1.1.3/src/cmsearch.c:489:60: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-A")) { if ((afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL) cm_Fail("Failed to open alignment file %s for writing\n", esl_opt_GetString(go, "-A")); }
data/infernal-1.1.3/src/cmsearch.c:490:60: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) cm_Fail("Failed to open tabular output file %s for writing\n", esl_opt_GetString(go, "--tblout")); }
data/infernal-1.1.3/src/cmsearch.c:1092:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmsearch.c:1116:40: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "-o") && (ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
data/infernal-1.1.3/src/cmsearch.c:1120:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((afp = fopen(esl_opt_GetString(go, "-A"), "w")) == NULL)
data/infernal-1.1.3/src/cmsearch.c:1124:48: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (esl_opt_IsOn(go, "--tblout") && (tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL)
data/infernal-1.1.3/src/cmsearch.c:1492:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for reporting errors */
data/infernal-1.1.3/src/cmsearch.c:2497:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[512];
data/infernal-1.1.3/src/cmsim.c:214:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->ifp = fopen(esl_opt_GetString(go, "--ifile"), "w")) == NULL)
data/infernal-1.1.3/src/cmsim.c:218:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((cfg->rfp = fopen(esl_opt_GetString(go, "--rfile"), "w")) == NULL)
data/infernal-1.1.3/src/cmsim.c:245:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cmsim.c:745:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dsq, sq->dsq, sizeof(ESL_DSQ) * (sq->n+2));
data/infernal-1.1.3/src/cmstat.c:72:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for error messages */
data/infernal-1.1.3/src/cmstat.c:240:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for error messages */
data/infernal-1.1.3/src/cp9-test.c:63:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE]; /* for error messages */
data/infernal-1.1.3/src/cp9_dp.c:1499:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cp9_dp.c:1643:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/cp9_modelmaker.c:2103:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(name, "seq%d", i+1);
data/infernal-1.1.3/src/cp9_trace.c:957:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/display.c:217:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ali->cseq+pos, "*[%*d]*", numwidth, qinset);
data/infernal-1.1.3/src/display.c:218:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ali->aseq+pos, "*[%*d]*", numwidth, tinset);
data/infernal-1.1.3/src/display.c:405:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ali->cseq+pos, "*[%*d]*", numwidth, qinset);
data/infernal-1.1.3/src/display.c:406:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ali->aseq+pos, "*[%*d]*", numwidth, tinset);
data/infernal-1.1.3/src/display.c:1270:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%02d:%02d:%02d.%02d", h,m,s,hs);
data/infernal-1.1.3/src/display.c:1272:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%02d:%02d:%02d", h,m,s);
data/infernal-1.1.3/src/impl_sse/sse_cm_dpsearch.c:824:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[cmERRBUFSIZE];
data/infernal-1.1.3/src/impl_sse/sse_cm_dpsmall.c:5319:57: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
else free_vjd_yshadow_deck((char **) shadow[v], i, j);
data/infernal-1.1.3/src/impl_sse/sse_cm_dpsmall.c:5756:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[cmERRBUFSIZE];
data/infernal-1.1.3/src/impl_sse/sse_cmcons_mscyk.c:1248:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[cmERRBUFSIZE];
data/infernal-1.1.3/src/impl_sse/sse_cmcons_mscyk.c:1449:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[cmERRBUFSIZE];
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:77:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:200:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((S0_OFILE = fopen(strcat(fname,".s0.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 0 glbf file for writing!"); }
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:200:27: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
if ((S0_OFILE = fopen(strcat(fname,".s0.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 0 glbf file for writing!"); }
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:202:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((S1_OFILE = fopen(strcat(fname,".s1.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 1 glbf file for writing!"); }
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:202:27: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
if ((S1_OFILE = fopen(strcat(fname,".s1.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 1 glbf file for writing!"); }
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:204:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((S2_OFILE = fopen(strcat(fname,".s2.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 2 glbf file for writing!"); }
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:204:27: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
if ((S2_OFILE = fopen(strcat(fname,".s2.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 2 glbf file for writing!"); }
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:206:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((S3_OFILE = fopen(strcat(fname,".s3.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 3 glbf file for writing!"); }
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:206:27: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
if ((S3_OFILE = fopen(strcat(fname,".s3.glbf"),"w")) == NULL) { cm_Fail("Couldn't open stage 3 glbf file for writing!"); }
data/infernal-1.1.3/src/infernal.h:2040:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/infernal.h:2175:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/itest_brute.c:170:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/itest_brute.c:222:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *ofp = fopen(cmpfile, "w");
data/infernal-1.1.3/src/prior.c:111:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pri->tsetnum = atoi(tok);
data/infernal-1.1.3/src/rnamat.c:485:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char linebuf[256];
data/infernal-1.1.3/src/rnamat.c:486:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char fullbuf[16384];
data/infernal-1.1.3/src/rnamat.c:642:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen (matfile, "r");
data/infernal-1.1.3/src/rnamat.c:854:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char degen_string[13] = "XRYMKSWHBVDN\0";
data/infernal-1.1.3/src/rnamat.c:855:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char rna_string[5] = "ACGU\0";
data/infernal-1.1.3/src/sub_cm-test.c:110:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/trcyk.c:39:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/truncyk.c:1464:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
((char **) shadow[v])[j][d] = USED_EL;
data/infernal-1.1.3/src/truncyk.c:1466:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
((char **)L_shadow[v])[j][d] = USED_EL;
data/infernal-1.1.3/src/truncyk.c:1467:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
((char **)R_shadow[v])[j][d] = USED_EL;
data/infernal-1.1.3/src/truncyk.c:1475:50: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) ((char **)shadow[v])[j][d] = yoffset;
data/infernal-1.1.3/src/truncyk.c:1480:50: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) ((char **)L_shadow[v])[j][d] = yoffset;
data/infernal-1.1.3/src/truncyk.c:1486:50: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) ((char **)R_shadow[v])[j][d] = yoffset;
data/infernal-1.1.3/src/truncyk.c:1638:46: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][1] = USED_EL; }
data/infernal-1.1.3/src/truncyk.c:1639:46: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][1] = USED_EL; }
data/infernal-1.1.3/src/truncyk.c:1646:46: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)shadow[v])[j][d] = USED_EL; }
data/infernal-1.1.3/src/truncyk.c:1653:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1659:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1665:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1672:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1678:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1734:48: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **) shadow[v])[j][d] = USED_EL; }
data/infernal-1.1.3/src/truncyk.c:1735:46: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = USED_EL; }
data/infernal-1.1.3/src/truncyk.c:1743:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1750:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1764:53: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1771:53: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1781:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1788:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1818:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1825:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1883:48: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **) shadow[v])[j][d] = USED_EL; }
data/infernal-1.1.3/src/truncyk.c:1884:46: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = USED_EL; }
data/infernal-1.1.3/src/truncyk.c:1892:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1898:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1912:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1919:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1937:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1943:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1950:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:1958:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[v])[j][d] = yoffset; }
data/infernal-1.1.3/src/truncyk.c:2063:42: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **) shadow[0])[j0][W] = USED_LOCAL_BEGIN; }
data/infernal-1.1.3/src/truncyk.c:2064:40: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)L_shadow[0])[j0][W] = USED_LOCAL_BEGIN; }
data/infernal-1.1.3/src/truncyk.c:2065:40: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ret_shadow != NULL ) { ((char **)R_shadow[0])[j0][W] = USED_LOCAL_BEGIN; }
data/infernal-1.1.3/src/truncyk.c:3984:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
yoffset = ((char **) shadow[v])[j][d];
data/infernal-1.1.3/src/truncyk.c:3989:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
yoffset = ((char **) L_shadow[v])[j][d];
data/infernal-1.1.3/src/truncyk.c:3994:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
yoffset = ((char **) R_shadow[v])[j][d];
data/infernal-1.1.3/src/truncyk_check.c:59:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char errbuf[eslERRBUFSIZE];
data/infernal-1.1.3/src/truncyk_check.c:107:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((regressfp = fopen(regressfile, "w")) == NULL)
data/infernal-1.1.3/easel/easel.c:589:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(s);
data/infernal-1.1.3/easel/easel.c:709:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(*buf);
data/infernal-1.1.3/easel/easel.c:723:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(s);
data/infernal-1.1.3/easel/easel.c:833:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (n < 0) n = strlen(s);
data/infernal-1.1.3/easel/easel.c:888:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (ldest < 0) len1 = ((*dest == NULL) ? 0 : strlen(*dest));
data/infernal-1.1.3/easel/easel.c:891:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (lsrc < 0) len2 = (( src == NULL) ? 0 : strlen(src));
data/infernal-1.1.3/easel/easel.c:994:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (*ldest < 0) *ldest = ( (*dest) ? strlen(*dest) : 0);
data/infernal-1.1.3/easel/easel.c:995:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( lsrc < 0) lsrc = ( (*src) ? strlen(src) : 0);
data/infernal-1.1.3/easel/easel.c:1233:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n1 = strlen(format) * 2; /* initial guess at string size needed */
data/infernal-1.1.3/easel/easel.c:1431:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (n < 0) n = strlen(s);
data/infernal-1.1.3/easel/easel.c:1576:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(s[i]);
data/infernal-1.1.3/easel/easel.c:1654:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(tail, sizeof(char) * (strlen(path)+1)); /* a little overkill */
data/infernal-1.1.3/easel/easel.c:1693:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
esl_pos_t n1 = strlen(filename) - n_ignore;
data/infernal-1.1.3/easel/easel.c:1745:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nd = (dir != NULL)? strlen(dir) : 0;
data/infernal-1.1.3/easel/easel.c:1746:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nf = strlen(file);
data/infernal-1.1.3/easel/easel.c:1807:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nf = (lastdot == NULL)? strlen(filename) : lastdot-filename;
