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/phyml-3.3.20200621/src/alrt.c
Examining data/phyml-3.3.20200621/src/alrt.h
Examining data/phyml-3.3.20200621/src/ancestral.c
Examining data/phyml-3.3.20200621/src/ancestral.h
Examining data/phyml-3.3.20200621/src/avx.c
Examining data/phyml-3.3.20200621/src/avx.h
Examining data/phyml-3.3.20200621/src/beagle_utils.h
Examining data/phyml-3.3.20200621/src/bionj.c
Examining data/phyml-3.3.20200621/src/bionj.h
Examining data/phyml-3.3.20200621/src/checkpoint.c
Examining data/phyml-3.3.20200621/src/checkpoint.h
Examining data/phyml-3.3.20200621/src/cl.c
Examining data/phyml-3.3.20200621/src/cl.h
Examining data/phyml-3.3.20200621/src/date.c
Examining data/phyml-3.3.20200621/src/date.h
Examining data/phyml-3.3.20200621/src/draw.c
Examining data/phyml-3.3.20200621/src/draw.h
Examining data/phyml-3.3.20200621/src/eigen.c
Examining data/phyml-3.3.20200621/src/eigen.h
Examining data/phyml-3.3.20200621/src/free.c
Examining data/phyml-3.3.20200621/src/free.h
Examining data/phyml-3.3.20200621/src/geo.c
Examining data/phyml-3.3.20200621/src/geo.h
Examining data/phyml-3.3.20200621/src/help.c
Examining data/phyml-3.3.20200621/src/help.h
Examining data/phyml-3.3.20200621/src/init.c
Examining data/phyml-3.3.20200621/src/init.h
Examining data/phyml-3.3.20200621/src/interface.c
Examining data/phyml-3.3.20200621/src/interface.h
Examining data/phyml-3.3.20200621/src/invitee.c
Examining data/phyml-3.3.20200621/src/invitee.h
Examining data/phyml-3.3.20200621/src/io.c
Examining data/phyml-3.3.20200621/src/io.h
Examining data/phyml-3.3.20200621/src/lk.h
Examining data/phyml-3.3.20200621/src/m4.c
Examining data/phyml-3.3.20200621/src/m4.h
Examining data/phyml-3.3.20200621/src/main.c
Examining data/phyml-3.3.20200621/src/make.c
Examining data/phyml-3.3.20200621/src/make.h
Examining data/phyml-3.3.20200621/src/mcmc.c
Examining data/phyml-3.3.20200621/src/mcmc.h
Examining data/phyml-3.3.20200621/src/mg.c
Examining data/phyml-3.3.20200621/src/mg.h
Examining data/phyml-3.3.20200621/src/mixt.c
Examining data/phyml-3.3.20200621/src/mixt.h
Examining data/phyml-3.3.20200621/src/models.c
Examining data/phyml-3.3.20200621/src/models.h
Examining data/phyml-3.3.20200621/src/mpi_boot.c
Examining data/phyml-3.3.20200621/src/mpi_boot.h
Examining data/phyml-3.3.20200621/src/mxml.h
Examining data/phyml-3.3.20200621/src/nexus.c
Examining data/phyml-3.3.20200621/src/nexus.h
Examining data/phyml-3.3.20200621/src/optimiz.c
Examining data/phyml-3.3.20200621/src/optimiz.h
Examining data/phyml-3.3.20200621/src/pars.c
Examining data/phyml-3.3.20200621/src/pars.h
Examining data/phyml-3.3.20200621/src/phyrex.c
Examining data/phyml-3.3.20200621/src/phyrex.h
Examining data/phyml-3.3.20200621/src/rates.c
Examining data/phyml-3.3.20200621/src/rates.h
Examining data/phyml-3.3.20200621/src/rrw.c
Examining data/phyml-3.3.20200621/src/rrw.h
Examining data/phyml-3.3.20200621/src/rw.c
Examining data/phyml-3.3.20200621/src/rw.h
Examining data/phyml-3.3.20200621/src/rwrapper.c
Examining data/phyml-3.3.20200621/src/rwrapper.h
Examining data/phyml-3.3.20200621/src/simu.c
Examining data/phyml-3.3.20200621/src/simu.h
Examining data/phyml-3.3.20200621/src/slfv.c
Examining data/phyml-3.3.20200621/src/slfv.h
Examining data/phyml-3.3.20200621/src/spr.c
Examining data/phyml-3.3.20200621/src/spr.h
Examining data/phyml-3.3.20200621/src/sse.c
Examining data/phyml-3.3.20200621/src/sse.h
Examining data/phyml-3.3.20200621/src/stats.c
Examining data/phyml-3.3.20200621/src/stats.h
Examining data/phyml-3.3.20200621/src/tbe.c
Examining data/phyml-3.3.20200621/src/tbe.h
Examining data/phyml-3.3.20200621/src/times.c
Examining data/phyml-3.3.20200621/src/times.h
Examining data/phyml-3.3.20200621/src/tiporder.c
Examining data/phyml-3.3.20200621/src/tiporder.h
Examining data/phyml-3.3.20200621/src/utilities.h
Examining data/phyml-3.3.20200621/src/xml.c
Examining data/phyml-3.3.20200621/src/xml.h
Examining data/phyml-3.3.20200621/src/utilities.c
Examining data/phyml-3.3.20200621/src/beagle_utils.c
Examining data/phyml-3.3.20200621/src/lk.c
FINAL RESULTS:
data/phyml-3.3.20200621/src/mpi_boot.c:411:91: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, ". Sequence file : [%s]\n\n", Basename(io->in_align_file)); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:416:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:424:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:426:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "\n", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:429:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, ". Data\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:431:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Nb of \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:433:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Likelihood\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:435:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Discrete \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:438:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Number of \tGamma shape\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:440:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Proportion of\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:443:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Transition/ \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:445:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Nucleotides frequencies \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:449:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "Instantaneous rate matrix \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:451:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "\n", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:454:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, " set\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:456:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "taxa\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:458:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "loglk \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:460:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "gamma model\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:463:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "categories\tparameter \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:465:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "invariant \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:468:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "transversion\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:470:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "f(A) f(C) f(G) f(T) \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:474:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "[A---------C---------G---------T------]\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:476:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "\n", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:480:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, " \t \t \t \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:482:9: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, " \t \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:483:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, " \t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:484:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "purines pyrimid.\t", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:485:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "\n", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:488:5: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, "\n", T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:494:3: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:496:53: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%d \t",tree->n_otu); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:498:52: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%.5f\t",tree->c_lnL); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:501:56: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
(tree->mod->ras->n_catg>1)?("Yes"):("No ")); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:505:73: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%d \t",tree->mod->ras->n_catg); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:506:73: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%.3f \t",tree->mod->ras->alpha->v); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:509:70: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%.3f \t",tree->mod->ras->pinvar->v); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:513:69: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%.3f \t",tree->mod->kappa->v); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:519:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:522:7: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:527:72: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%8.5f ",tree->mod->e_frq->pi->v[0]); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:528:72: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%8.5f ",tree->mod->e_frq->pi->v[1]); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:529:72: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%8.5f ",tree->mod->e_frq->pi->v[2]); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:530:72: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
snprintf(tmp, T_MAX_LINE, "%8.5f\t",tree->mod->e_frq->pi->v[3]); strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:542:13: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:545:15: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:548:13: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:552:13: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/mpi_boot.c:556:13: [5] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is high; the length parameter
appears to be a constant, instead of computing the number of characters
left.
strncat (s, tmp, T_MAX_LINE);
data/phyml-3.3.20200621/src/ancestral.c:536:7: [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(tree->io->out_ancestral_seq_file,tree->io->out_file);
data/phyml-3.3.20200621/src/ancestral.c:540:11: [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(tree->io->out_ancestral_seq_file,tree->io->run_id_string);
data/phyml-3.3.20200621/src/ancestral.c:547:7: [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(tree->io->out_ancestral_tree_file,tree->io->out_file);
data/phyml-3.3.20200621/src/ancestral.c:551:11: [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(tree->io->out_ancestral_tree_file,tree->io->run_id_string);
data/phyml-3.3.20200621/src/cl.c:181:13: [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(io->weight_file, optarg);
data/phyml-3.3.20200621/src/cl.c:199:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.c:210:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.c:219:17: [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(io->in_coord_file, optarg);
data/phyml-3.3.20200621/src/cl.c:306:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.c:317:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.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(io->in_constraint_tree_file, optarg);
data/phyml-3.3.20200621/src/cl.c:467:6: [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,optarg);
data/phyml-3.3.20200621/src/cl.c:469:6: [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(io->mod->aa_rate_mat_file->s,s);
data/phyml-3.3.20200621/src/cl.c:488:6: [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(io->clade_list_file,optarg);
data/phyml-3.3.20200621/src/cl.c:512:17: [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(io->run_id_string,optarg);
data/phyml-3.3.20200621/src/cl.c:860:21: [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(io->mod->custom_mod_string->s,optarg);
data/phyml-3.3.20200621/src/cl.c:1245:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.c:1257:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.c:1266:3: [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(io->in_align_file, optarg);
data/phyml-3.3.20200621/src/cl.c:1269:3: [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(io->out_file, optarg);
data/phyml-3.3.20200621/src/cl.c:1270:3: [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(io->out_tree_file,optarg);
data/phyml-3.3.20200621/src/cl.c:1279:3: [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(io->out_stats_file,optarg);
data/phyml-3.3.20200621/src/cl.c:1290:3: [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(io->out_summary_file,optarg);
data/phyml-3.3.20200621/src/cl.c:1390:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.c:1401:3: [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 (tmp, optarg);
data/phyml-3.3.20200621/src/cl.c:1410:3: [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(io->in_tree_file, optarg);
data/phyml-3.3.20200621/src/cl.c:1554:7: [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(io->out_ps_file,io->in_align_file);
data/phyml-3.3.20200621/src/cl.c:1598:7: [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(io->out_lk_file,io->in_align_file);
data/phyml-3.3.20200621/src/cl.c:1600:60: [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).
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1607:7: [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(io->out_trace_file,io->in_align_file);
data/phyml-3.3.20200621/src/cl.c:1609:63: [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).
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1616:7: [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(io->out_json_trace_file,io->in_align_file);
data/phyml-3.3.20200621/src/cl.c:1618:68: [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).
if(io->append_run_ID) { strcat(io->out_json_trace_file,"_"); strcat(io->out_json_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1626:7: [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(io->out_trees_file,io->in_align_file);
data/phyml-3.3.20200621/src/cl.c:1628:63: [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).
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1635:7: [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(io->out_boot_tree_file,io->in_align_file);
data/phyml-3.3.20200621/src/cl.c:1637:67: [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).
if(io->append_run_ID) { strcat(io->out_boot_tree_file,"_"); strcat(io->out_boot_tree_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1641:7: [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(io->out_boot_stats_file,io->in_align_file);
data/phyml-3.3.20200621/src/cl.c:1643:68: [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).
if(io->append_run_ID) { strcat(io->out_boot_stats_file,"_"); strcat(io->out_boot_stats_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1652:7: [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(io->out_tree_file,io->run_id_string);
data/phyml-3.3.20200621/src/cl.c:1653:7: [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(io->out_stats_file,io->run_id_string);
data/phyml-3.3.20200621/src/geo.c:1769:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(fscanf(fp,"%s",s) == EOF) break;
data/phyml-3.3.20200621/src/init.c:524:7: [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(mat->name[i],data->c_seq[i]->name);
data/phyml-3.3.20200621/src/init.c:795:12: [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).
if(name) strcpy(new_node->name,name);
data/phyml-3.3.20200621/src/init.c:3587:7: [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(mcmc->out_filename,filename);
data/phyml-3.3.20200621/src/init.c:3591:7: [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(s,mcmc->io->in_align_file);
data/phyml-3.3.20200621/src/init.c:3593:7: [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(s,mcmc->out_filename);
data/phyml-3.3.20200621/src/init.c:3597:7: [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(s,mcmc->io->in_align_file);
data/phyml-3.3.20200621/src/init.c:3599:7: [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(s,mcmc->out_filename);
data/phyml-3.3.20200621/src/init.c:3603:7: [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(s,mcmc->io->in_align_file);
data/phyml-3.3.20200621/src/init.c:3605:7: [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(s,mcmc->out_filename);
data/phyml-3.3.20200621/src/interface.c:78:7: [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(io->mod->aa_rate_mat_file->s,filename);
data/phyml-3.3.20200621/src/interface.c:135:7: [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(io->out_lk_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:138:60: [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).
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:144:7: [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(io->out_trace_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:147:63: [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).
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:153:7: [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(io->out_trees_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:156:63: [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).
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:162:7: [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(io->out_boot_tree_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:165:67: [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).
if(io->append_run_ID) { strcat(io->out_boot_tree_file,"_"); strcat(io->out_boot_tree_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:168:7: [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(io->out_boot_stats_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:171:68: [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).
if(io->append_run_ID) { strcat(io->out_boot_stats_file,"_"); strcat(io->out_boot_stats_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:179:7: [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(io->out_tree_file,io->run_id_string);
data/phyml-3.3.20200621/src/interface.c:180:7: [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(io->out_stats_file,io->run_id_string);
data/phyml-3.3.20200621/src/interface.c:213:3: [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.
system("cls");
data/phyml-3.3.20200621/src/interface.c:283:3: [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(io->out_stats_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:286:3: [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(io->out_tree_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.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(io->out_lk_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:415:3: [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(buff,(io->n_data_sets > 1)?("yes"):("no"));
data/phyml-3.3.20200621/src/interface.c:416:8: [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).
buff=strcat(buff,(io->n_data_sets > 1)?(s):("\0"));
data/phyml-3.3.20200621/src/interface.c:422:8: [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(s,io->run_id_string);
data/phyml-3.3.20200621/src/interface.c:655:7: [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(s,(io->mod->s_opt->opt_kappa)?("estimated"):("fixed"));
data/phyml-3.3.20200621/src/interface.c:675:3: [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,io->mod->s_opt->opt_pinvar?"estimated":"fixed");
data/phyml-3.3.20200621/src/interface.c:676:3: [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(s,io->mod->s_opt->opt_pinvar?"":" (p-invar = ");
data/phyml-3.3.20200621/src/interface.c:715:7: [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(s,(io->mod->s_opt->opt_alpha)?("estimated"):("fixed"));
data/phyml-3.3.20200621/src/interface.c:716:7: [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(s,io->mod->s_opt->opt_alpha?"":" (alpha = ");
data/phyml-3.3.20200621/src/interface.c:836:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(rr+strlen(rr),"%s = ",rr_param[j]);
data/phyml-3.3.20200621/src/interface.c:1591:6: [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(io->out_trees_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:1637:3: [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,(io->do_boot || io->do_tbe)?("yes"):("no"));
data/phyml-3.3.20200621/src/interface.c:1638:33: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
if(io->n_boot_replicates > 0) sprintf(s+strlen(s)," (%d replicate%s%s)",
data/phyml-3.3.20200621/src/interface.c:1745:5: [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(io->out_boot_tree_file,io->in_align_file);
data/phyml-3.3.20200621/src/interface.c:1749:5: [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(io->out_boot_stats_file,io->in_align_file);
data/phyml-3.3.20200621/src/invitee.c:93:4: [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(io -> out_tree_file, XML_Search_Attribute(n_cur, "user.tree") -> value);
data/phyml-3.3.20200621/src/invitee.c:180:4: [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(mon_list[i], n_m -> child -> attr -> value);
data/phyml-3.3.20200621/src/invitee.c:252:5: [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(io -> in_align_file, XML_Search_Attribute(n_cur, "user.alignment") -> value);
data/phyml-3.3.20200621/src/invitee.c:266:5: [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(io -> data[i] -> name, n_r -> child -> attr -> value);
data/phyml-3.3.20200621/src/invitee.c:268:19: [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(io -> data[i] -> state, s);
data/phyml-3.3.20200621/src/invitee.c:326:19: [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(clade_name, n_r -> child -> attr -> value);//reached clade names n_r -> child -> attr -> value
data/phyml-3.3.20200621/src/io.c:82:11: [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((*s_tree),subs[i]);
data/phyml-3.3.20200621/src/io.c:86:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf((*s_tree)+strlen((*s_tree))-1,"%s",");\0");
data/phyml-3.3.20200621/src/io.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(d->name,s_tree_d);
data/phyml-3.3.20200621/src/io.c:316:3: [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(sub_tp,s_d);
data/phyml-3.3.20200621/src/io.c:323:7: [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(sub_tp,s_d);
data/phyml-3.3.20200621/src/io.c:355:3: [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(sub_tp,s_d);
data/phyml-3.3.20200621/src/io.c:362:7: [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(sub_tp,s_d);
data/phyml-3.3.20200621/src/io.c:406:3: [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(sub_tp,s_d);
data/phyml-3.3.20200621/src/io.c:414:7: [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(sub_tp,s_d);
data/phyml-3.3.20200621/src/io.c:463:7: [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(s_tmp,subtrees[0]);
data/phyml-3.3.20200621/src/io.c:465:7: [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(s_tmp,subtrees[1]);
data/phyml-3.3.20200621/src/io.c:470:36: [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).
