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/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/binposplugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/largefiles.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/vmdplugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/src/binposplugin.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/dcdplugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/endianswap.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/largefiles.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/vmdplugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/endianswap.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/vmddir.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/vmdplugin.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/bwlzh.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/bwt.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/coder.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/dict.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/fixpoint.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/huffman.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/lz77.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/merge_sort.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/mtf.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/my64bit.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/rle.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/tng_compress.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/vals16.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/warnmalloc.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/compression/widemuldiv.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/tng/md5.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/tng/tng_io.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/tng/tng_io.hpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/tng/tng_io_fwd.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/include/tng/version.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwt.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/coder.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/dict.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/fixpoint.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/huffman.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/huffmem.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/lz77.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/merge_sort.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/mtf.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/rle.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/vals16.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/warnmalloc.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/widemuldiv.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/md5.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/include/ms_stdint.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/include/trr_header.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/include/xdr_seek.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/include/xdrfile.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/include/xdrfile_trr.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/include/xdrfile_xtc.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdr_seek.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile_trr.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile_xtc.c
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/dridkernels.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/geometry.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/math_patch.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/moments.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/msvccompat.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/neighborlist.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/neighbors.hpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/sasa.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/vectorize.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/vectorize_neon.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/include/vectorize_sse.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/dridkernels.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/dssp.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/geometry.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/kernels/anglekernels.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/kernels/dihedralkernels.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/kernels/distancekernels.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/moments.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/neighborlist.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/neighbors.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/geometry/src/sasa.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/Munkres.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/center.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/euclidean_permutation.hpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/fancy_index.hpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/msvccompat.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/rotation.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/sse_swizzle.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/theobald_rmsd.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/util_arm.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/include/util_sse.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/Munkres.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/center.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/center_arm.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/center_sse.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/euclidean_permutation.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/fancy_index.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/rotation.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/rotation_arm.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/rotation_sse.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/theobald_rmsd.cpp
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/theobald_rmsd_arm.h
Examining data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/rmsd/src/theobald_rmsd_sse.h
FINAL RESULTS:
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:722:17: [5] (race) chmod:
This accepts filename arguments; if an attacker can move those files, a
race condition results. (CWE-362). Use fchmod( ) instead.
if( chmod(dirsub.c_str(), mode) < 0 )
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:729:13: [5] (race) chmod:
This accepts filename arguments; if an attacker can move those files, a
race condition results. (CWE-362). Use fchmod( ) instead.
if( chmod(dpslash.c_str(), mode) < 0 )
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:731:13: [5] (race) chmod:
This accepts filename arguments; if an attacker can move those files, a
race condition results. (CWE-362). Use fchmod( ) instead.
if( chmod((dpslash + "not_hashed").c_str(), mode) < 0 )
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:76:9: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
DWORD access;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:87:5: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
access |= GENERIC_READ;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:89:5: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
access |= GENERIC_WRITE;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:113:32: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
fp = CreateFile(winfilename, access, sharing, security,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:745:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(time_str, "REMARKS Created %s", asctime(tmbuf));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/vmddir.h:55:3: [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(dirname, filename);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/coder.c:27:22: [4] (format) _snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
#define TNG_SNPRINTF _snprintf
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/coder.c:30:22: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
#define TNG_SNPRINTF snprintf
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:373:22: [4] (format) _snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
#define TNG_SNPRINTF _snprintf
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:376:22: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
#define TNG_SNPRINTF snprintf
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5405:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(data->block_name, block->name);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9286:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest->input_file_path, src->input_file_path);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9303:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest->output_file_path, src->output_file_path);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:11712:13: [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(block->name, tng_data->non_tr_data[i].block_name);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:11724:13: [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(block->name, tng_data->non_tr_particle_data[i].block_name);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15437:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*names[i], atom->name);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15439:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*types[i], atom->atom_type);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15441:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*res_names[i], res->name);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15443:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*chain_names[i], chain->name);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:113:20: [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.
# error Use system XDR libraries instead, or update xdrfile.c
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:2106:45: [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.
# error is larger than 4 bytes. Use your system XDR libraries
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:2456:36: [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.
# error non-IEEE floating point system, or you defined GROMACS yourself...
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:493:17: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if (getenv("DTRPLUGIN_VERBOSE")) fprintf(stderr,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1002:15: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if (getenv("DTRPLUGIN_VERBOSE"))
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1024:11: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if (getenv("DTRPLUGIN_VERBOSE"))
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1119:9: [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.
if (getenv("DTRPLUGIN_VERBOSE")) {
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:2141:8: [3] (random) setstate:
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.
in.setstate( std::ios::failbit );
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:68:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char database[81]; /**< database of origin, if any */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:69:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char accession[81]; /**< database accession code, if any */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:70:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char date[81]; /**< date/time stamp for this data */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:71:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char title[81]; /**< brief title for this data */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:94:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[16]; /**< required atom name string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:95:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char type[16]; /**< required atom type string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:96:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char resname[8]; /**< required residue name string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:98:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char segid[8]; /**< required segment name string, or "" */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:99:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chain[2]; /**< required chain name, or "" */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:102:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char altloc[2]; /**< optional PDB alternate location code */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:103:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char insertion[2]; /**< optional PDB insertion code */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:194:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char dataname[256]; /**< name of volumetric data set */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:315:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char basis_string[MOLFILE_BUFSIZ]; /**< basis name as "nice" string. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:316:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char runtitle[MOLFILE_BIGBUFSIZ]; /**< title of run. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:317:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char geometry[MOLFILE_BUFSIZ]; /**< type of provided geometry, XXX: remove?