data/infernal-1.1.3/easel/easel.c:1809:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (! new) ESL_ALLOC(new, sizeof(char) * (nf+strlen(sfx)+2)); /* '.' too */
data/infernal-1.1.3/easel/easel.c:1810:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(new, filename, nf);
data/infernal-1.1.3/easel/easel.c:1881:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
np = strlen(fname) + strlen(s) + 2; /* upper bound on full path len */
data/infernal-1.1.3/easel/easel.c:1881:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
np = strlen(fname) + strlen(s) + 2; /* upper bound on full path len */
data/infernal-1.1.3/easel/easel.c:1992:14: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
old_mode = umask(077);
data/infernal-1.1.3/easel/easel.c:1994:3: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
umask(old_mode);
data/infernal-1.1.3/easel/easel.c:2069:14: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
old_mode = umask(077);
data/infernal-1.1.3/easel/easel.c:2071:3: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
umask(old_mode);
data/infernal-1.1.3/easel/easel.c:2390:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L1 = strlen(pfx);
data/infernal-1.1.3/easel/easel.c:2391:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L2 = strlen(append);
data/infernal-1.1.3/easel/esl_alphabet.c:107:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(alphabet) != Kp) ESL_XEXCEPTION(eslEINVAL, "alphabet length != Kp");
data/infernal-1.1.3/easel/esl_alphabet.c:641:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(seq);
data/infernal-1.1.3/easel/esl_alphabet.c:928:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( n < 0) n = ( (s) ? strlen(s) : 0);
data/infernal-1.1.3/easel/esl_alphabet.c:1808:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(a->sym) != a->Kp) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_alphabet.c:1856:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (memcmp(dsq, expect, sizeof(ESL_DSQ) * (strlen(testseq)+2)) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_alphabet.c:1888:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (memcmp(dsq, expect, sizeof(ESL_DSQ) * (strlen(testseq)+2)) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_alphabet.c:1906:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (memcmp(dsq, expect, sizeof(ESL_DSQ) * (strlen(testseq)+2)) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_alphabet.c:1936:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (memcmp(dsq, expect, sizeof(ESL_DSQ) * (strlen(testseq)+2)) != 0) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_alphabet.c:2032:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (strlen(goodseq)+2));
data/infernal-1.1.3/easel/esl_alphabet.c:2062:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(goodseq);
data/infernal-1.1.3/easel/esl_alphabet.c:2117:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(goodseq);
data/infernal-1.1.3/easel/esl_alphabet.c:2152:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L1 = strlen(goodseq);
data/infernal-1.1.3/easel/esl_alphabet.c:2153:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L2 = strlen(addseq);
data/infernal-1.1.3/easel/esl_alphabet.c:2176:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L2 = strlen(badseq);
data/infernal-1.1.3/easel/esl_alphabet.c:2421:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(dnaseq);
data/infernal-1.1.3/easel/esl_arr2.c:25:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += sizeof(char) * (1 + strlen(s[i]));
data/infernal-1.1.3/easel/esl_arr3.c:28:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += sizeof(char) * (1 + strlen(s[i][j]));
data/infernal-1.1.3/easel/esl_buffer.c:149:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(path);
data/infernal-1.1.3/easel/esl_buffer.c:433:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
bf->n = (n == -1) ? strlen(p) : n;
data/infernal-1.1.3/easel/esl_buffer.c:2044:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (( n = read(fd, buf, filesize)) != filesize) esl_fatal("bad read()");
data/infernal-1.1.3/easel/esl_buffer.c:2650:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(tok) != n) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2660:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(tok) != n) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2759:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( (status = esl_buffer_OpenMem(s, strlen(s), &bf)) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:2761:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( n != strlen(s)) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_buffer.c:3045:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(s1)+1; fwrite(&n, sizeof(int), 1, fp); fwrite(s1, sizeof(char), n, fp);
data/infernal-1.1.3/easel/esl_buffer.c:3046:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(s2)+1; fwrite(&n, sizeof(int), 1, fp); fwrite(s2, sizeof(char), n, fp);
data/infernal-1.1.3/easel/esl_distance.c:1169:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(as[0]);
data/infernal-1.1.3/easel/esl_distance.c:1233:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(as[0]);
data/infernal-1.1.3/easel/esl_dsqdata.c:199:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC( dd->basename, sizeof(char) * (strlen(basename) + 6)); // +5 for .dsqx; +1 for \0
data/infernal-1.1.3/easel/esl_dsqdata.c:615:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(sq->name); if (n > max_namelen) max_namelen = n;
data/infernal-1.1.3/easel/esl_dsqdata.c:616:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(sq->acc); if (n > max_acclen) max_acclen = n;
data/infernal-1.1.3/easel/esl_dsqdata.c:617:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(sq->desc); if (n > max_desclen) max_desclen = n;
data/infernal-1.1.3/easel/esl_dsqdata.c:681:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(sq->name);
data/infernal-1.1.3/easel/esl_dsqdata.c:686:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(sq->acc);
data/infernal-1.1.3/easel/esl_dsqdata.c:691:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(sq->desc);
data/infernal-1.1.3/easel/esl_fileparser.c:348:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
blen = strlen(efp->buf);
data/infernal-1.1.3/easel/esl_fileparser.c:648:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((efp = esl_fileparser_CreateMapped(buffer, strlen(buffer))) == NULL)
data/infernal-1.1.3/easel/esl_gencode.c:437:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(aas, efp->buf+start, 64);
data/infernal-1.1.3/easel/esl_gencode.c:445:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(mline, efp->buf+start, 64);
data/infernal-1.1.3/easel/esl_gencode.c:453:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(base1, efp->buf+start, 64);
data/infernal-1.1.3/easel/esl_gencode.c:461:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(base2, efp->buf+start, 64);
data/infernal-1.1.3/easel/esl_gencode.c:469:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(base3, efp->buf+start, 64);
data/infernal-1.1.3/easel/esl_getopts.c:744:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ntot = strlen(g->argv[0]) + 1;
data/infernal-1.1.3/easel/esl_getopts.c:752:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (g->opt[i].type == eslARG_NONE) n = strlen(g->opt[i].name) + 1;
data/infernal-1.1.3/easel/esl_getopts.c:753:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else n = (strlen(g->opt[i].name) + strlen(g->val[i])) + 2;
data/infernal-1.1.3/easel/esl_getopts.c:753:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else n = (strlen(g->opt[i].name) + strlen(g->val[i])) + 2;
data/infernal-1.1.3/easel/esl_getopts.c:766:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(g->argv[j]) + 1;
data/infernal-1.1.3/easel/esl_getopts.c:1069:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(go->opt[i].name); /* "--foo" */
data/infernal-1.1.3/easel/esl_getopts.c:1075:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(go->opt[i].help) + 1; /* include " " in width */
data/infernal-1.1.3/easel/esl_getopts.c:1079:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(go->opt[i].defval) + 4; /* include " []" in width */
data/infernal-1.1.3/easel/esl_getopts.c:1083:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(go->opt[i].range) + 4; /* include " ()" in width */
data/infernal-1.1.3/easel/esl_getopts.c:1113:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(go->opt[i].name);
data/infernal-1.1.3/easel/esl_getopts.c:1224:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
arglen = strlen(optarg);
data/infernal-1.1.3/easel/esl_getopts.c:1301:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(optname); /* all of optname abbrev must match against the real name */
data/infernal-1.1.3/easel/esl_getopts.c:1308:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (n == strlen(g->opt[i].name)) { nexact++; break; } /* an exact match; can stop now (xref bug #e4) */
data/infernal-1.1.3/easel/esl_getopts.c:1414:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
{ n = strlen(g->argv[g->optind]); } /* and argptr == NULL from above. */
data/infernal-1.1.3/easel/esl_getopts.c:1620:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(val) > 1)
data/infernal-1.1.3/easel/esl_huffman.c:744:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(T);
data/infernal-1.1.3/easel/esl_huffman.c:785:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(T);
data/infernal-1.1.3/easel/esl_huffman.c:1030:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(text+n);
data/infernal-1.1.3/easel/esl_keyhash.c:273:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (n == -1) n = strlen(key);
data/infernal-1.1.3/easel/esl_mem.c:369:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( esl_memstrpfx_case(p+i, n-i, "infinity") ) { val = eslINFINITY; i += strlen("infinity"); m = 1; } // check "infinity" first, before "inf"
data/infernal-1.1.3/easel/esl_mem.c:370:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if ( esl_memstrpfx_case(p+i, n-i, "inf") ) { val = eslINFINITY; i += strlen("inf"); m = 1; }
data/infernal-1.1.3/easel/esl_mem.c:371:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if ( esl_memstrpfx_case(p+i, n-i, "nan") ) { val = eslNaN; i += strlen("nan"); m = 1; }
data/infernal-1.1.3/easel/esl_mem.c:1136:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
esl_mem_strtof(s, strlen(s), NULL, &(v2.f));
data/infernal-1.1.3/easel/esl_mem.c:1158:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(teststring);
data/infernal-1.1.3/easel/esl_mem.c:1224:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(p);
data/infernal-1.1.3/easel/esl_mem.c:1239:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(p);
data/infernal-1.1.3/easel/esl_mem.c:1257:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(p);
data/infernal-1.1.3/easel/esl_mpi.c:60:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (incount == -1 && type == MPI_CHAR) incount = strlen(inbuf) + 1;
data/infernal-1.1.3/easel/esl_mpi.c:101:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (incount == -1 && type == MPI_CHAR) incount = strlen(inbuf) + 1;
data/infernal-1.1.3/easel/esl_msa.c:461:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->name) n += sizeof(char) * (1 + strlen(msa->name));
data/infernal-1.1.3/easel/esl_msa.c:462:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->desc) n += sizeof(char) * (1 + strlen(msa->desc));
data/infernal-1.1.3/easel/esl_msa.c:463:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->acc) n += sizeof(char) * (1 + strlen(msa->acc));
data/infernal-1.1.3/easel/esl_msa.c:464:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->au) n += sizeof(char) * (1 + strlen(msa->au));
data/infernal-1.1.3/easel/esl_msa.c:1545:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (n == -1) n = strlen(p);
data/infernal-1.1.3/easel/esl_msa.c:1590:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (taglen == -1) taglen = strlen(tag);
data/infernal-1.1.3/easel/esl_msa.c:1591:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (vlen == -1) vlen = strlen(value);
data/infernal-1.1.3/easel/esl_msa.c:1639:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (taglen == -1) taglen = strlen(tag);
data/infernal-1.1.3/easel/esl_msa.c:1640:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (vlen == -1) vlen = strlen(value);
data/infernal-1.1.3/easel/esl_msa.c:1696:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n1 = strlen(msa->gs[tagidx][sqidx]);
data/infernal-1.1.3/easel/esl_msa.c:1697:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n2 = (vlen == -1 ? strlen(value) : vlen);
data/infernal-1.1.3/easel/esl_msa.c:2767:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((strlen(oldsyms) != strlen(newsyms)) && strlen(newsyms) != 1)
data/infernal-1.1.3/easel/esl_msa.c:2767:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((strlen(oldsyms) != strlen(newsyms)) && strlen(newsyms) != 1)