for(i=1;i<current_deg-1;i++) strcpy(subtrees[i],subtrees[i+1]);
data/phyml-3.3.20200621/src/io.c:661:19: [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(*s_tree,tree->io->long_tax_names[fils->num]);
data/phyml-3.3.20200621/src/io.c:666:21: [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(*s_tree,fils->name);
data/phyml-3.3.20200621/src/io.c:697:11: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(*s_tree+(int)strlen(*s_tree),format,MAX(0.0,mean_len));
data/phyml-3.3.20200621/src/io.c:793:11: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(*s_tree+(int)strlen(*s_tree),format,MAX(0.0,mean_len));
data/phyml-3.3.20200621/src/io.c:1316:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(fscanf(fp,"%s",line) == EOF)
data/phyml-3.3.20200621/src/io.c:1331:19: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(!fscanf(fp,"%s",line)) Exit("\n");
data/phyml-3.3.20200621/src/io.c:1372:11: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!fscanf(io->fp_in_align,format,data[i]->name)) Exit("\n");
data/phyml-3.3.20200621/src/io.c:1426:11: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!fscanf(io->fp_in_align,format,data[i]->name)) Exit("\n");
data/phyml-3.3.20200621/src/io.c:1471:19: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!fscanf(io->fp_in_align,format,line))
data/phyml-3.3.20200621/src/io.c:2338:14: [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(strcat(strcat(s,"user tree ("),io->in_tree_file),")");
data/phyml-3.3.20200621/src/io.c:2627:17: [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(s,io->in_tree_file);
data/phyml-3.3.20200621/src/io.c:2945:9: [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(s,Basename(io->in_tree_file));
data/phyml-3.3.20200621/src/io.c:3368:13: [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.
fprintf(stdout,fmt,catg,site,j,lk_left[catg*tree->n_pattern*tree->mod->ns + site*tree->mod->ns + j]);
data/phyml-3.3.20200621/src/io.c:3370:21: [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.
fprintf(stdout,fmt,catg,site,j,lk_left[catg*tree->mod->ns + site*tree->mod->ras->n_catg*tree->mod->ns + j]);
data/phyml-3.3.20200621/src/io.c:3390:21: [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.
fprintf(stdout,fmt,catg,site,j,lk_right[catg*tree->n_pattern*tree->mod->ns + site*tree->mod->ns + j]);
data/phyml-3.3.20200621/src/io.c:3392:21: [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.
fprintf(stdout,fmt,catg,site,j,lk_right[catg*tree->mod->ns + site*tree->mod->ras->n_catg*tree->mod->ns + j]);
data/phyml-3.3.20200621/src/io.c:3579:7: [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, ptr);
data/phyml-3.3.20200621/src/io.c:3584:7: [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, ptr);
data/phyml-3.3.20200621/src/io.c:3602:7: [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 (fp,format, ptr);
data/phyml-3.3.20200621/src/io.c:3607:7: [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 (fp,format, ptr);
data/phyml-3.3.20200621/src/io.c:3628:12: [4] (buffer) vfscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
rv = vfscanf(fp,format,ptr);
data/phyml-3.3.20200621/src/io.c:3634:8: [4] (buffer) vfscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
rv = vfscanf(fp,format,ptr);
data/phyml-3.3.20200621/src/io.c:3696:11: [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(clade_list[clade_size],s);
data/phyml-3.3.20200621/src/io.c:4003:7: [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(s,tree->io->in_align_file);
data/phyml-3.3.20200621/src/io.c:4885:11: [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(mod->custom_mod_string->s,model_code);
data/phyml-3.3.20200621/src/io.c:4905:11: [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(mod->aa_rate_mat_file->s,r_mat_file);
data/phyml-3.3.20200621/src/io.c:5033:11: [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(io->in_tree_file,starting_tree);
data/phyml-3.3.20200621/src/io.c:5053:7: [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(io->out_trees_file,io->in_align_file);
data/phyml-3.3.20200621/src/io.c:5055:63: [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).
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
data/phyml-3.3.20200621/src/io.c:5542:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(kv->value,"%s",s);
data/phyml-3.3.20200621/src/io.c:5825:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(kv->value,"%s",s);
data/phyml-3.3.20200621/src/io.c:6095:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6102:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6127:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6138:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6213:11: [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(disk->id,tk);
data/phyml-3.3.20200621/src/io.c:6239:15: [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(disk->ldsk->coord->id,tk+1);
data/phyml-3.3.20200621/src/io.c:6252:19: [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_ldsk->coord->id,tk);
data/phyml-3.3.20200621/src/io.c:6333:7: [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(lab->key,key);
data/phyml-3.3.20200621/src/io.c:6337:7: [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(lab->val,val);
data/phyml-3.3.20200621/src/io.c:6385:15: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(s_where+(int)strlen(s_where),"%s=%s",lab->key,lab->val);
data/phyml-3.3.20200621/src/lk.c:222:11: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!sscanf(state,format,&state_int))
data/phyml-3.3.20200621/src/lk.c:254:11: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!sscanf(state,format,&state_int))
data/phyml-3.3.20200621/src/m4.c:1477:3: [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,tree->io->in_align_file);
data/phyml-3.3.20200621/src/m4.c:1479:3: [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,tree->io->in_align_file);
data/phyml-3.3.20200621/src/m4.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(s,tree->io->in_align_file);
data/phyml-3.3.20200621/src/make.c:717:7: [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(cdata->c_seq[j]->name,sp_names_in[j]);
data/phyml-3.3.20200621/src/make.c:727:7: [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(cdata->c_seq_rm[j]->name,sp_names_out[j]);
data/phyml-3.3.20200621/src/make.c:1138:3: [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_attr->name,attr_name);
data/phyml-3.3.20200621/src/make.c:1141:3: [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_attr->value,attr_value);
data/phyml-3.3.20200621/src/mcmc.c:2654:7: [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(s,tree->mcmc->out_filename);
data/phyml-3.3.20200621/src/mcmc.c:2698:7: [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(s,tree->mcmc->out_filename);
data/phyml-3.3.20200621/src/mcmc.c:2846:7: [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(cpy->move_name[i],ori->move_name[i]);
data/phyml-3.3.20200621/src/mcmc.c:2858:7: [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(cpy->out_filename,filename);
data/phyml-3.3.20200621/src/mcmc.c:2862:7: [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(s,cpy->io->in_align_file);
data/phyml-3.3.20200621/src/mcmc.c:2864:7: [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(s,cpy->out_filename);
data/phyml-3.3.20200621/src/mcmc.c:2868:7: [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(s,cpy->io->in_align_file);
data/phyml-3.3.20200621/src/mcmc.c:2870:7: [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(s,cpy->out_filename);
data/phyml-3.3.20200621/src/mcmc.c:2874:7: [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(s,cpy->io->in_align_file);
data/phyml-3.3.20200621/src/mcmc.c:2876:7: [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(s,cpy->out_filename);
data/phyml-3.3.20200621/src/mixt.c:1899:7: [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(boot_out_file_name,out_attr->value);
data/phyml-3.3.20200621/src/mixt.c:1904:11: [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(boot_out_file_name,s);
data/phyml-3.3.20200621/src/mixt.c:1924:11: [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(buff,boot_out_attr->value);
data/phyml-3.3.20200621/src/mixt.c:1946:15: [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(orig_align,seqfile_attr->value);
data/phyml-3.3.20200621/src/mixt.c:1973:15: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(seqfile_attr->value,"%s_%d_%d",orig_align,elem,i);
data/phyml-3.3.20200621/src/nexus.c:126:4: [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(io->long_tax_names[io->size_tax_names-1],token);
data/phyml-3.3.20200621/src/nexus.c:212:3: [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(curr_parm->value,token);
data/phyml-3.3.20200621/src/nexus.c:244:3: [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(curr_parm->value,token);
data/phyml-3.3.20200621/src/phyrex.c:298:7: [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(mixt_tree->io->in_coord_file,coord_file);
data/phyml-3.3.20200621/src/phyrex.c:1809:3: [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(t->cpy->id,t->id);
data/phyml-3.3.20200621/src/phyrex.c:1822:3: [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(t->id,t->cpy->id);
data/phyml-3.3.20200621/src/phyrex.c:2933:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(fscanf(fp,"%s",s) == EOF) break;
data/phyml-3.3.20200621/src/phyrex.c:3388:11: [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(deme_names[n_demes],s+1);
data/phyml-3.3.20200621/src/slfv.c:1252:19: [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(s,ldsk_a_pop[i]->coord->id);
data/phyml-3.3.20200621/src/slfv.c:1678:7: [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(s,tree->young_disk->ldsk_a[i]->coord->id);
data/phyml-3.3.20200621/src/slfv.c:1952:7: [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(s,tree->young_disk->ldsk_a[i]->coord->id);
data/phyml-3.3.20200621/src/tiporder.c:526:8: [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(ref_tree->a_nodes[j]->name,ref_tree->io->long_tax_names[i]);
data/phyml-3.3.20200621/src/tiporder.c:1009:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(fscanf(fp_coord,"%s\t%lf\n",name,&z) == EOF) break;
data/phyml-3.3.20200621/src/tiporder.c:1053:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(fscanf(fp_coord,"%s\t%lf\t%lf\n",name,&lat,&lon) == EOF) break;
data/phyml-3.3.20200621/src/tiporder.c:1198:10: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(fscanf(fp_coord,"%s %lf\n",seqname,&lat) == EOF)
data/phyml-3.3.20200621/src/utilities.c:86:7: [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(subtrees[2],subtrees[1]);
data/phyml-3.3.20200621/src/utilities.c:88:24: [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).
for(j=0;j<2;j++) strcpy(subtrees[j],tmp_sub[j]);
data/phyml-3.3.20200621/src/utilities.c:93:7: [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(subtrees[2],subtrees[0]);
data/phyml-3.3.20200621/src/utilities.c:95:24: [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).
for(j=0;j<2;j++) strcpy(subtrees[j],tmp_sub[j]);
data/phyml-3.3.20200621/src/utilities.c:222:7: [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(sp_names[i],data[i]->name);
data/phyml-3.3.20200621/src/utilities.c:421:7: [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(cdata->c_seq[j]->name,data->c_seq[j]->name);
data/phyml-3.3.20200621/src/utilities.c:1228:3: [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(long_line,line);
data/phyml-3.3.20200621/src/utilities.c:1251:11: [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(long_line,cdata->c_seq[i]->name);
data/phyml-3.3.20200621/src/utilities.c:1302:7: [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(tree->a_nodes[i]->name,data->c_seq[i]->name);
data/phyml-3.3.20200621/src/utilities.c:2028:30: [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).
for(i=0;i<tree->n_otu;++i) strcpy(tree->a_nodes[i]->name,data->c_seq[i]->name);
data/phyml-3.3.20200621/src/utilities.c:2048:7: [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(sp_names_in[i],ori->c_seq[i]->name);
data/phyml-3.3.20200621/src/utilities.c:2055:7: [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(sp_names_out[i],ori->c_seq_rm[i]->name);
data/phyml-3.3.20200621/src/utilities.c:2064:7: [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->c_seq_rm[i]->name,ori->c_seq_rm[i]->name);
data/phyml-3.3.20200621/src/utilities.c:2105:7: [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->c_seq[i]->name,ori->c_seq[i]->name);
data/phyml-3.3.20200621/src/utilities.c:2611:15: [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(daughter->name,tree->data->c_seq_rm[i]->name);
data/phyml-3.3.20200621/src/utilities.c:2913:13: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
ret = sscanf(c,format,state);
data/phyml-3.3.20200621/src/utilities.c:3074:15: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!sscanf(c,format,state))
data/phyml-3.3.20200621/src/utilities.c:3752:3: [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(cpy->modelname->s,ori->modelname->s);
data/phyml-3.3.20200621/src/utilities.c:3753:3: [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(cpy->custom_mod_string->s,ori->custom_mod_string->s);
data/phyml-3.3.20200621/src/utilities.c:4901:15: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!sscanf(statea,format,&a))
data/phyml-3.3.20200621/src/utilities.c:4907:15: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
if(!sscanf(stateb,format,&b))
data/phyml-3.3.20200621/src/utilities.c:5009:7: [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(cpy->a_nodes[i]->name,ori->a_nodes[i]->name);
data/phyml-3.3.20200621/src/utilities.c:8972:7: [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(cpy->a_nodes[i]->name,ori->a_nodes[i]->name);
data/phyml-3.3.20200621/src/utilities.c:11920:3: [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(to->id,from->id);
data/phyml-3.3.20200621/src/utilities.c:11945:3: [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(to->id,from->id);
data/phyml-3.3.20200621/src/utilities.c:11956:7: [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(to->tax_list[i],from->tax_list[i]);
data/phyml-3.3.20200621/src/xml.c:129:7: [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(io->run_id_string,s);
data/phyml-3.3.20200621/src/xml.c:135:3: [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(io->out_file,outputfile);
data/phyml-3.3.20200621/src/xml.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(io->out_tree_file,outputfile);
data/phyml-3.3.20200621/src/xml.c:137:3: [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(io->out_stats_file,outputfile);
data/phyml-3.3.20200621/src/xml.c:159:58: [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).
if(io->append_run_ID) { strcat(io->out_tree_file,"_"); strcat(io->out_tree_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:160:59: [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).
if(io->append_run_ID) { strcat(io->out_stats_file,"_"); strcat(io->out_stats_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:188:11: [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(io->out_trace_file,outputfile);
data/phyml-3.3.20200621/src/xml.c:190:67: [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).
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:208:11: [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(io->out_json_trace_file,outputfile);
data/phyml-3.3.20200621/src/xml.c:210:72: [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).
if(io->append_run_ID) { strcat(io->out_json_trace_file,"_"); strcat(io->out_json_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:225:7: [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(io->out_lk_file,outputfile);
data/phyml-3.3.20200621/src/xml.c:227:60: [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).