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:319:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char version_string[MOLFILE_BUFSIZ]; /**< QM code version information. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/include/molfile_plugin.h:459:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char info[MOLFILE_BUFSIZ]; /**< string for additional type info */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/src/binposplugin.c:47:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char lenbuf[4];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/src/binposplugin.c:49:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char magicchar[5];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/src/binposplugin.c:51:8: [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).
fd = fopen(path, "rb");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/src/binposplugin.c:77:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(lenbuf, (const char *)&igarb, 4);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/src/binposplugin.c:80:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((char *)&igarb, lenbuf, 4);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/binpos/src/binposplugin.c:209:8: [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).
fd = fopen(path, "wb");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/endianswap.h:68:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char byteArray[8];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:75:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char winfilename[8192];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:281:8: [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(filename, modestr);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:385:9: [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).
nfd = open(filename, oflag, 0666);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:68:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char database[81]; /**< database of origin, if any */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:69:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char accession[81]; /**< database accession code, if any */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:70:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char date[81]; /**< date/time stamp for this data */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:71:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char title[81]; /**< brief title for this data */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:94:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[16]; /**< required atom name string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:95:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char type[16]; /**< required atom type string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:96:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char resname[8]; /**< required residue name string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:98:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char segid[8]; /**< required segment name string, or "" */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:99:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chain[2]; /**< required chain name, or "" */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:102:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char altloc[2]; /**< optional PDB alternate location code */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:103:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char insertion[2]; /**< optional PDB insertion code */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:194:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char dataname[256]; /**< name of volumetric data set */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:315:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char basis_string[MOLFILE_BUFSIZ]; /**< basis name as "nice" string. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:316:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char runtitle[MOLFILE_BIGBUFSIZ]; /**< title of run. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:317:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char geometry[MOLFILE_BUFSIZ]; /**< type of provided geometry, XXX: remove?
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:319:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char version_string[MOLFILE_BUFSIZ]; /**< QM code version information. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/molfile_plugin.h:459:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char info[MOLFILE_BUFSIZ]; /**< string for additional type info */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:103:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hdrbuf[84]; /* char buffer used to store header */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:421:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pos, fixedcoords, 4*N);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:551:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fixedcoords, X, N*sizeof(float));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:552:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fixedcoords+N, Y, N*sizeof(float));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:553:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fixedcoords+2*N, Z, N*sizeof(float));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:688:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char title_string[200];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:691:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char time_str[81];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:695:3: [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(title_string, "CORD");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/endianswap.h:68:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char byteArray[8];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:100:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char database[81]; /**< database of origin, if any */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:101:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char accession[81]; /**< database accession code, if any */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:102:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char date[81]; /**< date/time stamp for this data */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:103:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char title[81]; /**< brief title for this data */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:126:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[16]; /**< required atom name string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:127:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char type[16]; /**< required atom type string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:128:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char resname[8]; /**< required residue name string */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:130:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char segid[8]; /**< required segment name string, or "" */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:131:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chain[2]; /**< required chain name, or "" */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:134:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char altloc[2]; /**< optional PDB alternate location code */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:135:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char insertion[2]; /**< optional PDB insertion code */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:226:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char dataname[256]; /**< name of volumetric data set */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:347:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char basis_string[MOLFILE_BUFSIZ]; /**< basis name as "nice" string. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:348:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char runtitle[MOLFILE_BIGBUFSIZ]; /**< title of run. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:349:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char geometry[MOLFILE_BUFSIZ]; /**< type of provided geometry, XXX: remove?