data/infernal-1.1.3/easel/esl_msa.c:2767:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((strlen(oldsyms) != strlen(newsyms)) && strlen(newsyms) != 1)
data/infernal-1.1.3/easel/esl_msa.c:2770:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
special = (strlen(newsyms) == 1 ? TRUE : FALSE);
data/infernal-1.1.3/easel/esl_msa.c:3168:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(msa->aseq[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: wrong length", idx);
data/infernal-1.1.3/easel/esl_msa.c:3175:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->ss && msa->ss[idx] && strlen(msa->ss[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: SS wrong length", idx);
data/infernal-1.1.3/easel/esl_msa.c:3176:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->sa && msa->sa[idx] && strlen(msa->sa[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: SA wrong length", idx);
data/infernal-1.1.3/easel/esl_msa.c:3177:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->pp && msa->pp[idx] && strlen(msa->pp[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: PP wrong length", idx);
data/infernal-1.1.3/easel/esl_msa.c:3181:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->ss_cons && strlen(msa->ss_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "SS_cons wrong length");
data/infernal-1.1.3/easel/esl_msa.c:3182:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->sa_cons && strlen(msa->sa_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "SA_cons wrong length");
data/infernal-1.1.3/easel/esl_msa.c:3183:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->pp_cons && strlen(msa->pp_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "PP_cons wrong length");
data/infernal-1.1.3/easel/esl_msa.c:3184:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->rf && strlen(msa->rf) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "RF wrong length");
data/infernal-1.1.3/easel/esl_msa.c:3185:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (msa->mm && strlen(msa->mm ) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "MM wrong length");
data/infernal-1.1.3/easel/esl_msafile.c:1298:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( esl_msafile_OpenMem(&abc, testmsa, strlen(testmsa), eslMSAFILE_STOCKHOLM, NULL, &afp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile2.c:172:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(filename);
data/infernal-1.1.3/easel/esl_msafile2.c:212:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(cmd, sizeof(char) * (n+1+strlen("gzip -dc ")));
data/infernal-1.1.3/easel/esl_msafile2.c:630:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(i = 0; i < msa->ngc; i++) maxgc = ESL_MAX(maxgc, strlen(msa->gc_tag[i]));
data/infernal-1.1.3/easel/esl_msafile2.c:639:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(i = 0; i < msa->ngf; i++) maxgf = ESL_MAX(maxgf, strlen(msa->gf_tag[i]));
data/infernal-1.1.3/easel/esl_msafile_afa.c:296:20: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (! msa->abc) strncpy(buf, msa->aseq[i] + pos, acpl);
data/infernal-1.1.3/easel/esl_msafile_clustal.c:353:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namelen = strlen(msa->sqname[i]);
data/infernal-1.1.3/easel/esl_msafile_clustal.c:372:20: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (! msa->abc) strncpy(buf, msa->aseq[i]+apos, cpl);
data/infernal-1.1.3/easel/esl_msafile_clustal.c:375:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, consline+apos, cpl);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:519:8: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->aseq[idx]+apos, rpl);
data/infernal-1.1.3/easel/esl_msafile_phylip.c:634:8: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->aseq[idx]+apos, rpl);
data/infernal-1.1.3/easel/esl_msafile_selex.c:304:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namelen = strlen(msa->sqname[i]);
data/infernal-1.1.3/easel/esl_msafile_selex.c:318:20: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (! msa->abc) strncpy(buf, msa->aseq[i]+apos, cpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1209:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
gslen = strlen(msa->gs_tag[i]);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1232:20: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (! msa->abc) strncpy(buf, msa->aseq[i] + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1237:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->ss[i] + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1242:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->sa[i] + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1247:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->pp[i] + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1253:8: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->gr[j][i] + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1260:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->ss_cons + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1264:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->sa_cons + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1268:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->pp_cons + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1272:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->rf + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1276:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->mm + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:1280:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, msa->gc[j] + currpos, acpl);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2371:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2421:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != expected_status) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msafile_stockholm.c:2432:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != eslOK) esl_fatal(msg);
data/infernal-1.1.3/easel/esl_msashuffle.c:448:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(x);
data/infernal-1.1.3/easel/esl_msashuffle.c:449:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(y) != L) ESL_XEXCEPTION(eslEINVAL, "sequences of different lengths in qrna shuffle");
data/infernal-1.1.3/easel/esl_randomseq.c:225:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(s);
data/infernal-1.1.3/easel/esl_randomseq.c:290:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(s);
data/infernal-1.1.3/easel/esl_randomseq.c:491:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int L = strlen(s);
data/infernal-1.1.3/easel/esl_randomseq.c:540:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(s);
data/infernal-1.1.3/easel/esl_randomseq.c:578:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(s);
data/infernal-1.1.3/easel/esl_randomseq.c:631:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(s);
data/infernal-1.1.3/easel/esl_randomseq.c:690:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
L = strlen(s);
data/infernal-1.1.3/easel/esl_randomseq.c:1687:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
K = strlen(alphabet);
data/infernal-1.1.3/easel/esl_randomseq.c:1981:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int L = strlen(testseq);
data/infernal-1.1.3/easel/esl_randomseq.c:2047:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int K = strlen(alphabet);
data/infernal-1.1.3/easel/esl_regexp.c:240:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(s, machine->ndfa->startp[elem], len);
data/infernal-1.1.3/easel/esl_regexp.c:282:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buffer, machine->ndfa->startp[elem], len);
data/infernal-1.1.3/easel/esl_regexp.c:643:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (OP(scan) == EXACTLY && strlen(OPERAND(scan)) >= len) {
data/infernal-1.1.3/easel/esl_regexp.c:645:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(OPERAND(scan));
data/infernal-1.1.3/easel/esl_regexp.c:1243:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(opnd);
data/infernal-1.1.3/easel/esl_regexp.c:1373:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*ret_count = strlen(ep->reginput);
data/infernal-1.1.3/easel/esl_regexp.c:1469:9: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
(void) strcpy(buf, ":");
data/infernal-1.1.3/easel/esl_regexp.c:1511:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(buf+strlen(buf), "OPEN%d", OP(op)-OPEN);
data/infernal-1.1.3/easel/esl_regexp.c:1523:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(buf+strlen(buf), "CLOSE%d", OP(op)-CLOSE);
data/infernal-1.1.3/easel/esl_regexp.c:1583:11: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
(void) strncpy(dst, prog->startp[no], len);
data/infernal-1.1.3/easel/esl_scorematrix.c:859:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
S->nc = strlen(S->outorder);
data/infernal-1.1.3/easel/esl_scorematrix.c:894:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(S->outorder, S->abc_r->sym, S->K);
data/infernal-1.1.3/easel/esl_scorematrix.c:945:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(S->outorder, S->abc_r->sym, S->abc_r->K);
data/infernal-1.1.3/easel/esl_sq.c:96:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int64_t n = strlen(seq);
data/infernal-1.1.3/easel/esl_sq.c:104:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(ss) != n) ESL_XEXCEPTION(eslEINVAL, "ss, seq lengths mismatch");
data/infernal-1.1.3/easel/esl_sq.c:785:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(ss) != sq->n) ESL_XEXCEPTION(eslEINVAL, "ss, seq lengths mismatch");
data/infernal-1.1.3/easel/esl_sq.c:1055:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(name);
data/infernal-1.1.3/easel/esl_sq.c:1093:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(acc);
data/infernal-1.1.3/easel/esl_sq.c:1133:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(desc);
data/infernal-1.1.3/easel/esl_sq.c:1171:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(source);
data/infernal-1.1.3/easel/esl_sq.c:1381:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int dlen = (sq->desc == NULL ? 0 : strlen(sq->desc));
data/infernal-1.1.3/easel/esl_sq.c:1382:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int newlen = (desc == NULL ? 0 : strlen(desc));
data/infernal-1.1.3/easel/esl_sq.c:1815:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(sq->ss, sizeof(char) * (strlen(ss)+2));
data/infernal-1.1.3/easel/esl_sq.c:1823:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(sq->xr[x], sizeof(char) * (strlen(xr[x])+2));
data/infernal-1.1.3/easel/esl_sq.c:2231:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(name)+1;
data/infernal-1.1.3/easel/esl_sq.c:2245:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(desc)+1;
data/infernal-1.1.3/easel/esl_sq.c:2259:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(acc)+1;
data/infernal-1.1.3/easel/esl_sq.c:2302:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int64_t n = strlen(seq);
data/infernal-1.1.3/easel/esl_sq.c:2423:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int64_t n = strlen(seq);
data/infernal-1.1.3/easel/esl_sq.c:2698:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(testseq);
data/infernal-1.1.3/easel/esl_sq.c:2749:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(testseq);
data/infernal-1.1.3/easel/esl_sqio.c:166:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(sqfp->filename, sizeof(char) * (strlen(filename) + 1));
data/infernal-1.1.3/easel/esl_sqio.c:190:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(list, sizeof(char) * (strlen(s1) + 1));
data/infernal-1.1.3/easel/esl_sqio.c:193:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(path, sizeof(char) * (strlen(filename) + strlen(list) + 3));
data/infernal-1.1.3/easel/esl_sqio.c:193:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(path, sizeof(char) * (strlen(filename) + strlen(list) + 3));
data/infernal-1.1.3/easel/esl_sqio.c:198:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(s1);
data/infernal-1.1.3/easel/esl_sqio.c:358:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return sqfp->read(sqfp, sq);
data/infernal-1.1.3/easel/esl_sqio.c:1140:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(sq->name);
data/infernal-1.1.3/easel/esl_sqio.c:1144:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(sq->acc);
data/infernal-1.1.3/easel/esl_sqio.c:1148:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(sq->desc);
data/infernal-1.1.3/easel/esl_sqio.c:1179:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(cache->filename, strlen(seqfile) + 1);
data/infernal-1.1.3/easel/esl_sqio.c:1210:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hdr_ptr += strlen(sq->name) + 1;
data/infernal-1.1.3/easel/esl_sqio.c:1217:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hdr_ptr += strlen(sq->acc) + 1;
data/infernal-1.1.3/easel/esl_sqio.c:1224:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hdr_ptr += strlen(sq->desc) + 1;
data/infernal-1.1.3/easel/esl_sqio.c:1604:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ( (n = read(fd, buf, bufsize)) > 0)