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:384:7: [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(io->in_align_file,alignment);
data/phyml-3.3.20200621/src/xml.c:1546:3: [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(attr->value,s);
data/phyml-3.3.20200621/src/xml.c:1588:3: [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(n->id,id);
data/phyml-3.3.20200621/src/xml.c:1598:3: [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(n->value,val);
data/phyml-3.3.20200621/src/xml.c:2119:3: [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(cpy_root->name,root->name);
data/phyml-3.3.20200621/src/xml.c:2122:16: [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(root->id) strcpy(cpy_root->id,root->id);
data/phyml-3.3.20200621/src/xml.c:2125:19: [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(root->value) strcpy(cpy_root->value,root->value);
data/phyml-3.3.20200621/src/xml.c:2346:11: [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(cal->id,calib_id);
data/phyml-3.3.20200621/src/xml.c:2404:53: [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).
for(i=0;i<clade_size;++i) strcpy(clade->tax_list[i],xclade[i]);
data/phyml-3.3.20200621/src/xml.c:2413:27: [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(clade->id,clade_id);
data/phyml-3.3.20200621/src/cl.c:144:11: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
c = getopt_long(argc,argv,"qi:d:m:b:n:t:f:zk:v:c:a:u:ho:s:x:g:l:ep",longopts,&idx);
data/phyml-3.3.20200621/src/date.c:251:3: [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(seed);
data/phyml-3.3.20200621/src/geo.c:50:3: [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(seed);
data/phyml-3.3.20200621/src/geo.c:159:3: [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(seed);
data/phyml-3.3.20200621/src/help.c:34:9: [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.
cha = getenv("OS");
data/phyml-3.3.20200621/src/invitee.c:47:3: [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(NULL));
data/phyml-3.3.20200621/src/invitee.c:517:3: [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(r_seed);
data/phyml-3.3.20200621/src/invitee.c:2004:3: [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(NULL));
data/phyml-3.3.20200621/src/m4.c:55:3: [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(r_seed);
data/phyml-3.3.20200621/src/main.c:92:3: [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(r_seed);
data/phyml-3.3.20200621/src/main.c:452:3: [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(r_seed);
data/phyml-3.3.20200621/src/mcmc.h:89:59: [3] (random) random:
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.
void MCMC_Pair_Rates_Constraint(t_node *a, t_node *d, int random, int traversal, t_tree *tree);
data/phyml-3.3.20200621/src/mcmc.h:90:53: [3] (random) random:
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.
void MCMC_Times_And_Rates(t_node *a, t_node *d, int random, int traversal, t_tree *tree);
data/phyml-3.3.20200621/src/phyrex.c:303:3: [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(seed);
data/phyml-3.3.20200621/src/phyrex.c:492:3: [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(seed);
data/phyml-3.3.20200621/src/tiporder.c:261:3: [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(NULL)); rand();
data/phyml-3.3.20200621/src/alrt.c:192:27: [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 ALRTCHI2: { strcpy(method,"aLRT"); break; }
data/phyml-3.3.20200621/src/alrt.c:193:27: [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 MINALRTCHI2SH: { strcpy(method,"aLRT"); break; }
data/phyml-3.3.20200621/src/alrt.c:194:27: [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 ALRTSTAT: { strcpy(method,"aLRT"); break; }
data/phyml-3.3.20200621/src/alrt.c:195:27: [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 SH: { strcpy(method,"SH"); break; }
data/phyml-3.3.20200621/src/alrt.c:196:27: [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 ABAYES: { strcpy(method,"aBayes"); break; }
data/phyml-3.3.20200621/src/ancestral.c:119:7: [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,"mutmap.");
data/phyml-3.3.20200621/src/ancestral.c:120:7: [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(s+strlen(s),"%d.",tree->io->r_seed);
data/phyml-3.3.20200621/src/ancestral.c:121:7: [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(s+strlen(s),"%d",i);
data/phyml-3.3.20200621/src/ancestral.c:122:12: [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).
fp = fopen(s,"a");
data/phyml-3.3.20200621/src/ancestral.c:537:7: [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(tree->io->out_ancestral_seq_file,"_phyml_ancestral_");
data/phyml-3.3.20200621/src/ancestral.c:543:7: [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(tree->io->out_ancestral_seq_file,"seq.txt");
data/phyml-3.3.20200621/src/ancestral.c:548:7: [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(tree->io->out_ancestral_tree_file,"_phyml_ancestral_");
data/phyml-3.3.20200621/src/ancestral.c:554:7: [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(tree->io->out_ancestral_tree_file,"tree.txt");
data/phyml-3.3.20200621/src/cl.c:155:12: [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).
if ((!atoi(optarg)) || (atoi(optarg) < 1) || (atoi(optarg) > DECIMAL_DIG -3))
data/phyml-3.3.20200621/src/cl.c:155:30: [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(optarg)) || (atoi(optarg) < 1) || (atoi(optarg) > DECIMAL_DIG -3))
data/phyml-3.3.20200621/src/cl.c:155:52: [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(optarg)) || (atoi(optarg) < 1) || (atoi(optarg) > DECIMAL_DIG -3))
data/phyml-3.3.20200621/src/cl.c:162:19: [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).
io->precision = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:198:3: [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 (tmp, "\n. The file name'");
data/phyml-3.3.20200621/src/cl.c:200:3: [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 (tmp, "' is too long.\n");
data/phyml-3.3.20200621/src/cl.c:209:3: [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 (tmp, "\n. The file '");
data/phyml-3.3.20200621/src/cl.c:211:3: [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 (tmp, "' doesn't exist.\n");
data/phyml-3.3.20200621/src/cl.c:234:40: [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).
io->beagle_resource = (int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:288:28: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
io->mcmc->in_fp_par = fopen(optarg,"r");
data/phyml-3.3.20200621/src/cl.c:305:3: [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 (tmp, "\n. The file name'");
data/phyml-3.3.20200621/src/cl.c:307:3: [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 (tmp, "' is too long.\n");
data/phyml-3.3.20200621/src/cl.c:316:3: [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 (tmp, "\n. The file '");
data/phyml-3.3.20200621/src/cl.c:318:3: [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 (tmp, "' doesn't exist.\n");
data/phyml-3.3.20200621/src/cl.c:475:28: [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).
io->boot_prog_every = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:541:41: [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).
io->mod->s_opt->pars_thresh = (int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:588:33: [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).
io->mod->m4mod->n_h = (int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:671:39: [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).
io->random_boot_seq_order = (int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:676:31: [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).
io->collapse_boot = (int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:681:24: [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).
io->r_seed = (int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:706:36: [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).
io->mod->s_opt->wim_n_rgrft = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:711:36: [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).
io->mod->s_opt->wim_n_globl = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:716:37: [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).
io->mod->s_opt->wim_max_dist = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:721:36: [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).
io->mod->s_opt->wim_n_optim = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:726:35: [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).
io->mod->s_opt->wim_n_best = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:747:37: [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).
io->mod->s_opt->brent_it_max = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:758:38: [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).
io->mod->s_opt->n_rand_starts = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:812:7: [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(io->mod->modelname->s, "HKY85\0");
data/phyml-3.3.20200621/src/cl.c:836:7: [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(io->mod->modelname->s, "LG\0");
data/phyml-3.3.20200621/src/cl.c:868:21: [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(io->mod->modelname->s, "custom");
data/phyml-3.3.20200621/src/cl.c:1111:36: [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).
io->n_boot_replicates = (int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:1123:12: [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).
else if (atoi(optarg)==0)
data/phyml-3.3.20200621/src/cl.c:1135:30: [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).
io->ratio_test = -(int)atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:1142:12: [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).
if ((!atoi(optarg)) || (atoi(optarg) < 0))
data/phyml-3.3.20200621/src/cl.c:1142:30: [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(optarg)) || (atoi(optarg) < 0))
data/phyml-3.3.20200621/src/cl.c:1152:26: [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).
io->mod->ras->n_catg = atoi(optarg);
data/phyml-3.3.20200621/src/cl.c:1244:3: [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 (tmp, "\n. The file name'");
data/phyml-3.3.20200621/src/cl.c:1246:3: [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 (tmp, "' is too long.\n");
data/phyml-3.3.20200621/src/cl.c:1256:3: [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 (tmp, "\n. The file '");
data/phyml-3.3.20200621/src/cl.c:1258:3: [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 (tmp, "' does not exist.\n");
data/phyml-3.3.20200621/src/cl.c:1272:3: [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(io->out_tree_file,"_phyml_tree");
data/phyml-3.3.20200621/src/cl.c:1274:3: [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(io->out_tree_file,"_m4_tree");
data/phyml-3.3.20200621/src/cl.c:1276:3: [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(io->out_tree_file,"_phyrex_tree");
data/phyml-3.3.20200621/src/cl.c:1281:3: [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(io->out_stats_file,"_phyml_stats");
data/phyml-3.3.20200621/src/cl.c:1283:3: [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(io->out_stats_file,"_m4_stats");
data/phyml-3.3.20200621/src/cl.c:1285:3: [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(io->out_stats_file,"_phyrex_stats");
data/phyml-3.3.20200621/src/cl.c:1291:3: [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(io->out_summary_file,"_phyrex_summary");
data/phyml-3.3.20200621/src/cl.c:1366:12: [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).
if ((!atoi(optarg)) || (atoi(optarg) < 0))
data/phyml-3.3.20200621/src/cl.c:1366:30: [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(optarg)) || (atoi(optarg) < 0))
data/phyml-3.3.20200621/src/cl.c:1374:29: [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 io->n_data_sets = atoi (optarg);
data/phyml-3.3.20200621/src/cl.c:1389:3: [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 (tmp, "\n. The file name'");
data/phyml-3.3.20200621/src/cl.c:1391:3: [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 (tmp, "' is too long.\n");
data/phyml-3.3.20200621/src/cl.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 (tmp, "\n. The file '");
data/phyml-3.3.20200621/src/cl.c:1402:3: [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 (tmp, "' doesn't exist.\n");
data/phyml-3.3.20200621/src/cl.c:1555:7: [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(io->out_ps_file, "_mc_tree.ps");
data/phyml-3.3.20200621/src/cl.c:1599:7: [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(io->out_lk_file, "_phyml_lk");
data/phyml-3.3.20200621/src/cl.c:1601:7: [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(io->out_lk_file, ".txt");
data/phyml-3.3.20200621/src/cl.c:1608:7: [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(io->out_trace_file,"_phyml_trace");
data/phyml-3.3.20200621/src/cl.c:1610:7: [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(io->out_trace_file,".txt");
data/phyml-3.3.20200621/src/cl.c:1617:7: [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(io->out_json_trace_file,"_phyml_trace");
data/phyml-3.3.20200621/src/cl.c:1619:7: [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(io->out_json_trace_file,".json");
data/phyml-3.3.20200621/src/cl.c:1627:7: [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(io->out_trees_file,"_phyml_rand_trees");
data/phyml-3.3.20200621/src/cl.c:1629:7: [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(io->out_trees_file,".txt");
data/phyml-3.3.20200621/src/cl.c:1636:7: [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(io->out_boot_tree_file,"_phyml_boot_trees");
data/phyml-3.3.20200621/src/cl.c:1638:7: [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(io->out_boot_tree_file,".txt");
data/phyml-3.3.20200621/src/cl.c:1642:7: [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(io->out_boot_stats_file,"_phyml_boot_stats");
data/phyml-3.3.20200621/src/cl.c:1644:7: [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(io->out_boot_stats_file,".txt");
data/phyml-3.3.20200621/src/cl.c:1658:7: [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(io->out_tree_file,".txt");
data/phyml-3.3.20200621/src/cl.c:1659:7: [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(io->out_stats_file,".txt");
data/phyml-3.3.20200621/src/cl.c:1664:3: [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(io->out_summary_file,".txt");
data/phyml-3.3.20200621/src/date.c:62:15: [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).
fp_xml_in = fopen(xml_filename,"r");
data/phyml-3.3.20200621/src/date.c:132:7: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/date.c:152:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/date.c:158:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/date.c:164:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/date.c:170:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/date.c:176:15: [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(mixt_tree->rates->model_name,"lognormal (uncorrelated)");
data/phyml-3.3.20200621/src/date.c:182:15: [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(mixt_tree->rates->model_name,"lognormal (uncorrelated)");
data/phyml-3.3.20200621/src/date.c:188:15: [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(mixt_tree->rates->model_name,"strict clock");
data/phyml-3.3.20200621/src/date.c:194:15: [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(mixt_tree->rates->model_name,"strict clock");
data/phyml-3.3.20200621/src/draw.c:20:21: [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).
ps_tree = (FILE *)fopen(file_name,"w");
data/phyml-3.3.20200621/src/geo.c:149:3: [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(s,"geo.out");
data/phyml-3.3.20200621/src/geo.c:151:3: [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(s+strlen(s),".%d",pid);
data/phyml-3.3.20200621/src/geo.c:153:8: [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(s,"w");
data/phyml-3.3.20200621/src/geo.c:169:24: [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).
t->ldscape_sz = (int)atoi(argv[1]);
data/phyml-3.3.20200621/src/geo.c:171:24: [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_tax = (int)atoi(argv[2]);
data/phyml-3.3.20200621/src/geo.c:1135:7: [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(tree->a_nodes[i]->name+1,"%d",i);
data/phyml-3.3.20200621/src/help.c:44:7: [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(BOLD, "\033[00;01m");
data/phyml-3.3.20200621/src/help.c:45:7: [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(FLAT, "\033[00;00m");
data/phyml-3.3.20200621/src/help.c:46:7: [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(LINE, "\033[00;04m");
data/phyml-3.3.20200621/src/init.c:285:3: [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(com[0]->name,"dimensions");
data/phyml-3.3.20200621/src/init.c:291:3: [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(com[0]->parm[0]->name,"ntax");
data/phyml-3.3.20200621/src/init.c:298:3: [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(com[0]->parm[1]->name,"nchar");
data/phyml-3.3.20200621/src/init.c:306:3: [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(com[1]->name,"format");
data/phyml-3.3.20200621/src/init.c:312:3: [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(com[1]->parm[0]->name,"datatype");
data/phyml-3.3.20200621/src/init.c:319:3: [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(com[1]->parm[1]->name,"respectcase");
data/phyml-3.3.20200621/src/init.c:326:3: [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(com[1]->parm[2]->name,"missing");
data/phyml-3.3.20200621/src/init.c:333:3: [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(com[1]->parm[3]->name,"gap");
data/phyml-3.3.20200621/src/init.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(com[1]->parm[4]->name,"symbols");
data/phyml-3.3.20200621/src/init.c:347:3: [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(com[1]->parm[5]->name,"equate");
data/phyml-3.3.20200621/src/init.c:354:3: [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(com[1]->parm[6]->name,"matchchar");
data/phyml-3.3.20200621/src/init.c:361:3: [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(com[1]->parm[7]->name,"transpose");
data/phyml-3.3.20200621/src/init.c:368:3: [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(com[1]->parm[8]->name,"interleave");
data/phyml-3.3.20200621/src/init.c:375:3: [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(com[1]->parm[9]->name,"items");
data/phyml-3.3.20200621/src/init.c:382:3: [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(com[1]->parm[10]->name,"statesformat");
data/phyml-3.3.20200621/src/init.c:390:3: [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(com[2]->name,"eliminate");
data/phyml-3.3.20200621/src/init.c:397:3: [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(com[3]->name,"taxlabels");
data/phyml-3.3.20200621/src/init.c:404:3: [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(com[4]->name,"charstatelabels");
data/phyml-3.3.20200621/src/init.c:411:3: [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(com[5]->name,"charlabels");
data/phyml-3.3.20200621/src/init.c:418:3: [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(com[6]->name,"statelabels");
data/phyml-3.3.20200621/src/init.c:425:3: [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(com[7]->name,"matrix");
data/phyml-3.3.20200621/src/init.c:432:3: [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(com[7]->parm[0]->name,"matrix");
data/phyml-3.3.20200621/src/init.c:440:3: [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(com[8]->name,"begin");
data/phyml-3.3.20200621/src/init.c:447:3: [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(com[8]->parm[0]->name,"data");
data/phyml-3.3.20200621/src/init.c:455:3: [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(com[8]->parm[1]->name,"trees");
data/phyml-3.3.20200621/src/init.c:463:3: [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(com[8]->parm[2]->name,"taxa");
data/phyml-3.3.20200621/src/init.c:472:3: [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(com[9]->name,"end");
data/phyml-3.3.20200621/src/init.c:479:3: [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(com[10]->name,"translate");
data/phyml-3.3.20200621/src/init.c:485:3: [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(com[10]->parm[0]->name,"translate");
data/phyml-3.3.20200621/src/init.c:493:3: [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(com[11]->name,"tree");
data/phyml-3.3.20200621/src/init.c:499:3: [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(com[11]->parm[0]->name,"tree");
data/phyml-3.3.20200621/src/init.c:560:3: [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(io->nt_or_cd,"nucleotides");
data/phyml-3.3.20200621/src/init.c:634:3: [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(mod->modelname->s,"HKY85");
data/phyml-3.3.20200621/src/init.c:635:3: [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(mod->custom_mod_string->s,"000000");
data/phyml-3.3.20200621/src/init.c:3589:7: [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(mcmc->out_filename+strlen(mcmc->out_filename),".%d",pid);
data/phyml-3.3.20200621/src/init.c:3594:7: [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(s,".stats");
data/phyml-3.3.20200621/src/init.c:3595:28: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mcmc->out_fp_stats = fopen(s,"w");
data/phyml-3.3.20200621/src/init.c:3600:7: [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(s,".trees");
data/phyml-3.3.20200621/src/init.c:3601:28: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mcmc->out_fp_trees = fopen(s,"w");
data/phyml-3.3.20200621/src/init.c:3606:7: [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(s,".constree");
data/phyml-3.3.20200621/src/init.c:3607:31: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mcmc->out_fp_constree = fopen(s,"w");
data/phyml-3.3.20200621/src/interface.c:136:7: [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(io->out_lk_file, "_phyml_lk.txt");
data/phyml-3.3.20200621/src/interface.c:145:7: [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(io->out_trace_file,"_phyml_trace.txt");
data/phyml-3.3.20200621/src/interface.c:154:7: [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(io->out_trees_file,"_phyml_trees.txt");
data/phyml-3.3.20200621/src/interface.c:163:7: [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(io->out_boot_tree_file,"_phyml_boot_trees.txt");
data/phyml-3.3.20200621/src/interface.c:169:7: [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(io->out_boot_stats_file,"_phyml_boot_stats.txt");
data/phyml-3.3.20200621/src/interface.c:250:11: [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).
while((!atoi(n_data_sets)) || (atoi(n_data_sets) < 0))
data/phyml-3.3.20200621/src/interface.c:250:34: [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).
while((!atoi(n_data_sets)) || (atoi(n_data_sets) < 0))
data/phyml-3.3.20200621/src/interface.c:257:26: [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).