data/infernal-1.1.3/easel/esl_sqio.c:2317:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
status = esl_sqio_Parse(test, strlen(test), sq, format);
data/infernal-1.1.3/easel/esl_sqio.c:2354:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
printf("%-40s length: %8ld desclen: %lu\n", sq->name, (long) sq->L, (unsigned long) strlen(sq->desc));
data/infernal-1.1.3/easel/esl_sqio.h:55:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int (*read) (struct esl_sqio_s *sqfp, ESL_SQ *sq);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:215:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(filename);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:220:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(cmd, sizeof(char) * (n+1+strlen("gzip -dc ")));
data/infernal-1.1.3/easel/esl_sqio_ascii.c:373:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(sqfp->filename);
data/infernal-1.1.3/easel/esl_sqio_ascii.c:3151:28: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
else strncpy(buf, sq->seq+pos, 60);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:266:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(filename);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:335:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(filename);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:425:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(ncbi->vols[vol].name, sizeof(char) * strlen(dbptr) + 5);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:539:3: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fgetc(ncbi->fppsq);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1417:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(name);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:1460:3: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fgetc(ncbi->fppsq);
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2164:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (x = 0; x < strlen(ncbisym); ++x) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2165:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (y = 0; y < strlen(abc->sym); ++y) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2173:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (y >= strlen(abc->sym)) return eslEFORMAT;
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2212:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (x = 0; x < strlen(ncbisym); ++x) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2213:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (y = 0; y < strlen(abc->sym); ++y) {
data/infernal-1.1.3/easel/esl_sqio_ncbi.c:2221:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (y >= strlen(abc->sym)) return eslEFORMAT;
data/infernal-1.1.3/easel/esl_ssi.c:727:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(filename);
data/infernal-1.1.3/easel/esl_ssi.c:861:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(key)+1;
data/infernal-1.1.3/easel/esl_ssi.c:940:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(alias)+1;
data/infernal-1.1.3/easel/esl_ssi.c:1088:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(ns->ptmpfile) > 256 || strlen(ns->ptmpfile) > 256)
data/infernal-1.1.3/easel/esl_ssi.c:1088:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(ns->ptmpfile) > 256 || strlen(ns->ptmpfile) > 256)
data/infernal-1.1.3/easel/esl_ssi.c:1134:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(fk, ns->filenames[i], ns->flen);
data/infernal-1.1.3/easel/esl_ssi.c:1148:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant character.
if (ns->nprimary) strncpy(pk, "", ns->plen);
data/infernal-1.1.3/easel/esl_ssi.c:1154:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pk, pkey.key, ns->plen); // strncpy() pads w/ nulls, and we count on that behavior.
data/infernal-1.1.3/easel/esl_ssi.c:1166:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant character.
if (ns->nprimary) strncpy(pk, "", ns->plen);
data/infernal-1.1.3/easel/esl_ssi.c:1170:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pk, ns->pkeys[i].key, ns->plen);
data/infernal-1.1.3/easel/esl_ssi.c:1186:27: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant character.
if (ns->nsecondary) strncpy(sk, "", ns->slen);
data/infernal-1.1.3/easel/esl_ssi.c:1192:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(sk, skey.key, ns->slen); // slen > 0 if there are any secondary keys.
data/infernal-1.1.3/easel/esl_ssi.c:1193:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pk, skey.pkey, ns->plen);
data/infernal-1.1.3/easel/esl_ssi.c:1203:27: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant character.
if (ns->nsecondary) strncpy(sk, "", ns->slen);
data/infernal-1.1.3/easel/esl_ssi.c:1207:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(sk, ns->skeys[i].key, ns->slen);
data/infernal-1.1.3/easel/esl_ssi.c:1208:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pk, ns->skeys[i].pkey, ns->plen);
data/infernal-1.1.3/easel/esl_stack.c:861:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(str);
data/infernal-1.1.3/easel/esl_stack.c:973:7: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(esl_rnd_Roll(r, 100)+1); /* 1..100 usec delay */
data/infernal-1.1.3/easel/esl_stack.c:989:7: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(esl_rnd_Roll(r, 100)+1); /* 1..100 usec delay */
data/infernal-1.1.3/easel/esl_wuss.c:648:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(oldss);
data/infernal-1.1.3/easel/esl_wuss.c:803:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(ss);
data/infernal-1.1.3/easel/miniapps/cmd_downsample.c:39:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
status = esl_mem_strtoi64(Marg, strlen(Marg), 10, &nc, &M);
data/infernal-1.1.3/easel/miniapps/cmd_downsample.c:40:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (status != eslOK || nc != strlen(Marg)) esl_fatal("First argument is an integer: number of data elements to take from <infile>");
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:770:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(amask_len != (int) strlen(amask)) { ESL_FAIL(eslEINVAL, errbuf, "write_rf_given_alen(), passed in mask len (%d) is not equal to actual mask length (%d)\n", amask_len, (int) strlen(amask)); }
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:770:179: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(amask_len != (int) strlen(amask)) { ESL_FAIL(eslEINVAL, errbuf, "write_rf_given_alen(), passed in mask len (%d) is not equal to actual mask length (%d)\n", amask_len, (int) strlen(amask)); }
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:811:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(mask_for_rf_len != (int) strlen(mask_for_rf)) { ESL_FAIL(eslEINVAL, errbuf, "write_rf_given_rflen(), passed in mask len (%d) is not equal to actual mask length (%d).\n", mask_for_rf_len, (int) strlen(mask_for_rf)); }
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:811:199: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(mask_for_rf_len != (int) strlen(mask_for_rf)) { ESL_FAIL(eslEINVAL, errbuf, "write_rf_given_rflen(), passed in mask len (%d) is not equal to actual mask length (%d).\n", mask_for_rf_len, (int) strlen(mask_for_rf)); }
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:1043:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uaend = uastart + strlen(uasubseq) - 1;
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:1462:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
masklen = strlen(xmask);
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:2875:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(rf) != msa->alen) ESL_FAIL(eslEINCOMPAT, errbuf, "'#=GF %s <RF sequence>' markup is of length %d but it must be equal to aln length (%" PRId64 ").", msa->gf_tag[f], (int) strlen(rf), msa->alen);
data/infernal-1.1.3/easel/miniapps/esl-alimanip.c:2875:183: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(rf) != msa->alen) ESL_FAIL(eslEINCOMPAT, errbuf, "'#=GF %s <RF sequence>' markup is of length %d but it must be equal to aln length (%" PRId64 ").", msa->gf_tag[f], (int) strlen(rf), msa->alen);
data/infernal-1.1.3/easel/miniapps/esl-alimerge.c:241:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namewidth = ESL_MAX(namewidth, strlen(tmpstr));
data/infernal-1.1.3/easel/miniapps/esl-alimerge.c:1795:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(s[i]);
data/infernal-1.1.3/easel/miniapps/esl-compalign.c:344:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(ni = 0; ni < ka->nseq; ni++) namewidth = ESL_MAX(namewidth, strlen(ka->sqname[ni]));
data/infernal-1.1.3/easel/miniapps/esl-construct.c:231:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(i = 0; i < msa->nseq; i++) namewidth = ESL_MAX(namewidth, strlen(msa->sqname[i]));
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:173:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (gapsym != NULL && strlen(gapsym) != 1)
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:450:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
special = (strlen(newsyms) == 1 ? TRUE : FALSE);
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:691:8: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(aseqbuf, aseq + apos, acpl);
data/infernal-1.1.3/easel/miniapps/esl-reformat.c:918:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rlen = strlen(rstring);
data/infernal-1.1.3/easel/miniapps/esl-shuffle.c:293:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(targ, sq->seq + pos, L);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1676:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(text[1], sizeof(char) * (strlen("as the least ambiguous nt that represents >= 1.00") + 1));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1688:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(text[2], sizeof(char) * (strlen("Capitalized nts occur in >= 1.00 fraction of sequences") + 1));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1766:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(((int) strlen(text)) <= max_chars_per_line) {
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1771:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if(((int) strlen(text)) > ((2 * max_chars_per_line) - 6)) {
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1776:119: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_FAIL(eslEINVAL, errbuf, "add_text_to_scheme_colorlegend(), text is %d chars, max allowed is %d (%s)\n", (int) strlen(text), ((2 * max_chars_per_line) - 6), text);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1790:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = (int) strlen(text);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1817:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(((int) strlen(text)) > (max_chars_per_line)) {
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1818:120: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_FAIL(eslEINVAL, errbuf, "add_text_to_onecell_colorlegend(), text is %d chars, max allowed is %d (%s)\n", (int) strlen(text), max_chars_per_line, text);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1887:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int textlen = (int) strlen(text);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1967:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
mask_file_len = (int) strlen(ps->mask);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:1968:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
maskdiff_file_len = (int) strlen(maskdiff_file);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:2145:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(occl->celltext == NULL || (strlen(occl->celltext) > 0)) {
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:3460:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namewidth = ESL_MAX(namewidth, strlen(msa->sqname[i]));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:5338:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if((strlen(mask_file) + strlen(mask_desc)) > (ps->desc_max_chars*2 - 2)) { /* desc would be too long, shorten mask_file so desc is legal */
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:5338:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if((strlen(mask_file) + strlen(mask_desc)) > (ps->desc_max_chars*2 - 2)) { /* desc would be too long, shorten mask_file so desc is legal */
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:5340:84: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if((status = esl_strcat(&(mask_desc), -1, mask_file, ((ps->desc_max_chars*2) - strlen(mask_desc) - 5))) != eslOK) ESL_FAIL(status, errbuf, "error copying mask file name string");
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6181:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
model_width = ESL_MAX(strlen("model"), (int) strlen(ps->modelname));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6181:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