io->n_data_set_asked = atoi(n_data_sets);
data/phyml-3.3.20200621/src/interface.c:285:3: [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(io->out_stats_file,"_phyml_stats.txt");
data/phyml-3.3.20200621/src/interface.c:288:3: [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(io->out_tree_file,"_phyml_tree.txt");
data/phyml-3.3.20200621/src/interface.c:291:3: [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(io->out_lk_file,"_phyml_lk.txt");
data/phyml-3.3.20200621/src/interface.c:400:31: [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.
if(io->datatype == NT) strcpy(s,"DNA");
data/phyml-3.3.20200621/src/interface.c:401:31: [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.
else if(io->datatype == AA) strcpy(s,"AA");
data/phyml-3.3.20200621/src/interface.c:402:8: [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.
else strcpy(s,"Generic");
data/phyml-3.3.20200621/src/interface.c:414:3: [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(s," (%d sets)",io->n_data_sets);
data/phyml-3.3.20200621/src/interface.c:421:26: [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.
if(!io->append_run_ID) strcpy(s,"none");
data/phyml-3.3.20200621/src/interface.c:463:10: [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).
while((!atoi(c)) || (atoi(c) < 0))
data/phyml-3.3.20200621/src/interface.c:463:23: [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).
while((!atoi(c)) || (atoi(c) < 0))
data/phyml-3.3.20200621/src/interface.c:470:20: [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).
io->n_data_sets = atoi(c);
data/phyml-3.3.20200621/src/interface.c:505:6: [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(io->mod->modelname->s,"LG");
data/phyml-3.3.20200621/src/interface.c:511:6: [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(io->mod->modelname->s,"JC69");
data/phyml-3.3.20200621/src/interface.c:512:6: [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(io->nt_or_cd,"natural numbers");
data/phyml-3.3.20200621/src/interface.c:519:6: [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(io->mod->modelname->s,"HKY85");
data/phyml-3.3.20200621/src/interface.c:520:6: [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(io->nt_or_cd,"nucleotides");
data/phyml-3.3.20200621/src/interface.c:657:12: [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.
else strcat(s," (ts/tv = ");
data/phyml-3.3.20200621/src/interface.c:666:4: [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((char *)(s+(int)strlen(s)),"%3.2f)",io->mod->kappa->v);
data/phyml-3.3.20200621/src/interface.c:684:7: [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((char *)(s+strlen((char *)s)),"%3.2f)",io->mod->ras->pinvar->v);
data/phyml-3.3.20200621/src/interface.c:724:4: [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(s+strlen(s),"%3.2f)",io->mod->ras->alpha->v);
data/phyml-3.3.20200621/src/interface.c:821:6: [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(rr_param[0],"A<->C");
data/phyml-3.3.20200621/src/interface.c:822:6: [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(rr_param[1],"A<->G");
data/phyml-3.3.20200621/src/interface.c:823:6: [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(rr_param[2],"A<->T");
data/phyml-3.3.20200621/src/interface.c:824:6: [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(rr_param[3],"C<->G");
data/phyml-3.3.20200621/src/interface.c:825:6: [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(rr_param[4],"C<->T");
data/phyml-3.3.20200621/src/interface.c:826:6: [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(rr_param[5],"G<->T");
data/phyml-3.3.20200621/src/interface.c:831:3: [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(rr,"\n. [");
data/phyml-3.3.20200621/src/interface.c:888:7: [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(bases[0],". f(A)> ");
data/phyml-3.3.20200621/src/interface.c:889:7: [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(bases[1],". f(C)> ");
data/phyml-3.3.20200621/src/interface.c:890:7: [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(bases[2],". f(G)> ");
data/phyml-3.3.20200621/src/interface.c:891:7: [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(bases[3],". f(T)> ");
data/phyml-3.3.20200621/src/interface.c:1020:10: [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).
while((!atoi(c)) || (atoi(c) < 0))
data/phyml-3.3.20200621/src/interface.c:1020:23: [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).
while((!atoi(c)) || (atoi(c) < 0))
data/phyml-3.3.20200621/src/interface.c:1027:25: [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).
io->mod->ras->n_catg = atoi(c);
data/phyml-3.3.20200621/src/interface.c:1406:12: [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 0: { strcpy(s,"BioNJ"); break; }
data/phyml-3.3.20200621/src/interface.c:1407:12: [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 1: { strcpy(s,"parsimony"); break; }
data/phyml-3.3.20200621/src/interface.c:1408:12: [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 2: { strcpy(s,"user tree"); break; }
data/phyml-3.3.20200621/src/interface.c:1419:12: [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 0: { strcpy(s,"BioNJ"); break; }
data/phyml-3.3.20200621/src/interface.c:1420:12: [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 2: { strcpy(s,"user tree"); break; }
data/phyml-3.3.20200621/src/interface.c:1439:4: [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,"SPR moves\0");
data/phyml-3.3.20200621/src/interface.c:1443:4: [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,"SPR moves\0");
data/phyml-3.3.20200621/src/interface.c:1447:4: [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,"SPR moves\0");
data/phyml-3.3.20200621/src/interface.c:1528:8: [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).
while(atoi(n) < 1)
data/phyml-3.3.20200621/src/interface.c:1535:34: [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).
io->mod->s_opt->n_rand_starts = atoi(n);
data/phyml-3.3.20200621/src/interface.c:1592:6: [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(io->out_trees_file,"_phyml_trees.txt");
data/phyml-3.3.20200621/src/interface.c:1650:7: [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,"no");
data/phyml-3.3.20200621/src/interface.c:1654:7: [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,"yes / aLRT statistics");
data/phyml-3.3.20200621/src/interface.c:1658:7: [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,"yes / Chi2-based supports");
data/phyml-3.3.20200621/src/interface.c:1662:7: [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,"yes / min of SH-like & Chi2-based supports");
data/phyml-3.3.20200621/src/interface.c:1666:7: [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,"yes / SH-like supports");
data/phyml-3.3.20200621/src/interface.c:1670:7: [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,"yes / aBayes supports");
data/phyml-3.3.20200621/src/interface.c:1723:14: [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).
while((!atoi(r)) || (atoi(r) < 0))
data/phyml-3.3.20200621/src/interface.c:1723:27: [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).
while((!atoi(r)) || (atoi(r) < 0))
data/phyml-3.3.20200621/src/interface.c:1730:30: [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).
io->n_boot_replicates = atoi(r);
data/phyml-3.3.20200621/src/interface.c:1747:5: [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(io->out_boot_tree_file,"_phyml_boot_trees.txt");
data/phyml-3.3.20200621/src/interface.c:1751:5: [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(io->out_boot_stats_file,"_phyml_boot_stats.txt");
data/phyml-3.3.20200621/src/invitee.c:58:19: [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 ((f =(FILE *)fopen(xml_file, "r")) == NULL)
data/phyml-3.3.20200621/src/invitee.c:265:19: [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(io -> in_align_file, "invitee");
data/phyml-3.3.20200621/src/invitee.c:532:28: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
c_seq[i] -> state = (char *)mCalloc(data[0] -> len + 1,sizeof(char));
data/phyml-3.3.20200621/src/invitee.c:2503:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cResult[mem];
data/phyml-3.3.20200621/src/invitee.c:2505:3: [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(cResult, "%d%d", int1, int2);
data/phyml-3.3.20200621/src/invitee.c:2506:10: [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(cResult);
data/phyml-3.3.20200621/src/io.c:83:11: [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((*s_tree),",\0");
data/phyml-3.3.20200621/src/io.c:232:23: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
s_tree_d = (char *)mCalloc(strlen(subs[0])+strlen(subs[1])+5,sizeof(char));
data/phyml-3.3.20200621/src/io.c:407:3: [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(sub_tp,"[\0");
data/phyml-3.3.20200621/src/io.c:415:7: [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(sub_tp,"[\0");
data/phyml-3.3.20200621/src/io.c:462:7: [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(s_tmp,"(\0");
data/phyml-3.3.20200621/src/io.c:464:7: [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(s_tmp,",\0");
data/phyml-3.3.20200621/src/io.c:466:7: [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(s_tmp,")#NULL\0"); /* Add the label 'NULL' to identify a non-existing edge */
data/phyml-3.3.20200621/src/io.c:627:9: [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(s+(int)strlen(s),"%d",tree->a_nodes[tree->n_otu+i]->num);
data/phyml-3.3.20200621/src/io.c:629:9: [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(s+(int)strlen(s),"%d",tree->n_root->num);
data/phyml-3.3.20200621/src/io.c:648:3: [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(format,"%%.%df",tree->bl_ndigits);
data/phyml-3.3.20200621/src/io.c:668:21: [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.
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num+1);
data/phyml-3.3.20200621/src/io.c:673:15: [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.
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num+1);
data/phyml-3.3.20200621/src/io.c:678:11: [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.
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num+1);
data/phyml-3.3.20200621/src/io.c:772:19: [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.
sprintf(*s_tree+(int)strlen(*s_tree),"%.0f",fils->b[p]->support_val);
data/phyml-3.3.20200621/src/io.c:776:19: [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.
sprintf(*s_tree+(int)strlen(*s_tree),"%f",fils->b[p]->support_val);
data/phyml-3.3.20200621/src/io.c:781:15: [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.
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num);
data/phyml-3.3.20200621/src/io.c:839:11: [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.
char s[10],t[6]="NEXUS";
data/phyml-3.3.20200621/src/io.c:877:7: [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 s[10],t[6]="NEXUS";
data/phyml-3.3.20200621/src/io.c:1360:3: [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(format, "%%%ds", T_MAX_NAME);
data/phyml-3.3.20200621/src/io.c:1414:3: [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(format, "%%%ds", T_MAX_NAME);
data/phyml-3.3.20200621/src/io.c:1623:7: [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 open,maxopen;
data/phyml-3.3.20200621/src/io.c:1642:13: [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).
maxopen = open;
data/phyml-3.3.20200621/src/io.c:1669:10: [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).
if(open>maxopen) maxopen = open;
data/phyml-3.3.20200621/src/io.c:1669:34: [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).
if(open>maxopen) maxopen = open;
data/phyml-3.3.20200621/src/io.c:1747:7: [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(s,"Site");
data/phyml-3.3.20200621/src/io.c:1750:7: [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(s,"P(D|M)");
data/phyml-3.3.20200621/src/io.c:1753:7: [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(s,"Scaler");
data/phyml-3.3.20200621/src/io.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(s,"Pattern");
data/phyml-3.3.20200621/src/io.c:1763:15: [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.
sprintf(s,"P*(D|M,rr[%d]=%5.4f)",catg+1,tree->mod->ras->gamma_rr->v[catg]);
data/phyml-3.3.20200621/src/io.c:1767:11: [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.
sprintf(s,"Posterior mean");
data/phyml-3.3.20200621/src/io.c:1774:11: [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.
sprintf(s,"P(D|M,rr[0]=0)");
data/phyml-3.3.20200621/src/io.c:1778:7: [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(s,"NDistinctStates");
data/phyml-3.3.20200621/src/io.c:2246:11: [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.
char s[2]="-";
data/phyml-3.3.20200621/src/io.c:2273:30: [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).
while(!(fp = (FILE *)fopen(s,"r")) && ++open_test<10)
data/phyml-3.3.20200621/src/io.c:2282:22: [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).
fp = (FILE *)fopen(s,"w");
data/phyml-3.3.20200621/src/io.c:2287:22: [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).
fp = (FILE *)fopen(s,"a");
data/phyml-3.3.20200621/src/io.c:2292:22: [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).
fp = (FILE *)fopen(s,"w+");
data/phyml-3.3.20200621/src/io.c:2311:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char format[8];
data/phyml-3.3.20200621/src/io.c:2338:21: [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(strcat(strcat(s,"user tree ("),io->in_tree_file),")");
data/phyml-3.3.20200621/src/io.c:2344:32: [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(io->in_tree == 0) strcat(s,"BioNJ");
data/phyml-3.3.20200621/src/io.c:2345:32: [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(io->in_tree == 1) strcat(s,"parsimony");
data/phyml-3.3.20200621/src/io.c:2348:9: [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(s,"random tree");
data/phyml-3.3.20200621/src/io.c:2624:17: [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 0: { strcpy(s,"BioNJ"); break; }
data/phyml-3.3.20200621/src/io.c:2625:17: [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 1: { strcpy(s,"parsimony"); break; }
data/phyml-3.3.20200621/src/io.c:2626:17: [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 2: { strcpy(s,"user tree (");
data/phyml-3.3.20200621/src/io.c:2846:26: [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.
if(io->datatype == NT) strcpy(s,"dna");
data/phyml-3.3.20200621/src/io.c:2847:31: [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.
else if(io->datatype == AA) strcpy(s,"aa");
data/phyml-3.3.20200621/src/io.c:2848:8: [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.
else strcpy(s,"generic");
data/phyml-3.3.20200621/src/io.c:2942:15: [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 0: { strcpy(s,"BioNJ"); break; }
data/phyml-3.3.20200621/src/io.c:2943:15: [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 1: { strcpy(s,"parsimony"); break; }
data/phyml-3.3.20200621/src/io.c:2944:15: [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 2: { strcpy(s,"user tree (");
data/phyml-3.3.20200621/src/io.c:4004:7: [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(s,", ");
data/phyml-3.3.20200621/src/io.c:4129:19: [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,"Empirical");
data/phyml-3.3.20200621/src/io.c:4133:19: [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,"Model");
data/phyml-3.3.20200621/src/io.c:4194:3: [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(param,"Partition element ");
data/phyml-3.3.20200621/src/io.c:4316:3: [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(param,"State frequencies ");
data/phyml-3.3.20200621/src/io.c:4332:3: [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(param,"Branch lengths ");
data/phyml-3.3.20200621/src/io.c:4347:3: [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(param,"Rate matrix ");
data/phyml-3.3.20200621/src/io.c:5049:39: [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).
mod->s_opt->n_rand_starts = atoi(n_rand_starts);
data/phyml-3.3.20200621/src/io.c:5054:7: [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(io->out_trees_file,"_phyml_rand_trees");
data/phyml-3.3.20200621/src/io.c:5056:7: [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(io->out_trees_file,".txt");
data/phyml-3.3.20200621/src/io.c:5436:3: [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(state->key,"state");
data/phyml-3.3.20200621/src/io.c:5451:3: [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(kv->key,"type");
data/phyml-3.3.20200621/src/io.c:5453:3: [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(kv->value,"t_num");
data/phyml-3.3.20200621/src/io.c:5460:3: [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(kv->key,"id");
data/phyml-3.3.20200621/src/io.c:5462:3: [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(kv->value,"state_num");
data/phyml-3.3.20200621/src/io.c:5469:3: [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(kv->key,"value");
data/phyml-3.3.20200621/src/io.c:5471:3: [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(kv->value,"%d",mixt_tree->json_num);
data/phyml-3.3.20200621/src/io.c:5488:3: [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(kv->key,"type");
data/phyml-3.3.20200621/src/io.c:5490:3: [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(kv->value,"t_time");
data/phyml-3.3.20200621/src/io.c:5496:3: [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(kv->key,"id");
data/phyml-3.3.20200621/src/io.c:5498:3: [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(kv->value,"time");
data/phyml-3.3.20200621/src/io.c:5505:3: [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(kv->key,"value");
data/phyml-3.3.20200621/src/io.c:5508:3: [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(kv->value,"%d",(int)(t_end-mixt_tree->t_beg));
data/phyml-3.3.20200621/src/io.c:5522:3: [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(kv->key,"type");
data/phyml-3.3.20200621/src/io.c:5524:3: [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(kv->value,"t_tree");
data/phyml-3.3.20200621/src/io.c:5530:3: [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(kv->key,"id");
data/phyml-3.3.20200621/src/io.c:5532:3: [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(kv->value,"tree");
data/phyml-3.3.20200621/src/io.c:5539:3: [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(kv->key,"value");
data/phyml-3.3.20200621/src/io.c:5558:3: [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(kv->key,"type");
data/phyml-3.3.20200621/src/io.c:5560:3: [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(kv->value,"t_param");
data/phyml-3.3.20200621/src/io.c:5566:3: [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(kv->key,"id");
data/phyml-3.3.20200621/src/io.c:5568:3: [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(kv->value,"likelihood");
data/phyml-3.3.20200621/src/io.c:5575:3: [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(kv->key,"value");
data/phyml-3.3.20200621/src/io.c:5577:3: [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(kv->value,"%G",mixt_tree->c_lnL);
data/phyml-3.3.20200621/src/io.c:5615:17: [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(kv->key,"type");
data/phyml-3.3.20200621/src/io.c:5617:17: [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(kv->value,"t_param");
data/phyml-3.3.20200621/src/io.c:5623:17: [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(kv->key,"id");
data/phyml-3.3.20200621/src/io.c:5625:17: [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(kv->value,"tstv");
data/phyml-3.3.20200621/src/io.c:5626:17: [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.