model_width = ESL_MAX(strlen("model"), (int) strlen(ps->modelname));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6238:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
desc_width = ESL_MAX((int) strlen(desc_string), (int) strlen(ps->descA[page]));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6238:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
desc_width = ESL_MAX((int) strlen(desc_string), (int) strlen(ps->descA[page]));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6952:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(desc) > (ps->desc_max_chars*2.)) esl_fatal("Error reading --dfile, description length (%d) exceeds max allowed (%d)", strlen(desc), (ps->desc_max_chars*2));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6952:130: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(desc) > (ps->desc_max_chars*2.)) esl_fatal("Error reading --dfile, description length (%d) exceeds max allowed (%d)", strlen(desc), (ps->desc_max_chars*2));
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6961:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(legheader) > ps->legx_max_chars) esl_fatal("Error reading --dfile, legend header length (%d) exceeds max allowed (%d)", strlen(legheader), ps->legx_max_chars);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:6961:132: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(legheader) > ps->legx_max_chars) esl_fatal("Error reading --dfile, legend header length (%d) exceeds max allowed (%d)", strlen(legheader), ps->legx_max_chars);
data/infernal-1.1.3/easel/miniapps/esl-ssdraw.c:7101:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(((int) strlen(s)) != 1) esl_fatal("Read multi-character string (%s) for consensus nucleotide %d on line %d of expertfile %s\n", s, cpos, efp->linenumber, efile);
data/infernal-1.1.3/hmmer/profmark/rocplot.c:290:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qlen = strlen(query);
data/infernal-1.1.3/hmmer/profmark/rocplot.c:291:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int tlen = strlen(target);
data/infernal-1.1.3/hmmer/src/cachedb.c:119:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
i = strlen(ptr);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:127:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
i = strlen(ptr);
data/infernal-1.1.3/hmmer/src/cachedb_shard.c:404:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
i = strlen(ptr);
data/infernal-1.1.3/hmmer/src/generic_viterbi.c:451:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int L = strlen(targ);
data/infernal-1.1.3/hmmer/src/hmmc2.c:301:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(buffer);
data/infernal-1.1.3/hmmer/src/hmmc2.c:327:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(seq);
data/infernal-1.1.3/hmmer/src/hmmc2.c:412:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(seq);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1094:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((n = read(data->sock_fd, ptr, remaining)) < 0) {
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1193:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
status = esl_sqio_Parse(ptr, strlen(ptr), seq, eslSQFILE_DAEMON);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1203:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
status = p7_hmmfile_OpenBuffer(ptr, strlen(ptr), &hfp);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1231:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = n + strlen(opt_str) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1234:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = n + strlen(seq->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1235:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = n + strlen(seq->desc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1242:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->name != NULL) n = n + strlen(hmm->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1243:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->acc != NULL) n = n + strlen(hmm->acc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1244:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->desc != NULL) n = n + strlen(hmm->desc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1258:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd->srch.opts_length = strlen(opt_str) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1269:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(seq->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1273:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(seq->desc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1298:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->name) { n = strlen(hmm->name) + 1; memcpy(ptr, hmm->name, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1299:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->acc) { n = strlen(hmm->acc) + 1; memcpy(ptr, hmm->acc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1300:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->desc) { n = strlen(hmm->desc) + 1; memcpy(ptr, hmm->desc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1418:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(targs->ip_addr, inet_ntoa(addr.sin_addr), addrlen);
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1684:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (parent->seq_db != NULL) n += strlen(parent->seq_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1685:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (parent->hmm_db != NULL) n += strlen(parent->hmm_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1704:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(cmd->init.sid, parent->seq_db->id, sizeof(cmd->init.sid));
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1708:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p += strlen(parent->seq_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1720:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p += strlen(parent->hmm_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr.c:1850:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(worker->ip_addr, inet_ntoa(addr.sin_addr), addrlen);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1133:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((n = read(data->sock_fd, ptr, remaining)) < 0) {
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1232:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
status = esl_sqio_Parse(ptr, strlen(ptr), seq, eslSQFILE_DAEMON);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1242:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
status = p7_hmmfile_OpenBuffer(ptr, strlen(ptr), &hfp);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1270:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = n + strlen(opt_str) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1273:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = n + strlen(seq->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1274:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = n + strlen(seq->desc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1281:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->name != NULL) n = n + strlen(hmm->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1282:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->acc != NULL) n = n + strlen(hmm->acc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1283:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->desc != NULL) n = n + strlen(hmm->desc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1297:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd->srch.opts_length = strlen(opt_str) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1308:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(seq->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1312:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(seq->desc) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1337:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->name) { n = strlen(hmm->name) + 1; memcpy(ptr, hmm->name, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1338:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->acc) { n = strlen(hmm->acc) + 1; memcpy(ptr, hmm->acc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1339:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->desc) { n = strlen(hmm->desc) + 1; memcpy(ptr, hmm->desc, n); ptr += n; }
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1457:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(targs->ip_addr, inet_ntoa(addr.sin_addr), addrlen);
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1724:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (parent->seq_db != NULL) n += strlen(parent->seq_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1725:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (parent->hmm_db != NULL) n += strlen(parent->hmm_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1744:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(cmd->init.sid, parent->seq_db->id, sizeof(cmd->init.sid));
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1748:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p += strlen(parent->seq_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1762:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
p += strlen(parent->hmm_db->name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdmstr_shard.c:1888:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(worker->ip_addr, inet_ntoa(addr.sin_addr), addrlen);
data/infernal-1.1.3/hmmer/src/hmmdutils.c:147:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((bytes = read(fd, ptr, remaining)) <= 0) {
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:391:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
desc = name + strlen(name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:392:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dsq = (ESL_DSQ *) (desc + strlen(desc) + 1);
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:426:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (thmm.name) { hmm->name = strdup(p); p += strlen(hmm->name) + 1; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:427:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (thmm.acc) { hmm->acc = strdup(p); p += strlen(hmm->acc) + 1; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr.c:428:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (thmm.desc) { hmm->desc = strdup(p); p += strlen(hmm->desc) + 1; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:418:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
desc = name + strlen(name) + 1;
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:419:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dsq = (ESL_DSQ *) (desc + strlen(desc) + 1);
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:453:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (thmm.name) { hmm->name = strdup(p); p += strlen(hmm->name) + 1; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:454:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (thmm.acc) { hmm->acc = strdup(p); p += strlen(hmm->acc) + 1; }
data/infernal-1.1.3/hmmer/src/hmmdwrkr_shard.c:455:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (thmm.desc) { hmm->desc = strdup(p); p += strlen(hmm->desc) + 1; }
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:93:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(om->name);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:132:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(om->acc);
data/infernal-1.1.3/hmmer/src/impl_sse/io.c:141:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(om->desc);
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:155:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->name != NULL) len += strlen(om->name) + 1;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:156:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->acc != NULL) len += strlen(om->acc) + 1;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:157:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->desc != NULL) len += strlen(om->desc) + 1;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:158:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->rf != NULL) len += strlen(om->rf) + 1;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:159:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->mm != NULL) len += strlen(om->mm) + 1;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:160:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->cs != NULL) len += strlen(om->cs) + 1;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:161:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->consensus != NULL) len += strlen(om->consensus) + 1;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:259:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->name != NULL) ? strlen(om->name)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:263:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->acc != NULL) ? strlen(om->acc)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:267:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->desc != NULL) ? strlen(om->desc)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:271:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->rf != NULL) ? strlen(om->rf)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:275:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->mm != NULL) ? strlen(om->mm)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:279:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->cs != NULL) ? strlen(om->cs)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_sse/mpi.c:283:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->consensus != NULL) ? strlen(om->consensus)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:98:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(om->name);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:134:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(om->acc);