sprintf(kv->value+strlen(kv->value),"%d",n_tstv);
data/phyml-3.3.20200621/src/io.c:5632:17: [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(kv->key,"value");
data/phyml-3.3.20200621/src/io.c:5634:17: [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.
sprintf(kv->value,"%G",tree->mod->kappa->v);
data/phyml-3.3.20200621/src/io.c:5680:17: [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(kv->key,"type");
data/phyml-3.3.20200621/src/io.c:5682:17: [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(kv->value,"t_param");
data/phyml-3.3.20200621/src/io.c:5688:17: [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(kv->key,"id");
data/phyml-3.3.20200621/src/io.c:5690:17: [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(kv->value,"alpha");
data/phyml-3.3.20200621/src/io.c:5691:17: [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.
sprintf(kv->value+strlen(kv->value),"%d",n_alpha);
data/phyml-3.3.20200621/src/io.c:5697:17: [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(kv->key,"value");
data/phyml-3.3.20200621/src/io.c:5699:17: [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.
sprintf(kv->value,"%G",tree->mod->ras->alpha->v);
data/phyml-3.3.20200621/src/io.c:5728:9: [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(kv->key,"type");
data/phyml-3.3.20200621/src/io.c:5730:9: [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(kv->value,"t_param");
data/phyml-3.3.20200621/src/io.c:5736:9: [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(kv->key,"id");
data/phyml-3.3.20200621/src/io.c:5738:9: [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(kv->value,"tree_size");
data/phyml-3.3.20200621/src/io.c:5739:9: [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(kv->value+strlen(kv->value),"%d",tree_num);
data/phyml-3.3.20200621/src/io.c:5745:9: [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(kv->key,"value");
data/phyml-3.3.20200621/src/io.c:5747:9: [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(kv->value,"%G",Get_Tree_Size(tree));
data/phyml-3.3.20200621/src/io.c:5782:3: [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(state->key,"state");
data/phyml-3.3.20200621/src/io.c:5797:3: [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(kv->key,"state_num");
data/phyml-3.3.20200621/src/io.c:5799:3: [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(kv->value,"%d",mixt_tree->json_num);
data/phyml-3.3.20200621/src/io.c:5808:3: [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(kv->key,"time");
data/phyml-3.3.20200621/src/io.c:5811:3: [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(kv->value,"%d",(int)(t_end-mixt_tree->t_beg));
data/phyml-3.3.20200621/src/io.c:5822:3: [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(kv->key,"tree");
data/phyml-3.3.20200621/src/io.c:5837:3: [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(kv->key,"likelihood");
data/phyml-3.3.20200621/src/io.c:5839:3: [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(kv->value,"%G",mixt_tree->c_lnL);
data/phyml-3.3.20200621/src/io.c:5873:17: [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(kv->key,"tstv");
data/phyml-3.3.20200621/src/io.c:5874:17: [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.
sprintf(kv->key+strlen(kv->key),"%d",n_tstv);
data/phyml-3.3.20200621/src/io.c:5876:17: [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.
sprintf(kv->value,"%G",tree->mod->kappa->v);
data/phyml-3.3.20200621/src/io.c:5916:17: [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(kv->key,"alpha");
data/phyml-3.3.20200621/src/io.c:5917:17: [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.
sprintf(kv->key+strlen(kv->key),"%d",n_alpha);
data/phyml-3.3.20200621/src/io.c:5919:17: [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.
sprintf(kv->value,"%G",tree->mod->ras->alpha->v);
data/phyml-3.3.20200621/src/io.c:5943:9: [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(kv->key,"tree_size");
data/phyml-3.3.20200621/src/io.c:5944:9: [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(kv->key+strlen(kv->key),"%d",tree_num);
data/phyml-3.3.20200621/src/io.c:5946:9: [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(kv->value,"%G",Get_Tree_Size(tree));
data/phyml-3.3.20200621/src/io.c:6079:8: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
fp = tmpfile();
data/phyml-3.3.20200621/src/io.c:6183:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *tk,*s,delim[4]="\n\r ";
data/phyml-3.3.20200621/src/lk.c:220:7: [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 format[6];
data/phyml-3.3.20200621/src/lk.c:221:7: [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(format,"%%%dd",state_len);
data/phyml-3.3.20200621/src/lk.c:252:7: [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 format[6];
data/phyml-3.3.20200621/src/lk.c:253:7: [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(format,"%%%dd",state_len);
data/phyml-3.3.20200621/src/m4.c:1101:6: [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(tree->a_edges[br]->labels[tree->a_edges[br]->n_labels],"FASTER");
data/phyml-3.3.20200621/src/m4.c:1103:6: [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(tree->a_edges[br]->labels[tree->a_edges[br]->n_labels],"SLOWER");
data/phyml-3.3.20200621/src/m4.c:1478:23: [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.
fp_nocov = Openfile(strcat(s,"_nocov"),1);
data/phyml-3.3.20200621/src/m4.c:1480:23: [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.
fp_cov = Openfile(strcat(s,"_cov"),1);
data/phyml-3.3.20200621/src/m4.c:1482:21: [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.
fp_obs = Openfile(strcat(s,"_obs"),1);
data/phyml-3.3.20200621/src/make.c:716:37: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
cdata->c_seq[j]->name = (char *)mCalloc((int)(strlen(sp_names_in[j])+1),sizeof(char));
data/phyml-3.3.20200621/src/make.c:726:40: [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.
cdata->c_seq_rm[j]->name = (char *)mCalloc((int)(strlen(sp_names_out[j])+1),sizeof(char));
data/phyml-3.3.20200621/src/mcmc.c:2514:7: [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(format,"%%.%df\t",tree->mcmc->nd_t_digits);
data/phyml-3.3.20200621/src/mcmc.c:2655:7: [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(s,".means");
data/phyml-3.3.20200621/src/mcmc.c:2659:28: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
mcmc->out_fp_means = fopen(s,"w");
data/phyml-3.3.20200621/src/mcmc.c:2699:7: [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(s,".lasts");
data/phyml-3.3.20200621/src/mcmc.c:2703:27: [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).
mcmc->out_fp_last = fopen(s,"w");
data/phyml-3.3.20200621/src/mcmc.c:2860:7: [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(cpy->out_filename+strlen(cpy->out_filename),"_%d",pid);
data/phyml-3.3.20200621/src/mcmc.c:2865:7: [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(s,"_stats");
data/phyml-3.3.20200621/src/mcmc.c:2866:27: [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).
cpy->out_fp_stats = fopen(s,"w");
data/phyml-3.3.20200621/src/mcmc.c:2871:7: [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(s,"_trees");
data/phyml-3.3.20200621/src/mcmc.c:2872:27: [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).
cpy->out_fp_trees = fopen(s,"w");
data/phyml-3.3.20200621/src/mcmc.c:2877:7: [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(s,"_constree");
data/phyml-3.3.20200621/src/mcmc.c:2878:30: [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).
cpy->out_fp_constree = fopen(s,"w");
data/phyml-3.3.20200621/src/mcmc.c:5999:3: [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(mcmc->move_name[mcmc->num_move_br_r],"br_rate");
data/phyml-3.3.20200621/src/mcmc.c:6000:3: [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(mcmc->move_name[mcmc->num_move_nd_r],"nd_rate");
data/phyml-3.3.20200621/src/mcmc.c:6001:3: [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(mcmc->move_name[mcmc->num_move_times],"times");
data/phyml-3.3.20200621/src/mcmc.c:6002:3: [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(mcmc->move_name[mcmc->num_move_times_and_rates],"times_and_rates");
data/phyml-3.3.20200621/src/mcmc.c:6003:3: [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(mcmc->move_name[mcmc->num_move_times_and_rates_root],"times_and_rates_root");
data/phyml-3.3.20200621/src/mcmc.c:6004:3: [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(mcmc->move_name[mcmc->num_move_root_time],"root_time");
data/phyml-3.3.20200621/src/mcmc.c:6005:3: [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(mcmc->move_name[mcmc->num_move_nu],"nu");
data/phyml-3.3.20200621/src/mcmc.c:6006:3: [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(mcmc->move_name[mcmc->num_move_clock_r],"clock");
data/phyml-3.3.20200621/src/mcmc.c:6007:3: [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(mcmc->move_name[mcmc->num_move_tree_height],"tree_height");
data/phyml-3.3.20200621/src/mcmc.c:6008:3: [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(mcmc->move_name[mcmc->num_move_time_slice],"time_slice");
data/phyml-3.3.20200621/src/mcmc.c:6009:3: [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(mcmc->move_name[mcmc->num_move_subtree_height],"subtree_height");
data/phyml-3.3.20200621/src/mcmc.c:6010:3: [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(mcmc->move_name[mcmc->num_move_kappa],"kappa");
data/phyml-3.3.20200621/src/mcmc.c:6011:3: [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(mcmc->move_name[mcmc->num_move_rr],"rr");
data/phyml-3.3.20200621/src/mcmc.c:6012:3: [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(mcmc->move_name[mcmc->num_move_spr],"spr");
data/phyml-3.3.20200621/src/mcmc.c:6013:3: [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(mcmc->move_name[mcmc->num_move_spr_weighted],"spr_weighted");
data/phyml-3.3.20200621/src/mcmc.c:6014:3: [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(mcmc->move_name[mcmc->num_move_spr_local],"spr_local");
data/phyml-3.3.20200621/src/mcmc.c:6015:3: [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(mcmc->move_name[mcmc->num_move_spr_root],"spr_root");
data/phyml-3.3.20200621/src/mcmc.c:6016:3: [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(mcmc->move_name[mcmc->num_move_tree_rates],"tree_rates");
data/phyml-3.3.20200621/src/mcmc.c:6017:3: [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(mcmc->move_name[mcmc->num_move_subtree_rates],"subtree_rates");
data/phyml-3.3.20200621/src/mcmc.c:6018:3: [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(mcmc->move_name[mcmc->num_move_updown_nu_cr],"updown_nu_cr");
data/phyml-3.3.20200621/src/mcmc.c:6019:3: [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(mcmc->move_name[mcmc->num_move_ras],"ras");
data/phyml-3.3.20200621/src/mcmc.c:6020:3: [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(mcmc->move_name[mcmc->num_move_updown_t_cr],"updown_t_cr");
data/phyml-3.3.20200621/src/mcmc.c:6021:3: [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(mcmc->move_name[mcmc->num_move_cov_rates],"cov_rates");
data/phyml-3.3.20200621/src/mcmc.c:6022:3: [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(mcmc->move_name[mcmc->num_move_cov_switch],"cov_switch");
data/phyml-3.3.20200621/src/mcmc.c:6023:3: [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(mcmc->move_name[mcmc->num_move_birth_rate],"birth_rate");
data/phyml-3.3.20200621/src/mcmc.c:6024:3: [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(mcmc->move_name[mcmc->num_move_death_rate],"death_rate");
data/phyml-3.3.20200621/src/mcmc.c:6025:3: [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(mcmc->move_name[mcmc->num_move_birth_death_updown],"birth_death_updown");
data/phyml-3.3.20200621/src/mcmc.c:6026:3: [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(mcmc->move_name[mcmc->num_move_updown_t_br],"updown_t_br");
data/phyml-3.3.20200621/src/mcmc.c:6027:3: [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(mcmc->move_name[mcmc->num_move_jump_calibration],"jump_calibration");
data/phyml-3.3.20200621/src/mcmc.c:6028:3: [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(mcmc->move_name[mcmc->num_move_geo_lambda],"geo_lambda");
data/phyml-3.3.20200621/src/mcmc.c:6029:3: [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(mcmc->move_name[mcmc->num_move_geo_sigma],"geo_sigma");
data/phyml-3.3.20200621/src/mcmc.c:6030:3: [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(mcmc->move_name[mcmc->num_move_geo_tau],"geo_tau");
data/phyml-3.3.20200621/src/mcmc.c:6031:3: [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(mcmc->move_name[mcmc->num_move_geo_updown_tau_lbda],"geo_updown_tau_lbda");
data/phyml-3.3.20200621/src/mcmc.c:6032:3: [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(mcmc->move_name[mcmc->num_move_geo_updown_lbda_sigma],"geo_updown_lbda_sigma");
data/phyml-3.3.20200621/src/mcmc.c:6033:3: [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(mcmc->move_name[mcmc->num_move_geo_dum],"geo_dum");
data/phyml-3.3.20200621/src/mcmc.c:6034:3: [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(mcmc->move_name[mcmc->num_move_phyrex_lbda],"phyrex_lbda");
data/phyml-3.3.20200621/src/mcmc.c:6035:3: [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(mcmc->move_name[mcmc->num_move_phyrex_mu],"phyrex_mu");
data/phyml-3.3.20200621/src/mcmc.c:6036:3: [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(mcmc->move_name[mcmc->num_move_phyrex_rad],"phyrex_rad");
data/phyml-3.3.20200621/src/mcmc.c:6037:3: [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(mcmc->move_name[mcmc->num_move_phyrex_indel_disk],"phyrex_indel_disk");
data/phyml-3.3.20200621/src/mcmc.c:6038:3: [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(mcmc->move_name[mcmc->num_move_phyrex_move_disk_ud],"phyrex_move_disk_ud");
data/phyml-3.3.20200621/src/mcmc.c:6039:3: [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(mcmc->move_name[mcmc->num_move_phyrex_swap_disk],"phyrex_swap_disk");
data/phyml-3.3.20200621/src/mcmc.c:6040:3: [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(mcmc->move_name[mcmc->num_move_phyrex_indel_hit],"phyrex_indel_hit");
data/phyml-3.3.20200621/src/mcmc.c:6041:3: [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(mcmc->move_name[mcmc->num_move_phyrex_spr],"phyrex_spr");
data/phyml-3.3.20200621/src/mcmc.c:6042:3: [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(mcmc->move_name[mcmc->num_move_phyrex_spr_local],"phyrex_spr_local");
data/phyml-3.3.20200621/src/mcmc.c:6043:3: [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(mcmc->move_name[mcmc->num_move_phyrex_scale_times],"phyrex_scale_times");
data/phyml-3.3.20200621/src/mcmc.c:6044:3: [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(mcmc->move_name[mcmc->num_move_phyrex_ldscape_lim],"phyrex_ldscape_lim");
data/phyml-3.3.20200621/src/mcmc.c:6045:3: [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(mcmc->move_name[mcmc->num_move_phyrex_sigsq],"phyrex_sigsq");
data/phyml-3.3.20200621/src/mcmc.c:6046:3: [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(mcmc->move_name[mcmc->num_move_phyrex_neff],"phyrex_neff");
data/phyml-3.3.20200621/src/mcmc.c:6047:3: [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(mcmc->move_name[mcmc->num_move_phyrex_sim],"phyrex_sim");
data/phyml-3.3.20200621/src/mcmc.c:6048:3: [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(mcmc->move_name[mcmc->num_move_phyrex_traj],"phyrex_traj");
data/phyml-3.3.20200621/src/mcmc.c:6049:3: [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(mcmc->move_name[mcmc->num_move_phyrex_indel_disk_serial],"phyrex_indel_disk_serial");
data/phyml-3.3.20200621/src/mcmc.c:6050:3: [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(mcmc->move_name[mcmc->num_move_phyrex_sim_plus],"phyrex_sim_plus");
data/phyml-3.3.20200621/src/mcmc.c:6051:3: [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(mcmc->move_name[mcmc->num_move_phyrex_indel_hit_serial],"phyrex_indel_hit_serial");
data/phyml-3.3.20200621/src/mcmc.c:6052:3: [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(mcmc->move_name[mcmc->num_move_phyrex_ldsk_multi],"phyrex_ldsk_multi");
data/phyml-3.3.20200621/src/mcmc.c:6053:3: [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(mcmc->move_name[mcmc->num_move_phyrex_disk_multi],"phyrex_disk_multi");
data/phyml-3.3.20200621/src/mcmc.c:6054:3: [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(mcmc->move_name[mcmc->num_move_phyrex_ldsk_and_disk],"phyrex_ldsk_and_disk");
data/phyml-3.3.20200621/src/mcmc.c:6055:3: [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(mcmc->move_name[mcmc->num_move_phyrex_disk_given_ldsk],"phyrex_disk_given_ldsk");
data/phyml-3.3.20200621/src/mcmc.c:6056:3: [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(mcmc->move_name[mcmc->num_move_phyrex_ldsk_given_disk],"phyrex_ldsk_given_disk");
data/phyml-3.3.20200621/src/mcmc.c:6057:3: [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(mcmc->move_name[mcmc->num_move_phyrex_add_remove_jump],"phyrex_add_remove_jump");
data/phyml-3.3.20200621/src/mcmc.c:6058:3: [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(mcmc->move_name[mcmc->num_move_clade_change],"clade_change");
data/phyml-3.3.20200621/src/mcmc.c:6059:3: [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(mcmc->move_name[mcmc->num_move_phyrex_ldsk_tip_to_root],"phyrex_ldsk_tip_to_root");
data/phyml-3.3.20200621/src/mcmc.c:6060:3: [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(mcmc->move_name[mcmc->num_move_phyrex_sigsq_scale],"phyrex_sigsq_scale");
data/phyml-3.3.20200621/src/mixt.c:1891:7: [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(xml_boot_file_name,"phyml_boot_config.");
data/phyml-3.3.20200621/src/mixt.c:1893:7: [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(xml_boot_file_name+strlen(xml_boot_file_name),"%d",pid);
data/phyml-3.3.20200621/src/mixt.c:1894:7: [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(xml_boot_file_name,".xml");
data/phyml-3.3.20200621/src/mixt.c:1907:16: [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).