data/infernal-1.1.3/hmmer/src/impl_vmx/io.c:143:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(om->desc);
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:156:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->name != NULL) len += strlen(om->name) + 1;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:157:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->acc != NULL) len += strlen(om->acc) + 1;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:158:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->desc != NULL) len += strlen(om->desc) + 1;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:159:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->rf != NULL) len += strlen(om->rf) + 1;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:160:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->mm != NULL) len += strlen(om->mm) + 1;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:161:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->cs != NULL) len += strlen(om->cs) + 1;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:162:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (om->consensus != NULL) len += strlen(om->consensus) + 1;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:260:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->name != NULL) ? strlen(om->name)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:264:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->acc != NULL) ? strlen(om->acc)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:268:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->desc != NULL) ? strlen(om->desc)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:272:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->rf != NULL) ? strlen(om->rf)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:276:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->mm != NULL) ? strlen(om->mm)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:280:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->cs != NULL) ? strlen(om->cs)+1 : 0;
data/infernal-1.1.3/hmmer/src/impl_vmx/mpi.c:284:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = (om->consensus != NULL) ? strlen(om->consensus)+1 : 0;
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:134:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(sq->name);
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:138:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(sq->acc);
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:142:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(sq->source);
data/infernal-1.1.3/hmmer/src/makehmmerdb.c:146:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen(sq->desc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:139:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hmm_namelen = strlen(om->name); n += hmm_namelen + 1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:140:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hmm_acclen = (om->acc != NULL ? strlen(om->acc) : 0); n += hmm_acclen + 1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:141:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hmm_desclen = (om->desc != NULL ? strlen(om->desc) : 0); n += hmm_desclen + 1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:143:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_namelen = strlen(sq->name); n += sq_namelen + 1;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:144:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_acclen = strlen(sq->acc); n += sq_acclen + 1; /* sq->acc is "\0" when unset */
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:145:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_desclen = strlen(sq->desc); n += sq_desclen + 1; /* same for desc */
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:425:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->hmmname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:426:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->hmmacc); /* optional acc, desc fields: when not present, just "" ("\0") */
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:427:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->hmmdesc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:428:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->sqname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:429:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->sqacc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:430:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->sqdesc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:522:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hmmname_length = strlen(obj->hmmname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:525:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hmmacc_length = strlen(obj->hmmacc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:528:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
hmmdesc_length = strlen(obj->hmmdesc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:531:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sqname_length = strlen(obj->sqname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:534:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sqacc_length = strlen(obj->sqacc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:537:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sqdesc_length = strlen(obj->sqdesc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:786:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->rfline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:796:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->mmline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:806:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->csline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:816:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->model);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:821:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->mline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:827:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->aseq);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:837:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->ntseq);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:847:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->ppline);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:856:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->hmmname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:861:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->hmmacc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:866:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->hmmdesc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:871:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->sqname);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:876:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->sqacc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:881:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen(ret_obj->sqdesc);
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:935:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->hmmname); memcpy(ad->mem + pos, ad->hmmname, n); free(ad->hmmname); ad->hmmname = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:936:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->hmmacc); memcpy(ad->mem + pos, ad->hmmacc, n); free(ad->hmmacc); ad->hmmacc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:937:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->hmmdesc); memcpy(ad->mem + pos, ad->hmmdesc, n); free(ad->hmmdesc); ad->hmmdesc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:938:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->sqname); memcpy(ad->mem + pos, ad->sqname, n); free(ad->sqname); ad->sqname = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:939:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->sqacc); memcpy(ad->mem + pos, ad->sqacc, n); free(ad->sqacc); ad->sqacc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:940:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->sqdesc); memcpy(ad->mem + pos, ad->sqdesc, n); free(ad->sqdesc); ad->sqdesc = ad->mem+pos; pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:984:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->hmmname, sizeof(char) * n); memcpy(ad->hmmname, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:985:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->hmmacc, sizeof(char) * n); memcpy(ad->hmmacc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:986:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->hmmdesc, sizeof(char) * n); memcpy(ad->hmmdesc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:987:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->sqname, sizeof(char) * n); memcpy(ad->sqname, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:988:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->sqacc, sizeof(char) * n); memcpy(ad->sqacc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:989:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->mem+pos); ESL_ALLOC(ad->sqdesc, sizeof(char) * n); memcpy(ad->sqdesc, ad->mem+pos, n); pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1009:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->hmmname); if (ad->hmmname != ad->mem+pos) { free(ad->hmmname); ad->hmmname = ad->mem+pos; } pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1010:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->hmmacc); if (ad->hmmacc != ad->mem+pos) { free(ad->hmmacc); ad->hmmacc = ad->mem+pos; } pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1011:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->hmmname); if (ad->hmmdesc != ad->mem+pos) { free(ad->hmmdesc); ad->hmmdesc = ad->mem+pos; } pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1012:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->sqname); if (ad->sqname != ad->mem+pos) { free(ad->sqname); ad->sqname = ad->mem+pos; } pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1013:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->sqacc); if (ad->sqacc != ad->mem+pos) { free(ad->sqacc); ad->sqacc = ad->mem+pos; } pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1014:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = 1 + strlen(ad->sqname); if (ad->sqdesc != ad->mem+pos) { free(ad->sqdesc); ad->sqdesc = ad->mem+pos; } pos += n;
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1181:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namewidth = ESL_MAX(strlen(show_hmmname), strlen(show_seqname));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1181:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namewidth = ESL_MAX(strlen(show_hmmname), strlen(show_seqname));
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1209:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ad->csline != NULL) { strncpy(buf, ad->csline+pos, aliwidth); if (fprintf(fp, " %*s %s CS\n", namewidth+coordwidth+1, "", buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed"); }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1210:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ad->rfline != NULL) { strncpy(buf, ad->rfline+pos, aliwidth); if (fprintf(fp, " %*s %s RF\n", namewidth+coordwidth+1, "", buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed"); }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1211:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ad->mmline != NULL) { strncpy(buf, ad->mmline+pos, aliwidth); if (fprintf(fp, " %*s %s MM\n", namewidth+coordwidth+1, "", buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed"); }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1213:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ad->model+pos, aliwidth); if (fprintf(fp, " %*s %*d %s %-*d\n", namewidth, show_hmmname, coordwidth, k1, buf, coordwidth, k2) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed");