n_boot = atoi(bootstrap);
data/phyml-3.3.20200621/src/mixt.c:1927:11: [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.
sprintf(boot_out_attr->value+strlen(boot_out_attr->value),"_boot.%d",pid);
data/phyml-3.3.20200621/src/mixt.c:3695:11: [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.
sprintf(s,"Site");
data/phyml-3.3.20200621/src/mixt.c:3698:11: [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.
sprintf(s,"P(D|M)");
data/phyml-3.3.20200621/src/mixt.c:3701:11: [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.
sprintf(s,"Scaler");
data/phyml-3.3.20200621/src/mixt.c:3704:11: [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.
sprintf(s,"Pattern");
data/phyml-3.3.20200621/src/mixt.c:3711:19: [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.
sprintf(s,"P*(D|M,rr[%d]=%5.4f)",catg+1,mixt_tree->mod->ras->gamma_rr->v[catg]);
data/phyml-3.3.20200621/src/mixt.c:3715:15: [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.
sprintf(s,"Posterior mean");
data/phyml-3.3.20200621/src/mixt.c:3722:15: [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.
sprintf(s,"P(D|M,rr[0]=0)");
data/phyml-3.3.20200621/src/mixt.c:3726:11: [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.
sprintf(s,"NDistinctStates");
data/phyml-3.3.20200621/src/nexus.c:120:4: [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(io->short_tax_names[io->size_tax_names-1],"%d",tax_num);
data/phyml-3.3.20200621/src/phyrex.c:71:15: [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).
fp_xml_in = fopen(xml_filename,"r");
data/phyml-3.3.20200621/src/phyrex.c:141:7: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/phyrex.c:161:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/phyrex.c:167:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/phyrex.c:173:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/phyrex.c:179:15: [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(mixt_tree->rates->model_name,"geometric Brownian");
data/phyml-3.3.20200621/src/phyrex.c:185:15: [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(mixt_tree->rates->model_name,"lognormal (uncorrelated)");
data/phyml-3.3.20200621/src/phyrex.c:191:15: [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(mixt_tree->rates->model_name,"lognormal (uncorrelated)");
data/phyml-3.3.20200621/src/phyrex.c:197:15: [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(mixt_tree->rates->model_name,"strict clock");
data/phyml-3.3.20200621/src/phyrex.c:203:15: [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(mixt_tree->rates->model_name,"strict clock");
data/phyml-3.3.20200621/src/phyrex.c:481:18: [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).
n_otus = (int)atoi(argv[1]);
data/phyml-3.3.20200621/src/phyrex.c:488:18: [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).
seed = (int)atoi(argv[7]);
data/phyml-3.3.20200621/src/phyrex.c:489:18: [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).
modid = (int)atoi(argv[8]);
data/phyml-3.3.20200621/src/phyrex.c:3432:30: [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.
For(i,n_demes*(n_demes-1)) strcat(s,"1.0 ");
data/phyml-3.3.20200621/src/phyrex.c:3437:26: [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.
for(i=0;i<n_demes;i++) strcat(s,"1.0 ");
data/phyml-3.3.20200621/src/phyrex.c:3465:26: [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.
for(i=0;i<n_demes;i++) strcat(s,"1.0 ");
data/phyml-3.3.20200621/src/phyrex.c:3470:30: [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.
For(i,n_demes*(n_demes-1)) strcat(s,"1.0 ");
data/phyml-3.3.20200621/src/phyrex.c:4110:7: [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(tree->a_nodes[i]->label->key,"&location");
data/phyml-3.3.20200621/src/phyrex.c:4111:7: [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(tree->a_nodes[i]->label->val,"{%f,%f}",lat,lon);
data/phyml-3.3.20200621/src/phyrex.c:4112:7: [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(tree->a_nodes[i]->label->next->key,"location");
data/phyml-3.3.20200621/src/phyrex.c:4113:7: [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(tree->a_nodes[i]->label->next->val,"{%f,%f}",lat,lon);
data/phyml-3.3.20200621/src/phyrex.c:4132:11: [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.
sprintf(n->label->key,"&location");
data/phyml-3.3.20200621/src/phyrex.c:4133:11: [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.
sprintf(n->label->val,"{%f,%f}",lat,lon);
data/phyml-3.3.20200621/src/phyrex.c:4134:11: [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.
sprintf(n->label->next->key,"location");
data/phyml-3.3.20200621/src/phyrex.c:4135:11: [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.
sprintf(n->label->next->val,"{%f,%f}",lat,lon);
data/phyml-3.3.20200621/src/phyrex.c:4156:19: [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.
sprintf(n->label->key,"&location");
data/phyml-3.3.20200621/src/phyrex.c:4157:19: [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.
sprintf(n->label->val,"{%f,%f}",lat,lon);
data/phyml-3.3.20200621/src/phyrex.c:4158:19: [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.
sprintf(n->label->next->key,"location");
data/phyml-3.3.20200621/src/phyrex.c:4159:19: [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.
sprintf(n->label->next->val,"{%f,%f}",lat,lon);
data/phyml-3.3.20200621/src/phyrex.c:4182:7: [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(tree->a_edges[i]->label->key,"&rate");
data/phyml-3.3.20200621/src/phyrex.c:4183:7: [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(tree->a_edges[i]->label->val,"0.0");
data/phyml-3.3.20200621/src/phyrex.c:4185:7: [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(tree->a_edges[i]->label->next->key,"location.rate");
data/phyml-3.3.20200621/src/phyrex.c:4186:7: [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(tree->a_edges[i]->label->next->val,"0.0");
data/phyml-3.3.20200621/src/rates.c:3655:25: [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 GUINDON : {strcpy(s,"geometric Brownian"); break;}
data/phyml-3.3.20200621/src/rates.c:3656:25: [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 THORNE : {strcpy(s,"gbd"); break;}
data/phyml-3.3.20200621/src/rates.c:3657:25: [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 LOGNORMAL : {strcpy(s,"lognormal"); break;}
data/phyml-3.3.20200621/src/rates.c:3658:25: [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 STRICTCLOCK : {strcpy(s,"strict clock"); break;}
data/phyml-3.3.20200621/src/slfv.c:1249:24: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
s = (char *)mCalloc((int)strlen(ldsk_a_pop[i]->coord->id)+1+50,sizeof(char));
data/phyml-3.3.20200621/src/slfv.c:1251:19: [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.
sprintf(s,"%d_",i);
data/phyml-3.3.20200621/src/slfv.c:1254:19: [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(s,"_deme");
data/phyml-3.3.20200621/src/slfv.c:1255:19: [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.
sprintf(s+strlen(s),"%d",permut[j]);
data/phyml-3.3.20200621/src/slfv.c:1679:7: [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(s,"_deme0\0");
data/phyml-3.3.20200621/src/slfv.c:1953:7: [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(s,"_deme0\0");
data/phyml-3.3.20200621/src/stats.c:4065:8: [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("covariance","w");
data/phyml-3.3.20200621/src/tiporder.c:264:27: [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).
fp_tree_file = (FILE *)fopen(argv[1],"r");
data/phyml-3.3.20200621/src/tiporder.c:265:27: [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).
fp_coord_file = (FILE *)fopen(argv[2],"r");
data/phyml-3.3.20200621/src/tiporder.c:691:22: [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).
ps_tree = (FILE *)fopen("failed_tree.ps","w");
data/phyml-3.3.20200621/src/utilities.c:1220:11: [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 i,j,open;
data/phyml-3.3.20200621/src/utilities.c:1231:9: [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).
while(open)
data/phyml-3.3.20200621/src/utilities.c:1256:3: [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(long_line,");");
data/phyml-3.3.20200621/src/utilities.c:2137:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of 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(filename,"r");
data/phyml-3.3.20200621/src/utilities.c:2909:7: [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 format[6];
data/phyml-3.3.20200621/src/utilities.c:2912:7: [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(format,"%%%dd",stepsize);
data/phyml-3.3.20200621/src/utilities.c:3072:11: [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.
char format[6];
data/phyml-3.3.20200621/src/utilities.c:3073:11: [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.
sprintf(format,"%%%dd",stepsize);
data/phyml-3.3.20200621/src/utilities.c:4897:11: [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.
char format[6];
data/phyml-3.3.20200621/src/utilities.c:4899:11: [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.
sprintf(format,"%%%dd",stepsize);
data/phyml-3.3.20200621/src/utilities.c:7610:7: [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(tree->a_nodes[i]->name+1,"%d",i);
data/phyml-3.3.20200621/src/utilities.c:8986:5: [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(mod->modelname->s, "JC69");
data/phyml-3.3.20200621/src/utilities.c:8991:5: [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(mod->modelname->s, "K80");
data/phyml-3.3.20200621/src/utilities.c:8996:5: [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(mod->modelname->s, "F81");
data/phyml-3.3.20200621/src/utilities.c:9001:5: [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(mod->modelname->s, "HKY85");
data/phyml-3.3.20200621/src/utilities.c:9006:5: [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(mod->modelname->s, "F84");
data/phyml-3.3.20200621/src/utilities.c:9011:5: [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(mod->modelname->s, "TN93");
data/phyml-3.3.20200621/src/utilities.c:9016:5: [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(mod->modelname->s, "GTR");
data/phyml-3.3.20200621/src/utilities.c:9021:5: [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(mod->modelname->s, "Custom");
data/phyml-3.3.20200621/src/utilities.c:9026:5: [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(mod->modelname->s, "Dayhoff");
data/phyml-3.3.20200621/src/utilities.c:9031:5: [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(mod->modelname->s, "JTT");
data/phyml-3.3.20200621/src/utilities.c:9036:5: [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(mod->modelname->s, "MtREV");
data/phyml-3.3.20200621/src/utilities.c:9041:5: [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(mod->modelname->s, "LG");
data/phyml-3.3.20200621/src/utilities.c:9046:5: [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(mod->modelname->s, "WAG");
data/phyml-3.3.20200621/src/utilities.c:9051:5: [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(mod->modelname->s, "DCMut");
data/phyml-3.3.20200621/src/utilities.c:9056:5: [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(mod->modelname->s, "RtREV");
data/phyml-3.3.20200621/src/utilities.c:9061:5: [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(mod->modelname->s, "CpREV");
data/phyml-3.3.20200621/src/utilities.c:9066:5: [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(mod->modelname->s, "VT");
data/phyml-3.3.20200621/src/utilities.c:9071:5: [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(mod->modelname->s, "Blosum62");
data/phyml-3.3.20200621/src/utilities.c:9076:5: [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(mod->modelname->s, "MtMam");
data/phyml-3.3.20200621/src/utilities.c:9081:5: [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(mod->modelname->s, "MtArt");
data/phyml-3.3.20200621/src/utilities.c:9086:5: [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(mod->modelname->s, "HIVw");
data/phyml-3.3.20200621/src/utilities.c:9091:5: [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(mod->modelname->s, "HIVb");
data/phyml-3.3.20200621/src/utilities.c:9096:5: [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(mod->modelname->s, "AB");
data/phyml-3.3.20200621/src/utilities.c:9101:9: [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(mod->modelname->s, "Custom");
data/phyml-3.3.20200621/src/utilities.c:9106:9: [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(mod->modelname->s, "FLU");
data/phyml-3.3.20200621/src/utilities.c:11978:3: [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(s+strlen(s),"%c",c);
data/phyml-3.3.20200621/src/utilities.c:11982:3: [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(s+strlen(s),"%c",c);
data/phyml-3.3.20200621/src/utilities.c:12342:9: [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 alphabet[4]="ACGT";
data/phyml-3.3.20200621/src/utilities.c:12362:9: [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 alphabet[20]="ARNDCQEGHILKMFPSTWYV";
data/phyml-3.3.20200621/src/xml.c:29:8: [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(xml_filename,"r");
data/phyml-3.3.20200621/src/xml.c:133:42: [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).
if(s && strlen(s)>0) io->r_seed = (int)atoi(s);
data/phyml-3.3.20200621/src/xml.c:142:3: [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(io->out_tree_file,"_phytime_tree");
data/phyml-3.3.20200621/src/xml.c:144:3: [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(io->out_tree_file,"_phyrex_tree");
data/phyml-3.3.20200621/src/xml.c:146:3: [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(io->out_tree_file,"_phyml_tree");
data/phyml-3.3.20200621/src/xml.c:151:3: [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(io->out_stats_file,"_phytime_stats");
data/phyml-3.3.20200621/src/xml.c:153:3: [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(io->out_stats_file,"_phyrex_stats");
data/phyml-3.3.20200621/src/xml.c:155:3: [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(io->out_stats_file,"_phyml_stats");
data/phyml-3.3.20200621/src/xml.c:162:3: [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(io->out_stats_file,".txt");
data/phyml-3.3.20200621/src/xml.c:163:3: [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(io->out_tree_file,".txt");
data/phyml-3.3.20200621/src/xml.c:189:11: [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(io->out_trace_file,"_phyml_trace");
data/phyml-3.3.20200621/src/xml.c:191:11: [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(io->out_trace_file,".txt");
data/phyml-3.3.20200621/src/xml.c:209:11: [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(io->out_json_trace_file,"_phyml_trace");
data/phyml-3.3.20200621/src/xml.c:211:11: [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(io->out_json_trace_file,".json");
data/phyml-3.3.20200621/src/xml.c:226:7: [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(io->out_lk_file, "_phyml_lk");
data/phyml-3.3.20200621/src/xml.c:228:7: [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(io->out_lk_file, ".txt");
data/phyml-3.3.20200621/src/xml.c:2403:75: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
for(i=0;i<clade_size;++i) clade->tax_list[i] = (char *)mCalloc(strlen(xclade[i])+1,sizeof(char));
data/phyml-3.3.20200621/src/xml.c:2549:19: [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.
sprintf(val,"%f",((t_rmat *)(ds->obj))->rr->v[0]);
data/phyml-3.3.20200621/src/xml.c:2556:19: [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.
sprintf(val,"%f",((t_rmat *)(ds->obj))->rr->v[1]);
data/phyml-3.3.20200621/src/xml.c:2563:19: [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.
sprintf(val,"%f",((t_rmat *)(ds->obj))->rr->v[2]);
data/phyml-3.3.20200621/src/xml.c:2570:19: [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.
sprintf(val,"%f",((t_rmat *)(ds->obj))->rr->v[3]);
data/phyml-3.3.20200621/src/xml.c:2577:19: [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.
sprintf(val,"%f",((t_rmat *)(ds->obj))->rr->v[4]);
data/phyml-3.3.20200621/src/xml.c:2589:15: [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.
sprintf(val,"%f",((scalar_dbl *)(ds->obj))->v);
data/phyml-3.3.20200621/src/xml.c:2615:19: [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.
sprintf(val,"%f",((t_ras *)(parent->ds->obj))->gamma_rr->v[class]);
data/phyml-3.3.20200621/src/xml.c:2635:15: [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.
sprintf(val,"%f",((t_ras *)(parent->ds->obj))->alpha->v);
data/phyml-3.3.20200621/src/xml.c:2644:15: [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.
sprintf(val,"%f",((t_ras *)(parent->ds->obj))->alpha->v);
data/phyml-3.3.20200621/src/xml.c:2647:15: [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.
sprintf(val,"%f",((t_ras *)(parent->ds->obj))->pinvar->v);
data/phyml-3.3.20200621/src/xml.c:2673:19: [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.
sprintf(val,"%f",((t_ras *)(parent->ds->obj))->gamma_r_proba->v[class]);
data/phyml-3.3.20200621/src/xml.c:2679:19: [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.
sprintf(val,"%f",0.0);
data/phyml-3.3.20200621/src/ancestral.c:120:17: [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).
sprintf(s+strlen(s),"%d.",tree->io->r_seed);
data/phyml-3.3.20200621/src/ancestral.c:121:17: [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).
sprintf(s+strlen(s),"%d",i);
data/phyml-3.3.20200621/src/ancestral.c:541:11: [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(tree->io->out_ancestral_seq_file,"_");
data/phyml-3.3.20200621/src/ancestral.c:552:11: [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(tree->io->out_ancestral_tree_file,"_");
data/phyml-3.3.20200621/src/cl.c:195:9: [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(optarg) > T_MAX_FILE -11)
data/phyml-3.3.20200621/src/cl.c:302:9: [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(optarg) > T_MAX_FILE -11)
data/phyml-3.3.20200621/src/cl.c:509:16: [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).
if(strlen(optarg) > 0)
data/phyml-3.3.20200621/src/cl.c:861:25: [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 (strlen(io->mod->custom_mod_string->s) != 6)
data/phyml-3.3.20200621/src/cl.c:1241:10: [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).
if (strlen (optarg) > T_MAX_FILE -16)
data/phyml-3.3.20200621/src/cl.c:1386:9: [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(optarg) > T_MAX_FILE -11)
data/phyml-3.3.20200621/src/cl.c:1600:31: [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.