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1214:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ad->mline+pos, aliwidth); if (fprintf(fp, " %*s %s\n", namewidth+coordwidth+1, " ", buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed");
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1216:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ni > 0) { strncpy(buf, ad->aseq+pos, aliwidth); if (fprintf(fp, " %*s %*ld %s %-*ld\n", namewidth, show_seqname, coordwidth, i1, buf, coordwidth, i2) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed"); }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1217:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
else { strncpy(buf, ad->aseq+pos, aliwidth); if (fprintf(fp, " %*s %*s %s %*s\n", namewidth, show_seqname, coordwidth, "-", buf, coordwidth, "-") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed"); }
data/infernal-1.1.3/hmmer/src/p7_alidisplay.c:1219:34: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ad->ppline != NULL) { strncpy(buf, ad->ppline+pos, aliwidth); if (fprintf(fp, " %*s %s PP\n", namewidth+coordwidth+1, "", buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "alignment display write failed"); }
data/infernal-1.1.3/hmmer/src/p7_hit.c:178:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
name_size = strlen(obj->name) +1;
data/infernal-1.1.3/hmmer/src/p7_hit.c:182:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
acc_size = strlen(obj->acc) + 1;
data/infernal-1.1.3/hmmer/src/p7_hit.c:191:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
desc_size = strlen(obj->desc) + 1;
data/infernal-1.1.3/hmmer/src/p7_hit.c:514:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen((char *) ptr) +1;
data/infernal-1.1.3/hmmer/src/p7_hit.c:530:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen((char *) ptr) +1;
data/infernal-1.1.3/hmmer/src/p7_hit.c:547:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen((char *) ptr) +1;
data/infernal-1.1.3/hmmer/src/p7_hmm.c:414:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(name);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:452:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(acc);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:485:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(desc);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:519:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(argv[i]);
data/infernal-1.1.3/hmmer/src/p7_hmm.c:522:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(hmm->comlog) + 1; /* +1 for the \n we're going to add to the old comlog */
data/infernal-1.1.3/hmmer/src/p7_hmm.c:524:5: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(hmm->comlog, "\n");
data/infernal-1.1.3/hmmer/src/p7_hmm.c:533:7: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(hmm->comlog, " ");
data/infernal-1.1.3/hmmer/src/p7_hmm.c:1282:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->flags & p7H_RF) { if (hmm->rf == NULL || strlen(hmm->rf) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_RF flag up, but rf string is invalid"); }
data/infernal-1.1.3/hmmer/src/p7_hmm.c:1285:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->flags & p7H_MMASK) { if (hmm->mm == NULL || strlen(hmm->mm) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_MMASK flag up, but mm string is invalid"); }
data/infernal-1.1.3/hmmer/src/p7_hmm.c:1288:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->flags & p7H_CONS) { if (hmm->consensus == NULL || strlen(hmm->consensus) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CONS flag up, but consensus string is invalid"); }
data/infernal-1.1.3/hmmer/src/p7_hmm.c:1291:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->flags & p7H_CS) { if (hmm->cs == NULL || strlen(hmm->cs) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CS flag up, but cs string is invalid"); }
data/infernal-1.1.3/hmmer/src/p7_hmm.c:1294:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (hmm->flags & p7H_CA) { if (hmm->ca == NULL || strlen(hmm->ca) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CA flag up, but ca string is invalid"); }
data/infernal-1.1.3/hmmer/src/p7_hmmcache.c:82:28: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (status != eslEOF) { strncpy(errbuf, hfp->errbuf, eslERRBUFSIZE); goto ERROR; }
data/infernal-1.1.3/hmmer/src/p7_hmmcache.c:106:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += sizeof(char) * (strlen(cache->name) + 1);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:284:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(filename);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:342:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(envfile);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:399:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(hfp->fname); /* so, n = '\0', n-1 = 'm' */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:722:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size = 50 + strlen(HMMER_VERSION) + strlen(HMMER_DATE); /* HMMER version text */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:722:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size = 50 + strlen(HMMER_VERSION) + strlen(HMMER_DATE); /* HMMER version text */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:723:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size += 7 + strlen(hmm->name); /* NAME line */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:724:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size += (hmm->acc ? ( 7 + strlen(hmm->acc)) : 0); /* ACC line, if present */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:725:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size += (hmm->desc ? ( 7 + strlen(hmm->desc)) : 0); /* DESC line, if present */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:728:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size += 7 + strlen( esl_abc_DecodeType(hmm->abc->type)); /*ALPH tag */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:734:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size += (hmm->ctime != NULL ? (7 + strlen(hmm->ctime)) : 0); /*DATE line*/
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:746:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size += strlen(hmm->comlog);
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:912:16: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
if((offset = sprintf(ret_hmm + coffset, "\n")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:926:17: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
if((offset = sprintf(ret_hmm + coffset, "\n")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:938:16: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
if((offset = sprintf(ret_hmm + coffset, "\n")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:948:16: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
if((offset = sprintf(ret_hmm + coffset, "\n")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:1003:19: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
if ((offset = sprintf(ret_hmm + coffset, "\n")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2119:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*ret_str + *coffset, sptr, sizeof(char) * n); /* using strncpy lets us write fixed # of chars */
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2121:21: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
if ((offset = sprintf(*ret_str + *coffset, "\n")) < 0) return eslEWRITE;
data/infernal-1.1.3/hmmer/src/p7_hmmfile.c:2187:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(s) + 1;
data/infernal-1.1.3/hmmer/src/p7_tophits.c:536:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(h->unsrt[i].name);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:555:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(h->unsrt[i].acc);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:579:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(h->unsrt[i].acc);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:584:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(h->unsrt[i].name);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1236:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namew = strlen(th->hit[h]->acc);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1241:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namew = strlen(th->hit[h]->name);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1553:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qnamew = ESL_MAX(20, strlen(qname));
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1555:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qaccw = ((qacc != NULL) ? ESL_MAX(10, strlen(qacc)) : 10);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1658:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qnamew = ESL_MAX(20, strlen(qname));
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1660:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qaccw = (qacc ? ESL_MAX(10, strlen(qacc)) : 10);
data/infernal-1.1.3/hmmer/src/p7_tophits.c:1762:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qnamew = ESL_MAX(20, strlen(qname));
data/infernal-1.1.3/hmmer/src/p7_tophits.c:2187:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (p7_tophits_GetMaxNameLength(h3) != strlen(name)) esl_fatal("GetMaxNameLength() failed");
data/infernal-1.1.3/hmmer/src/seqmodel.c:242:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int L = strlen(seq);
data/infernal-1.1.3/rmark/rmark-rocplot.c:344:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qlen = strlen(query);
data/infernal-1.1.3/rmark/rmark-rocplot.c:345:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int tlen = strlen(target);
data/infernal-1.1.3/src/alphabet.c:390:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
i = (int) ((float)(strlen(s)) * esl_random(r));
data/infernal-1.1.3/src/alphabet.c:391:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
} while (i<0 || i>=strlen(s));
data/infernal-1.1.3/src/cm.c:2593:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(name);
data/infernal-1.1.3/src/cm.c:2631:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(acc);
data/infernal-1.1.3/src/cm.c:2664:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(desc);
data/infernal-1.1.3/src/cm.c:2771:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(argv[i]);
data/infernal-1.1.3/src/cm.c:2783:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += strlen(cm->comlog) + 1; /* +1 for the \n we're going to add to the old comlog */
data/infernal-1.1.3/src/cm.c:2785:5: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(cm->comlog, "\n");
data/infernal-1.1.3/src/cm.c:2794:7: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(cm->comlog, " ");
data/infernal-1.1.3/src/cm.c:3256:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->comlog != NULL) bytes += sizeof(char) * strlen(cm->comlog);
data/infernal-1.1.3/src/cm.c:3257:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->ctime != NULL) bytes += sizeof(char) * strlen(cm->ctime);
data/infernal-1.1.3/src/cm.c:3291:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->name != NULL) bytes += sizeof(char) * (strlen(cm->name) + 2);
data/infernal-1.1.3/src/cm.c:3292:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->acc != NULL) bytes += sizeof(char) * (strlen(cm->acc) + 2);
data/infernal-1.1.3/src/cm.c:3293:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->desc != NULL) bytes += sizeof(char) * (strlen(cm->desc) + 2);
data/infernal-1.1.3/src/cm.c:3294:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->rf != NULL) bytes += sizeof(char) * (strlen(cm->rf) + 2);
data/infernal-1.1.3/src/cm.c:3295:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->consensus != NULL) bytes += sizeof(char) * (strlen(cm->consensus) + 2);
data/infernal-1.1.3/src/cm_alidisplay.c:246:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cm_namelen = strlen(cm->name); n += cm_namelen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:247:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cm_acclen = (cm->acc != NULL ? strlen(cm->acc) : 0); n += cm_acclen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:248:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cm_desclen = (cm->desc != NULL ? strlen(cm->desc) : 0); n += cm_desclen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:249:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_namelen = strlen(sq->name); n += sq_namelen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:250:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_acclen = strlen(sq->acc); n += sq_acclen + 1; /* sq->acc is "\0" when unset */
data/infernal-1.1.3/src/cm_alidisplay.c:251:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_desclen = strlen(sq->desc); n += sq_desclen + 1; /* sq->desc is "\0" when unset */