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1609:31: [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.
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1618:31: [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.
if(io->append_run_ID) { strcat(io->out_json_trace_file,"_"); strcat(io->out_json_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1628:31: [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.
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1637:31: [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.
if(io->append_run_ID) { strcat(io->out_boot_tree_file,"_"); strcat(io->out_boot_tree_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1643:31: [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.
if(io->append_run_ID) { strcat(io->out_boot_stats_file,"_"); strcat(io->out_boot_stats_file,io->run_id_string); }
data/phyml-3.3.20200621/src/cl.c:1650:7: [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(io->out_tree_file,"_");
data/phyml-3.3.20200621/src/cl.c:1651:7: [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(io->out_stats_file,"_");
data/phyml-3.3.20200621/src/draw.c:476:23: [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).
curr_len = (int)strlen(tree->a_nodes[i]->name);
data/phyml-3.3.20200621/src/geo.c:151:13: [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).
sprintf(s+strlen(s),".%d",pid);
data/phyml-3.3.20200621/src/geo.c:1134:7: [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.
strcpy(tree->a_nodes[i]->name,"x");
data/phyml-3.3.20200621/src/geo.c:1771:10: [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).
if(strlen(s) > 0) for(tax=0;tax<tree->n_otu;tax++) if(!strcmp(tree->a_nodes[tax]->name,s)) break;
data/phyml-3.3.20200621/src/help.c:38:7: [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.
strcpy(BOLD, "");
data/phyml-3.3.20200621/src/help.c:39:7: [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.
strcpy(FLAT, "");
data/phyml-3.3.20200621/src/help.c:40:7: [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.
strcpy(LINE, "");
data/phyml-3.3.20200621/src/init.c:3589:34: [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).
sprintf(mcmc->out_filename+strlen(mcmc->out_filename),".%d",pid);
data/phyml-3.3.20200621/src/init.c:3592:7: [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(s,"_");
data/phyml-3.3.20200621/src/init.c:3598:7: [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(s,"_");
data/phyml-3.3.20200621/src/init.c:3604:7: [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(s,"_");
data/phyml-3.3.20200621/src/interface.c:138:31: [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.
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:147:31: [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.
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:156:31: [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.
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:165:31: [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.
if(io->append_run_ID) { strcat(io->out_boot_tree_file,"_"); strcat(io->out_boot_tree_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:171:31: [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.
if(io->append_run_ID) { strcat(io->out_boot_stats_file,"_"); strcat(io->out_boot_stats_file,io->run_id_string); }
data/phyml-3.3.20200621/src/interface.c:177:7: [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(io->out_tree_file,"_");
data/phyml-3.3.20200621/src/interface.c:178:7: [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(io->out_stats_file,"_");
data/phyml-3.3.20200621/src/interface.c:317:9: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:351:9: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:413:3: [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.
strcpy(s,"");
data/phyml-3.3.20200621/src/interface.c:433:21: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(choix != '\n') getchar(); /* \n */
data/phyml-3.3.20200621/src/interface.c:656:37: [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.
if(io->mod->s_opt->opt_kappa) strcat(s,"");
data/phyml-3.3.20200621/src/interface.c:662:4: [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((char *)s,"");
data/phyml-3.3.20200621/src/interface.c:666:28: [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).
sprintf((char *)(s+(int)strlen(s)),"%3.2f)",io->mod->kappa->v);
data/phyml-3.3.20200621/src/interface.c:680:7: [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(s,"");
data/phyml-3.3.20200621/src/interface.c:684:26: [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).
sprintf((char *)(s+strlen((char *)s)),"%3.2f)",io->mod->ras->pinvar->v);
data/phyml-3.3.20200621/src/interface.c:720:4: [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(s, "");
data/phyml-3.3.20200621/src/interface.c:724:14: [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).
sprintf(s+strlen(s),"%3.2f)",io->mod->ras->alpha->v);
data/phyml-3.3.20200621/src/interface.c:746:21: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(choix != '\n') getchar(); /* \n */
data/phyml-3.3.20200621/src/interface.c:791:6: [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).
if(strlen(io->mod->custom_mod_string->s) == 6)
data/phyml-3.3.20200621/src/interface.c:836:15: [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(rr+strlen(rr),"%s = ",rr_param[j]);
data/phyml-3.3.20200621/src/interface.c:839:3: [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.
sprintf(rr+strlen(rr)-3,"]");
data/phyml-3.3.20200621/src/interface.c:839:14: [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).
sprintf(rr+strlen(rr)-3,"]");
data/phyml-3.3.20200621/src/interface.c:953:13: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:961:13: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:975:11: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1053:13: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1061:13: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1075:11: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1143:13: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1151:13: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1165:11: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1485:21: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(choix != '\n') getchar(); /* \n */
data/phyml-3.3.20200621/src/interface.c:1638:43: [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(io->n_boot_replicates > 0) sprintf(s+strlen(s)," (%d replicate%s%s)",
data/phyml-3.3.20200621/src/interface.c:1684:21: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(choix != '\n') getchar(); /* \n */
data/phyml-3.3.20200621/src/interface.c:1737:11: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1770:11: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/interface.c:1887:25: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(choix != '\n') getchar();
data/phyml-3.3.20200621/src/interface.c:1897:9: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/invitee.c:153:78: [1] (buffer) strlen:
Does not handle 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_cur -> child -> value != NULL) data[i] -> state = (char *)mCalloc(strlen(n_cur -> child -> value) + 1,sizeof(char));
data/phyml-3.3.20200621/src/invitee.c:281:22: [1] (buffer) strlen:
Does not handle 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, n_taxa) if(strlen(io -> data[0] -> state) != strlen(io -> data[i] -> state))
data/phyml-3.3.20200621/src/invitee.c:281:56: [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).
For(i, n_taxa) if(strlen(io -> data[0] -> state) != strlen(io -> data[i] -> state))
data/phyml-3.3.20200621/src/invitee.c:300:34: [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).
io -> data[0] -> len = strlen(io -> data[0] -> state);
data/phyml-3.3.20200621/src/invitee.c:523:20: [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).
data[0] -> len = strlen(data[0] -> state);
data/phyml-3.3.20200621/src/io.c:36:18: [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).
for(i=0;i<(int)strlen((*s_tree));++i)
data/phyml-3.3.20200621/src/io.c:74:37: [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).
for(i=0;i<degree;i++) len += (strlen(subs[i])+1);
data/phyml-3.3.20200621/src/io.c:86:25: [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).
sprintf((*s_tree)+strlen((*s_tree))-1,"%s",");\0");
data/phyml-3.3.20200621/src/io.c:232:38: [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).
s_tree_d = (char *)mCalloc(strlen(subs[0])+strlen(subs[1])+5,sizeof(char));
data/phyml-3.3.20200621/src/io.c:232:54: [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).
s_tree_d = (char *)mCalloc(strlen(subs[0])+strlen(subs[1])+5,sizeof(char));
data/phyml-3.3.20200621/src/io.c:297:29: [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).
d->name = (char *)mCalloc(strlen(s_tree_d)+1,sizeof(char ));
data/phyml-3.3.20200621/src/io.c:312:31: [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).
sub_tp = (char *)mCalloc(10+strlen(s_d)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:330:44: [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).
b->support_val = atof((char *)p+(int)strlen(sub_tp));
data/phyml-3.3.20200621/src/io.c:332:15: [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).
p = p + strlen(sub_tp);
data/phyml-3.3.20200621/src/io.c:351:31: [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).
sub_tp = (char *)mCalloc(10+strlen(s_d)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:369:15: [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).
p = p + strlen(sub_tp);
data/phyml-3.3.20200621/src/io.c:400:35: [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).
sub_tp = (char *)mCalloc(3+(int)strlen(s_d)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:401:27: [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).
s_lab = (char *)mCalloc(strlen(s_a)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:421:13: [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).
p = p+strlen(sub_tp)-1;
data/phyml-3.3.20200621/src/io.c:432:13: [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).
s_lab[strlen(s_lab)]=']';
data/phyml-3.3.20200621/src/io.c:433:13: [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).
s_lab[strlen(s_lab)]='\0';
data/phyml-3.3.20200621/src/io.c:458:28: [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)strlen(subtrees[0])+1+
data/phyml-3.3.20200621/src/io.c:459:28: [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)strlen(subtrees[1])+1,
data/phyml-3.3.20200621/src/io.c:515:41: [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).
subs[(*degree)] = (char *)mCalloc(strlen(tree)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:516:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(subs[(*degree)],tree+posbeg,posend-posbeg+1);
data/phyml-3.3.20200621/src/io.c:620:10: [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).
s[(int)strlen(s)-1]=')';
data/phyml-3.3.20200621/src/io.c:622:53: [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(tree->n_root != NULL) Print_Labels(NULL,s+(int)strlen(s),tree->n_root->label);
data/phyml-3.3.20200621/src/io.c:627:24: [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).
sprintf(s+(int)strlen(s),"%d",tree->a_nodes[tree->n_otu+i]->num);
data/phyml-3.3.20200621/src/io.c:629:24: [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).
sprintf(s+(int)strlen(s),"%d",tree->n_root->num);
data/phyml-3.3.20200621/src/io.c:631:10: [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).
s[(int)strlen(s)]=';';
data/phyml-3.3.20200621/src/io.c:653:23: [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).
last_len = (int)strlen(*s_tree);
data/phyml-3.3.20200621/src/io.c:665:36: [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).
if(fils->name && strlen(fils->name) > 0)
data/phyml-3.3.20200621/src/io.c:668:42: [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).
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num+1);
data/phyml-3.3.20200621/src/io.c:673:36: [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).
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num+1);
data/phyml-3.3.20200621/src/io.c:678:32: [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).
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num+1);
data/phyml-3.3.20200621/src/io.c:689:42: [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).
Print_Labels(NULL,*s_tree+(int)strlen(*s_tree),fils->label);
data/phyml-3.3.20200621/src/io.c:691:26: [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).
(*s_tree)[(int)strlen(*s_tree)] = ':';
data/phyml-3.3.20200621/src/io.c:693:42: [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).
Print_Labels(NULL,*s_tree+(int)strlen(*s_tree),b->label);
data/phyml-3.3.20200621/src/io.c:697:32: [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).
sprintf(*s_tree+(int)strlen(*s_tree),format,MAX(0.0,mean_len));
data/phyml-3.3.20200621/src/io.c:700:22: [1] (buffer) strlen:
Does not handle 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_tree)[(int)strlen(*s_tree)] = ',';
data/phyml-3.3.20200621/src/io.c:704:29: [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).
(*available) -= ((int)strlen(*s_tree) - last_len);
data/phyml-3.3.20200621/src/io.c:712:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
PhyML_Fprintf(stderr,"\n. len=%d\n",(int)strlen(*s_tree));
data/phyml-3.3.20200621/src/io.c:720:53: [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).
(*s_tree) = (char *)mRealloc(*s_tree,(int)strlen(*s_tree)+3*(int)T_MAX_NAME,sizeof(char));
data/phyml-3.3.20200621/src/io.c:721:59: [1] (buffer) strlen:
Does not handle 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<3*(int)T_MAX_NAME;++i) (*s_tree)[(int)strlen(*s_tree)+i] = '\0';
data/phyml-3.3.20200621/src/io.c:729:22: [1] (buffer) strlen:
Does not handle 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_tree)[(int)strlen(*s_tree)]='(';
data/phyml-3.3.20200621/src/io.c:737:53: [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).
(*s_tree) = (char *)mRealloc(*s_tree,(int)strlen(*s_tree)+3*(int)T_MAX_NAME,sizeof(char));
data/phyml-3.3.20200621/src/io.c:738:59: [1] (buffer) strlen:
Does not handle 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<3*(int)T_MAX_NAME;++i) (*s_tree)[(int)strlen(*s_tree)+i] = '\0';
data/phyml-3.3.20200621/src/io.c:759:23: [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).
last_len = (int)strlen(*s_tree);
data/phyml-3.3.20200621/src/io.c:766:42: [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).
Print_Labels(NULL,*s_tree+(int)strlen(*s_tree),fils->label);
data/phyml-3.3.20200621/src/io.c:772:40: [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).
sprintf(*s_tree+(int)strlen(*s_tree),"%.0f",fils->b[p]->support_val);
data/phyml-3.3.20200621/src/io.c:776:40: [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).
sprintf(*s_tree+(int)strlen(*s_tree),"%f",fils->b[p]->support_val);
data/phyml-3.3.20200621/src/io.c:781:36: [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).
sprintf(*s_tree+(int)strlen(*s_tree),"%d",fils->num);
data/phyml-3.3.20200621/src/io.c:787:26: [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).
(*s_tree)[(int)strlen(*s_tree)] = ':';
data/phyml-3.3.20200621/src/io.c:789:42: [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).
Print_Labels(NULL,*s_tree+(int)strlen(*s_tree),b->label);
data/phyml-3.3.20200621/src/io.c:793:32: [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).
sprintf(*s_tree+(int)strlen(*s_tree),format,MAX(0.0,mean_len));
data/phyml-3.3.20200621/src/io.c:796:22: [1] (buffer) strlen:
Does not handle 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_tree)[(int)strlen(*s_tree)] = ',';
data/phyml-3.3.20200621/src/io.c:799:29: [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).
(*available) -= ((int)strlen(*s_tree) - last_len);
data/phyml-3.3.20200621/src/io.c:811:53: [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).
(*s_tree) = (char *)mRealloc(*s_tree,(int)strlen(*s_tree)+3*(int)T_MAX_NAME,sizeof(char));
data/phyml-3.3.20200621/src/io.c:812:59: [1] (buffer) strlen:
Does not handle 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<3*(int)T_MAX_NAME;++i) (*s_tree)[(int)strlen(*s_tree)+i] = '\0';
data/phyml-3.3.20200621/src/io.c:834:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c=fgetc(io->fp_in_align)) != EOF)
data/phyml-3.3.20200621/src/io.c:868:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c=fgetc(io->fp_in_tree)) != EOF)
data/phyml-3.3.20200621/src/io.c:1152:9: [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).
while(strlen(token) > 0);
data/phyml-3.3.20200621/src/io.c:1168:11: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/phyml-3.3.20200621/src/io.c:1178:15: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/phyml-3.3.20200621/src/io.c:1192:11: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/phyml-3.3.20200621/src/io.c:1215:15: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/phyml-3.3.20200621/src/io.c:1535:23: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=(char)fgetc(in);
data/phyml-3.3.20200621/src/io.c:1552:19: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=(char)fgetc(in);
data/phyml-3.3.20200621/src/io.c:1567:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = (char)fgetc(in);
data/phyml-3.3.20200621/src/io.c:1633:9: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=fgetc(fp_input_tree);
data/phyml-3.3.20200621/src/io.c:1649:13: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=fgetc(fp_input_tree);
data/phyml-3.3.20200621/src/io.c:1665:9: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=fgetc(fp_input_tree);
data/phyml-3.3.20200621/src/io.c:1904:25: [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(j<(int)strlen(cdata->c_seq[i]->name))
data/phyml-3.3.20200621/src/io.c:1998:21: [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).
if(j<(int)strlen(cdata->c_seq[i]->name))
data/phyml-3.3.20200621/src/io.c:2240:22: [1] (buffer) strlen:
Does not handle 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(j>=(int)strlen(mat->name[i])) putchar(' ');
data/phyml-3.3.20200621/src/io.c:2338:7: [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(strcat(strcat(s,"user tree ("),io->in_tree_file),")");
data/phyml-3.3.20200621/src/io.c:2628:17: [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(s,")"); break; }
data/phyml-3.3.20200621/src/io.c:2946:9: [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(s,")"); break; }
data/phyml-3.3.20200621/src/io.c:4002:36: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(tree->io->in_align_file)+2+2),sizeof(char));
data/phyml-3.3.20200621/src/io.c:4002:46: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(tree->io->in_align_file)+2+2),sizeof(char));
data/phyml-3.3.20200621/src/io.c:4009:10: [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).
s[(int)strlen(s)-2]=' ';
data/phyml-3.3.20200621/src/io.c:4010:10: [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).
s[(int)strlen(s)-1]='\0';
data/phyml-3.3.20200621/src/io.c:5055:31: [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.
if(io->append_run_ID) { strcat(io->out_trees_file,"_"); strcat(io->out_trees_file,io->run_id_string); }
data/phyml-3.3.20200621/src/io.c:5541:36: [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).
kv->value = (char *)mCalloc((int)strlen(s)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:5626:35: [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).
sprintf(kv->value+strlen(kv->value),"%d",n_tstv);
data/phyml-3.3.20200621/src/io.c:5691:35: [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).
sprintf(kv->value+strlen(kv->value),"%d",n_alpha);
data/phyml-3.3.20200621/src/io.c:5739:27: [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).
sprintf(kv->value+strlen(kv->value),"%d",tree_num);
data/phyml-3.3.20200621/src/io.c:5824:36: [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).
kv->value = (char *)mCalloc((int)strlen(s)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:5874:33: [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).
sprintf(kv->key+strlen(kv->key),"%d",n_tstv);
data/phyml-3.3.20200621/src/io.c:5917:33: [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).
sprintf(kv->key+strlen(kv->key),"%d",n_alpha);
data/phyml-3.3.20200621/src/io.c:5944:25: [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).
sprintf(kv->key+strlen(kv->key),"%d",tree_num);
data/phyml-3.3.20200621/src/io.c:5972:7: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(where);
data/phyml-3.3.20200621/src/io.c:6094:28: [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).
s = (char *)mCalloc((int)strlen(buff)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:6095:13: [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).