data/infernal-1.1.3/src/cm_alidisplay.c:686:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cm_namelen = strlen(cm->name); n += cm_namelen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:687:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cm_acclen = (cm->acc != NULL ? strlen(cm->acc) : 0); n += cm_acclen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:688:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cm_desclen = (cm->desc != NULL ? strlen(cm->desc) : 0); n += cm_desclen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:689:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_namelen = strlen(sq->name); n += sq_namelen + 1;
data/infernal-1.1.3/src/cm_alidisplay.c:690:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_acclen = strlen(sq->acc); n += sq_acclen + 1; /* sq->acc is "\0" when unset */
data/infernal-1.1.3/src/cm_alidisplay.c:691:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sq_desclen = strlen(sq->desc); n += sq_desclen + 1; /* sq->desc is "\0" when unset */
data/infernal-1.1.3/src/cm_alidisplay.c:925:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->cmname);
data/infernal-1.1.3/src/cm_alidisplay.c:926:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->cmacc); /* optional acc, desc fields: when not present, just "" ("\0") */
data/infernal-1.1.3/src/cm_alidisplay.c:927:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->cmdesc);
data/infernal-1.1.3/src/cm_alidisplay.c:928:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->sqname);
data/infernal-1.1.3/src/cm_alidisplay.c:929:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->sqacc);
data/infernal-1.1.3/src/cm_alidisplay.c:930:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n += 1 + strlen(ad->sqdesc);
data/infernal-1.1.3/src/cm_alidisplay.c:1171:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namewidth = ESL_MAX(strlen(show_cmname), strlen(show_seqname));
data/infernal-1.1.3/src/cm_alidisplay.c:1171:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namewidth = ESL_MAX(strlen(show_cmname), strlen(show_seqname));
data/infernal-1.1.3/src/cm_alidisplay.c:1237:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ad->ncline != NULL) { strncpy(buf, ad->ncline+pos, cur_aliwidth); fprintf(fp, " %*s %s %*sNC\n", namewidth+coordwidth+1, "", buf, aliwidth-cur_aliwidth, ""); }
data/infernal-1.1.3/src/cm_alidisplay.c:1238:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ad->csline+pos, cur_aliwidth); fprintf(fp, " %*s %s %*sCS\n", namewidth+coordwidth+1, "", buf, aliwidth-cur_aliwidth, "");
data/infernal-1.1.3/src/cm_alidisplay.c:1239:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ad->model+pos, cur_aliwidth); fprintf(fp, " %*s %*d %s %*s%-*d\n", namewidth, show_cmname, coordwidth, k1, buf, aliwidth-cur_aliwidth, "", coordwidth, k2);
data/infernal-1.1.3/src/cm_alidisplay.c:1240:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ad->mline+pos, cur_aliwidth); fprintf(fp, " %*s %s\n", namewidth+coordwidth+1, " ", buf);
data/infernal-1.1.3/src/cm_alidisplay.c:1241:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ni > 0) { strncpy(buf, ad->aseq+pos, cur_aliwidth); fprintf(fp, " %*s %*ld %s %*s%-*ld\n", namewidth, show_seqname, coordwidth, i1, buf, aliwidth-cur_aliwidth, "", coordwidth, i2); }
data/infernal-1.1.3/src/cm_alidisplay.c:1242:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
else { strncpy(buf, ad->aseq+pos, cur_aliwidth); fprintf(fp, " %*s %*s %s %*s%*s\n", namewidth, show_seqname, coordwidth, "-", buf, aliwidth-cur_aliwidth, "", coordwidth, "-"); }
data/infernal-1.1.3/src/cm_alidisplay.c:1243:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ad->ppline != NULL) { strncpy(buf, ad->ppline+pos, cur_aliwidth); fprintf(fp, " %*s %s %*sPP\n", namewidth+coordwidth+1, "", buf, aliwidth-cur_aliwidth, ""); }
data/infernal-1.1.3/src/cm_alidisplay.c:1244:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if (ad->rfline != NULL) { strncpy(buf, ad->rfline+pos, cur_aliwidth); fprintf(fp, " %*s %s %*sRF\n", namewidth+coordwidth+1, "", buf, aliwidth-cur_aliwidth, ""); }
data/infernal-1.1.3/src/cm_file.c:263:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int n = strlen(filename);
data/infernal-1.1.3/src/cm_file.c:327:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(envfile);
data/infernal-1.1.3/src/cm_file.c:425:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(cmfp->fname); /* so, n = '\0', n-1 = 'm' */
data/infernal-1.1.3/src/cm_file.c:922:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(s) + 1;
data/infernal-1.1.3/src/cm_file.c:3349:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((strncmp(s, "0x", 2) == 0 && (int) strlen(s) > 2) ||
data/infernal-1.1.3/src/cm_file.c:3350:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(strncmp(s, "0X", 2) == 0 && (int) strlen(s) > 2))
data/infernal-1.1.3/src/cm_file.c:3355:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (*s == '0' && (int) strlen(s) > 1)
data/infernal-1.1.3/src/cm_file.c:3476:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(comlog2print, sizeof(char) * (strlen(cm->comlog)+1));
data/infernal-1.1.3/src/cm_file.c:3478:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
while(x < strlen(cm->comlog) && cm->comlog[x] != '\n') { comlog2print[x] = cm->comlog[x]; x++; }
data/infernal-1.1.3/src/cm_parsetree.c:1171:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(msa->au, sizeof(char) * (strlen(INFERNAL_VERSION)+10));
data/infernal-1.1.3/src/cm_tophits.c:660:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
max = ESL_MAX(max, strlen(h->unsrt[i].name));
data/infernal-1.1.3/src/cm_tophits.c:681:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
max = ESL_MAX(max, strlen(h->unsrt[i].desc));
data/infernal-1.1.3/src/cm_tophits.c:702:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(h->unsrt[i].acc);
data/infernal-1.1.3/src/cm_tophits.c:728:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(h->unsrt[i].acc);
data/infernal-1.1.3/src/cm_tophits.c:733:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(h->unsrt[i].name);
data/infernal-1.1.3/src/cm_tophits.c:767:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(esl_keyhash_Get(clan_name_kh, h->unsrt[i].clan_idx)));
data/infernal-1.1.3/src/cm_tophits.c:1693:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namew = strlen(th->hit[h]->acc);
data/infernal-1.1.3/src/cm_tophits.c:1697:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namew = strlen(th->hit[h]->name);
data/infernal-1.1.3/src/cm_tophits.c:2234:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qnamew = ESL_MAX(20, strlen(qname));
data/infernal-1.1.3/src/cm_tophits.c:2235:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qaccw = ((qacc != NULL) ? ESL_MAX(9, strlen(qacc)) : 9);
data/infernal-1.1.3/src/cm_tophits.c:2339:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qnamew = ESL_MAX(20, strlen(qname));
data/infernal-1.1.3/src/cm_tophits.c:2340:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int qaccw = ((qacc != NULL) ? ESL_MAX(9, strlen(qacc)) : 9);
data/infernal-1.1.3/src/cm_tophits.c:3621:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (cm_tophits_GetMaxNameLength(h1) != strlen(name)) esl_fatal("GetMaxNameLength() failed");
data/infernal-1.1.3/src/cmalign.c:1959:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(i = first_idx; i < ndata; i++) namewidth = ESL_MAX(namewidth, strlen(dataA[i]->sq->name));
data/infernal-1.1.3/src/cmbuild.c:2384:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(map, sizeof(int) * strlen(aseq));
data/infernal-1.1.3/src/cmbuild.c:2387:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (i = 0; i < strlen(aseq); i++)
data/infernal-1.1.3/src/cmbuild.c:2653:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ndigits = strlen(cmsa[m]->name);
data/infernal-1.1.3/src/cmcalibrate.c:1495:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(cfg->tmpfile, (sizeof(char) * (strlen(cfg->cmfile) + 5)));
data/infernal-1.1.3/src/cmcalibrate.c:1958:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int namelen = strlen("irrelevant");
data/infernal-1.1.3/src/cmcalibrate.c:2239:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
seq_reqmb += N * sizeof(char) * strlen("irrelevant");
data/infernal-1.1.3/src/cmemit.c:336:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namelen = IntMaxDigits() + strlen("sample") + 1; /* IntMaxDigits() returns number of digits in INT_MAX */
data/infernal-1.1.3/src/cmemit.c:337:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->name != NULL) namelen += strlen(cm->name) + 1;
data/infernal-1.1.3/src/cmemit.c:505:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namelen = IntMaxDigits() + strlen("sample") + 1; /* IntMaxDigits() returns number of digits in INT_MAX */
data/infernal-1.1.3/src/cmemit.c:506:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(cm->name != NULL) namelen += strlen(cm->name) + 1;
data/infernal-1.1.3/src/cmscan.c:2709:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(src_sq->name)+1;
data/infernal-1.1.3/src/cmscan.c:2717:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(src_sq->desc)+1;
data/infernal-1.1.3/src/cmscan.c:2725:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(src_sq->acc)+1;
data/infernal-1.1.3/src/cmsearch.c:2209:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(tmp_filename, sizeof(char) * (strlen((*dbfp_ptr)->filename) + 1));
data/infernal-1.1.3/src/cp9_modelmaker.c:2551:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (alen != strlen(ss))
data/infernal-1.1.3/src/cp9_trace.c:1268:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ESL_ALLOC(msa->au, sizeof(char) * (strlen(INFERNAL_VERSION)+10));
data/infernal-1.1.3/src/display.c:535:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ali->rf+pos, linewidth);
data/infernal-1.1.3/src/display.c:539:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ali->top+pos, linewidth);
data/infernal-1.1.3/src/display.c:543:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ali->cstr+pos, linewidth);
data/infernal-1.1.3/src/display.c:547:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ali->cseq+pos, linewidth);
data/infernal-1.1.3/src/display.c:554:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ali->mid+pos, linewidth);
data/infernal-1.1.3/src/display.c:558:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ali->aseq+pos, linewidth);
data/infernal-1.1.3/src/display.c:575:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, ali->pcode+pos, linewidth);
data/infernal-1.1.3/src/impl_sse/sse_cmcons_mscyk.c:38:12: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
__m128i umask; /* underflow mask */
data/infernal-1.1.3/src/impl_sse/sse_cmcons_mscyk.c:53:33: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
ret_v = _mm_and_si128(ret_v, umask); /* underflow mask zeroes sum if an operand was zero (0 = -infty) */
data/infernal-1.1.3/src/impl_sse/sse_cmcons_mscyk.c:158:14: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
__m128i umask; /* underflow mask */
data/infernal-1.1.3/src/impl_sse/sse_cmcons_mscyk.c:500:76: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
vec_ntM_v[jp_v][v][d] = _mm_and_si128(vec_ntM_v[jp_v][v][d], umask);
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:197:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(cmfile) - 3 < length) length = strlen(cmfile) - 3;
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:197:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(cmfile) - 3 < length) length = strlen(cmfile) - 3;
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:198:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(fname,&cmfile[strlen(cmfile)-(length+4)],length);
data/infernal-1.1.3/src/impl_sse/sse_cmsearch.c:198:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(fname,&cmfile[strlen(cmfile)-(length+4)],length);
data/infernal-1.1.3/src/rnamat.c:499:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (fullbuf+fullbuf_used, linebuf, 16384-fullbuf_used-1);
data/infernal-1.1.3/src/rnamat.c:500:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullbuf_used += strlen(linebuf);
data/infernal-1.1.3/src/rnamat.c:510:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (fullmat->name, cp, i);
data/infernal-1.1.3/src/stats.c:41:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int namewidth = strlen(cm->name);
data/infernal-1.1.3/src/stats.c:183:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
namewidth = ESL_MAX(namewidth, strlen(sq->name));
ANALYSIS SUMMARY:
Hits = 2622
Lines analyzed = 355208 in approximately 21.46 seconds (16550 lines/second)
Physical Source Lines of Code (SLOC) = 219559
Hits@level = [0] 6930 [1] 610 [2] 1655 [3] 9 [4] 347 [5] 1
Hits@level+ = [0+] 9552 [1+] 2622 [2+] 2012 [3+] 357 [4+] 348 [5+] 1
Hits/KSLOC@level+ = [0+] 43.5054 [1+] 11.9421 [2+] 9.16382 [3+] 1.62599 [4+] 1.585 [5+] 0.00455458
Symlinks skipped = 1 (--allowlink overrides but see doc for security issue)
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.