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6101:32: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(buff)+1),sizeof(char));
data/phyml-3.3.20200621/src/io.c:6101:42: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(buff)+1),sizeof(char));
data/phyml-3.3.20200621/src/io.c:6102:13: [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).
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6114:39: [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).
s = (char *)mRealloc(s,(int)strlen(s)+9,sizeof(char));
data/phyml-3.3.20200621/src/io.c:6126:36: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(buff)+1),sizeof(char));
data/phyml-3.3.20200621/src/io.c:6126:46: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(buff)+1),sizeof(char));
data/phyml-3.3.20200621/src/io.c:6127:17: [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).
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6137:32: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(buff)+1),sizeof(char));
data/phyml-3.3.20200621/src/io.c:6137:42: [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).
s = (char *)mRealloc(s,(int)(strlen(s)+strlen(buff)+1),sizeof(char));
data/phyml-3.3.20200621/src/io.c:6138:13: [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).
sprintf(s+strlen(s),"%s",buff);
data/phyml-3.3.20200621/src/io.c:6308:28: [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).
if(s[0] != '[' || s[(int)strlen(s)-1] != ']')
data/phyml-3.3.20200621/src/io.c:6318:32: [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).
s_cpy = (char *)mCalloc((int)strlen(s)-1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:6319:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(s_cpy,s+1,(strlen(s)-2)*sizeof(char));
data/phyml-3.3.20200621/src/io.c:6319:22: [1] (buffer) strlen:
Does not handle 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(s_cpy,s+1,(strlen(s)-2)*sizeof(char));
data/phyml-3.3.20200621/src/io.c:6320:9: [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).
s_cpy[strlen(s)-2]='\0';
data/phyml-3.3.20200621/src/io.c:6332:34: [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).
lab->key = (char *)mCalloc(strlen(key)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:6336:34: [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).
lab->val = (char *)mCalloc(strlen(val)+1,sizeof(char));
data/phyml-3.3.20200621/src/io.c:6372:11: [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.
sprintf(s_where+(int)strlen(s_where),"[");
data/phyml-3.3.20200621/src/io.c:6372:32: [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).
sprintf(s_where+(int)strlen(s_where),"[");
data/phyml-3.3.20200621/src/io.c:6385:36: [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).
sprintf(s_where+(int)strlen(s_where),"%s=%s",lab->key,lab->val);
data/phyml-3.3.20200621/src/io.c:6386:37: [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(lab->next != NULL) sprintf(s_where+(int)strlen(s_where),",");
data/phyml-3.3.20200621/src/io.c:6386:58: [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).
if(lab->next != NULL) sprintf(s_where+(int)strlen(s_where),",");
data/phyml-3.3.20200621/src/io.c:6398:11: [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.
sprintf(s_where+(int)strlen(s_where),"]");
data/phyml-3.3.20200621/src/io.c:6398:32: [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).
sprintf(s_where+(int)strlen(s_where),"]");
data/phyml-3.3.20200621/src/m4.c:220:34: [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).
MPI_Bcast (most_likely_tree, strlen(most_likely_tree)+1, MPI_CHAR, 0, MPI_COMM_WORLD);
data/phyml-3.3.20200621/src/main.c:333:48: [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).
MPI_Bcast (most_likely_tree, strlen(most_likely_tree)+1, MPI_CHAR, 0, MPI_COMM_WORLD);
data/phyml-3.3.20200621/src/make.c:716:58: [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).
cdata->c_seq[j]->name = (char *)mCalloc((int)(strlen(sp_names_in[j])+1),sizeof(char));
data/phyml-3.3.20200621/src/make.c:726:61: [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).
cdata->c_seq_rm[j]->name = (char *)mCalloc((int)(strlen(sp_names_out[j])+1),sizeof(char));
data/phyml-3.3.20200621/src/make.c:1137:36: [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).
new_attr->name = (char *)mCalloc(strlen(attr_name)+1,sizeof(char));
data/phyml-3.3.20200621/src/make.c:1140:37: [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).
new_attr->value = (char *)mCalloc(strlen(attr_value)+1,sizeof(char));
data/phyml-3.3.20200621/src/make.c:1151:34: [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).
if(id) n->id = (char *)mCalloc(strlen(id)+1,sizeof(char));
data/phyml-3.3.20200621/src/make.c:1159:38: [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(val) n->value = (char *)mCalloc(strlen(val)+1,sizeof(char));
data/phyml-3.3.20200621/src/make.c:1169:45: [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).
if(name) new_node->name = (char *)mCalloc(strlen(name)+1,sizeof(char));
data/phyml-3.3.20200621/src/mcmc.c:2749:12: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar(); /* \n */
data/phyml-3.3.20200621/src/mcmc.c:2800:8: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar(); /* \n */
data/phyml-3.3.20200621/src/mcmc.c:2860:33: [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).
sprintf(cpy->out_filename+strlen(cpy->out_filename),"_%d",pid);
data/phyml-3.3.20200621/src/mcmc.c:2863:7: [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(s,"_");
data/phyml-3.3.20200621/src/mcmc.c:2869:7: [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(s,"_");
data/phyml-3.3.20200621/src/mcmc.c:2875:7: [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(s,"_");
data/phyml-3.3.20200621/src/mixt.c:1893:34: [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).
sprintf(xml_boot_file_name+strlen(xml_boot_file_name),"%d",pid);
data/phyml-3.3.20200621/src/mixt.c:1903:11: [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(boot_out_file_name,"_");
data/phyml-3.3.20200621/src/mixt.c:1918:11: [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.
strcpy(boot_attr->value,"0");
data/phyml-3.3.20200621/src/mixt.c:1927:40: [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).
sprintf(boot_out_attr->value+strlen(boot_out_attr->value),"_boot.%d",pid);
data/phyml-3.3.20200621/src/mpi_boot.c:562:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (bootStr, s, T_MAX_LINE);
data/phyml-3.3.20200621/src/nexus.c:21:18: [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).
tokenlen = strlen(token);
data/phyml-3.3.20200621/src/nexus.c:23:35: [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(tokenlen && (tokenlen == strlen(com_list[i]->name)))
data/phyml-3.3.20200621/src/nexus.c:59:18: [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).
tokenlen = strlen(token);
data/phyml-3.3.20200621/src/nexus.c:61:22: [1] (buffer) strlen:
Does not handle 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(tokenlen == strlen(curr_com->parm[i]->name))
data/phyml-3.3.20200621/src/nexus.c:90:12: [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).
}while(strlen(token) > 0);
data/phyml-3.3.20200621/src/nexus.c:119:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
io->short_tax_names[io->size_tax_names-1] = (char *)mCalloc(strlen(token)+1,sizeof(char));
data/phyml-3.3.20200621/src/nexus.c:125:63: [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).
io->long_tax_names[io->size_tax_names-1] = (char *)mCalloc(strlen(token)+1,sizeof(char));
data/phyml-3.3.20200621/src/nexus.c:130:12: [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).
}while(strlen(token) > 0);
data/phyml-3.3.20200621/src/nexus.c:242:9: [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).
For(i,strlen(token)) Lowercase(token+i);
data/phyml-3.3.20200621/src/nexus.c:312:35: [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(*token != '"' || *(token+strlen(token)-1) != '"')
data/phyml-3.3.20200621/src/nexus.c:371:13: [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(io->alphabet[0]);
data/phyml-3.3.20200621/src/nexus.c:374:7: [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(io->alphabet[i]) != len)
data/phyml-3.3.20200621/src/phyrex.c:2934:17: [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).
for(i=0;i<strlen(s);++i) if(s[i] == '#') break; /* skip comment */
data/phyml-3.3.20200621/src/phyrex.c:2935:15: [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(i != strlen(s)) continue;
data/phyml-3.3.20200621/src/phyrex.c:3387:49: [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).
deme_names[n_demes] = (char *)mCalloc(strlen(s+1)+1,sizeof(char));
data/phyml-3.3.20200621/src/slfv.c:1249:44: [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).
s = (char *)mCalloc((int)strlen(ldsk_a_pop[i]->coord->id)+1+50,sizeof(char));
data/phyml-3.3.20200621/src/slfv.c:1250:30: [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).
For(k,(int)strlen(ldsk_a_pop[i]->coord->id)+1+20) s[k]='\0';
data/phyml-3.3.20200621/src/slfv.c:1255:29: [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).
sprintf(s+strlen(s),"%d",permut[j]);
data/phyml-3.3.20200621/src/slfv.c:1677:27: [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).
s = (char *)mCalloc(strlen(tree->young_disk->ldsk_a[i]->coord->id)+1+20,sizeof(char));
data/phyml-3.3.20200621/src/slfv.c:1951:27: [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).
s = (char *)mCalloc(strlen(tree->young_disk->ldsk_a[i]->coord->id)+1+20,sizeof(char));
data/phyml-3.3.20200621/src/tiporder.c:525:58: [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).
ref_tree->a_nodes[j]->name = (char *)mCalloc((int)strlen(ref_tree->io->long_tax_names[i])+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:1250:11: [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(long_line,",");
data/phyml-3.3.20200621/src/utilities.c:1300:53: [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).
tree->a_nodes[i]->name = (char *)mCalloc((int)strlen(data->c_seq[i]->name)+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:2047:40: [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).
sp_names_in[i] = (char *)mCalloc(strlen(ori->c_seq[i]->name)+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:2054:41: [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).
sp_names_out[i] = (char *)mCalloc(strlen(ori->c_seq_rm[i]->name)+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:2609:53: [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).
daughter->name = (char *)mCalloc((int)strlen(tree->data->c_seq_rm[i]->name)+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:5006:47: [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).
cpy->a_nodes[i]->name = (char *)mCalloc(strlen(ori->a_nodes[i]->name)+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:7089:20: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else getchar();
data/phyml-3.3.20200621/src/utilities.c:7609:7: [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.
strcpy(tree->a_nodes[i]->name,"x");
data/phyml-3.3.20200621/src/utilities.c:8550:14: [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).
p = path + strlen(path) - 1;
data/phyml-3.3.20200621/src/utilities.c:8867:8: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
do c=fgetc(fp_input_tree);
data/phyml-3.3.20200621/src/utilities.c:8881:9: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=fgetc(fp_input_tree);
data/phyml-3.3.20200621/src/utilities.c:8888:9: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c=fgetc(fp_input_tree);
data/phyml-3.3.20200621/src/utilities.c:9169:11: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/phyml-3.3.20200621/src/utilities.c:9356:9: [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).
For(i,strlen(s))
data/phyml-3.3.20200621/src/utilities.c:9366:9: [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).
For(i,strlen(s))
data/phyml-3.3.20200621/src/utilities.c:9376:9: [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).
For(i,strlen(s))
data/phyml-3.3.20200621/src/utilities.c:10218:14: [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).
len = (int)strlen(in);
data/phyml-3.3.20200621/src/utilities.c:10237:14: [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).
len = (int)strlen(in);
data/phyml-3.3.20200621/src/utilities.c:11919:28: [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).
to->id = (char *)mCalloc(strlen(from->id)+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:11944:28: [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).
to->id = (char *)mCalloc(strlen(from->id)+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:11955:41: [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).
to->tax_list[i] = (char *)mCalloc(strlen(from->tax_list[i])+1,sizeof(char));
data/phyml-3.3.20200621/src/utilities.c:11976:3: [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.
strcpy(s," ");
data/phyml-3.3.20200621/src/utilities.c:11978:13: [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).
sprintf(s+strlen(s),"%c",c);
data/phyml-3.3.20200621/src/utilities.c:11980:3: [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(s," ");
data/phyml-3.3.20200621/src/utilities.c:11982:13: [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).
sprintf(s+strlen(s),"%c",c);
data/phyml-3.3.20200621/src/xml.c:111:23: [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(!outputfile || !(strlen(outputfile)>0))
data/phyml-3.3.20200621/src/xml.c:126:11: [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(s && strlen(s)>0)
data/phyml-3.3.20200621/src/xml.c:133:11: [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(s && strlen(s)>0) io->r_seed = (int)atoi(s);
data/phyml-3.3.20200621/src/xml.c:159:27: [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.
if(io->append_run_ID) { strcat(io->out_tree_file,"_"); strcat(io->out_tree_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:160:27: [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.
if(io->append_run_ID) { strcat(io->out_stats_file,"_"); strcat(io->out_stats_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:190:35: [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.
if(io->append_run_ID) { strcat(io->out_trace_file,"_"); strcat(io->out_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:210:35: [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.
if(io->append_run_ID) { strcat(io->out_json_trace_file,"_"); strcat(io->out_json_trace_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:227:31: [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.
if(io->append_run_ID) { strcat(io->out_lk_file,"_"); strcat(io->out_lk_file,io->run_id_string); }
data/phyml-3.3.20200621/src/xml.c:539:30: [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).
for(i=0;i<(int)strlen(list);++i) if(list[i] == ',') j++;
data/phyml-3.3.20200621/src/xml.c:553:50: [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(list[j] == ',' || j == (int)strlen(list))
data/phyml-3.3.20200621/src/xml.c:629:36: [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).
if(j != (int)strlen(list)-1) i = 0;
data/phyml-3.3.20200621/src/xml.c:1101:32: [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(j == (int)strlen(list)+1) break;
data/phyml-3.3.20200621/src/xml.c:1176:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1193:22: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1211:26: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1249:26: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1279:25: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if((c=fgetc(fp)) != '>')
data/phyml-3.3.20200621/src/xml.c:1354:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1363:19: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
quote = fgetc(fp);
data/phyml-3.3.20200621/src/xml.c:1387:22: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1399:22: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1416:47: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(c != EOF && isspace(c) != NO) c = fgetc(fp);
data/phyml-3.3.20200621/src/xml.c:1420:22: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF && isspace(c) != NO);
data/phyml-3.3.20200621/src/xml.c:1434:26: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:1453:26: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(fp)) != EOF)
data/phyml-3.3.20200621/src/xml.c:2345:37: [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).
cal->id = (char *)mCalloc(strlen(calib_id)+1,sizeof(char));
data/phyml-3.3.20200621/src/xml.c:2403:90: [1] (buffer) strlen:
Does not handle 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<clade_size;++i) clade->tax_list[i] = (char *)mCalloc(strlen(xclade[i])+1,sizeof(char));
data/phyml-3.3.20200621/src/xml.c:2412:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
clade->id = (char *)mCalloc(strlen(clade_id)+1,sizeof(char));
ANALYSIS SUMMARY:
Hits = 1127
Lines analyzed = 101048 in approximately 2.86 seconds (35275 lines/second)
Physical Source Lines of Code (SLOC) = 70900
Hits@level = [0] 264 [1] 280 [2] 554 [3] 16 [4] 228 [5] 49
Hits@level+ = [0+] 1391 [1+] 1127 [2+] 847 [3+] 293 [4+] 277 [5+] 49
Hits/KSLOC@level+ = [0+] 19.6192 [1+] 15.8956 [2+] 11.9464 [3+] 4.13258 [4+] 3.90691 [5+] 0.691114
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.