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:351:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char version_string[MOLFILE_BUFSIZ]; /**< QM code version information. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/molfile_plugin.h:491:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char info[MOLFILE_BUFSIZ]; /**< string for additional type info */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/vmddir.h:53:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char dirname[VMD_FILENAME_MAX];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/vmddir.h:56:3: [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(dirname, "\\*");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/include/vmddir.h:85:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp=fopen(filename, "rb")) != NULL) {
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:406:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE * fd = fopen( timekeys_path.c_str(), "rb" );
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:600:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf, data, count*sizeof(float));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:611:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf, data, count*sizeof(double));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:622:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf, data, count*sizeof(int32_t));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:630:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf, data, count*sizeof(uint32_t));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:660:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char answer[DD_RELPATH_MAXLEN];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:665:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(answer, "%03x/%03x/", d1, d2);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:667:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(answer, "%03x/", d1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:670:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(answer, "./");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:694:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen((dpslash + "not_hashed/.ddparams").c_str(), "w");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:705:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char sub[6];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:706:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(sub, "%03x/", i);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:713:6: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char subsub[6];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:714:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(subsub, "%03x", j);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:743:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen((dirslash + "not_hashed/.ddparams").c_str(), "r");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:746:12: [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((dirslash + ".ddparams").c_str(), "r");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:783:9: [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 buf[256];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:784:9: [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(buf, "invalid magic number: expected %d, got %d\n",
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:929:17: [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 meta_fd = open(metafile.c_str(), O_RDONLY|O_BINARY);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1124:14: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(fname.c_str(), O_RDONLY|O_BINARY);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1703:14: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(fname.c_str(), O_RDONLY|O_BINARY);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1905:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy( scalars, m->bytes, nbytes );
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1908:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy( fields, m->bytes, nbytes );
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1933:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cwd[4096];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1952:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fd = fopen(clickme_file.c_str(), "wb");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1963:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fd = fopen(metadata_file.c_str(), "wb");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:1970:21: [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).
timekeys_file = fopen( timekeys_path.c_str(), "wb" );
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:2046:18: [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).
frame_fd = open(filepath.c_str(),O_WRONLY|O_CREAT|O_BINARY,0666);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c:337:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzhhuff,bwlzhhufflen);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c:376:23: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzhhuff,bwlzhhufflen);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c:396:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f=fopen("len.dict","w");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c:401:19: [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).
f=fopen("off.dict","w");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c:406:19: [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).
f=fopen("len.time","w");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c:410:19: [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).
f=fopen("off.time","w");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwlzh.c:444:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzhhuff,bwlzhhufflen);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/bwt.c:137:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(indices+start,workarray,(end-start)*sizeof(int));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/huffmem.c:342:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char *huff_algo_names[N_HUFFMAN_ALGO]=
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/merge_sort.c:51:19: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(workarray+i*size,cbase+iright*size,size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/merge_sort.c:56:19: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(workarray+i*size,cbase+ileft*size,size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/merge_sort.c:66:23: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(workarray+i*size,cbase+iright*size,size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/merge_sort.c:71:23: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(workarray+i*size,cbase+ileft*size,size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/merge_sort.c:77:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cbase+start*size,workarray,(end-start)*size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:383:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data+bufloc,datablock,length);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:429:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data+bufloc,datablock,length);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:504:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data+bufloc,datablock,length);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:539:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data+bufloc,datablock,length);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:1569:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(posi,quant,natoms*3*sizeof *posi);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:1615:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(posi+natoms*3,quant+natoms*3,natoms*3*(nframes-1)*sizeof *posi);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:1716:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(veli,quant,natoms*3*sizeof *veli);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:1751:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(veli+natoms*3,quant+natoms*3,natoms*3*(nframes-1)*sizeof *veli);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:1828:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char *compress_algo_pos[TNG_COMPRESS_ALGO_MAX]={
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/tng_compress.c:1842:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char *compress_algo_vel[TNG_COMPRESS_ALGO_MAX]={
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:235:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char *instrnames[MAXINSTR]={
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:488:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(largeint,largeint_tmp,19*sizeof *largeint);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:551:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(largeint,largeint_tmp,19*sizeof *largeint);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:728:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char compress_buffer[18*4]; /* Holds compressed result for 3 large ints or up to 18 small ints. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:831:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(prevcoord, minint, 3*sizeof *prevcoord);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:1314:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char compress_buffer[18*4]; /* Holds compressed result for 3 large ints or up to 18 small ints. */
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:1339:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(prevcoord, minint, 3*sizeof *prevcoord);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:1362:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(large_ints, encode_ints, 3*sizeof *large_ints);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:1475:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(large_ints, encode_ints, 3*sizeof *large_ints);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc2.c:1480:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(prevcoord, large_ints, 3*sizeof *prevcoord);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:591:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(largeint, largeint_tmp, (n+1)*sizeof *largeint);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:849:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(xtc3_context.maxint, input, 3*sizeof *xtc3_context.maxint);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:850:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(xtc3_context.minint, input, 3*sizeof *xtc3_context.maxint);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:931:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(prevcoord, xtc3_context.minint, 3*sizeof *prevcoord);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1467:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzh_buf,bwlzh_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1485:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzh_buf,bwlzh_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1520:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,base_buf,base_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1527:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzh_buf,bwlzh_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1564:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,base_buf,base_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1571:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzh_buf,bwlzh_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1608:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,base_buf,base_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1615:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzh_buf,bwlzh_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1652:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,base_buf,base_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1659:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(output+outdata,bwlzh_buf,bwlzh_buf_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1731:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(prevcoord, large_ints, 3*sizeof *prevcoord);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/compression/xtc3.c:1840:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(prevcoord, minint, 3*sizeof *prevcoord);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/md5.c:194:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(xbuf, data, 64);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/md5.c:368:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pms->buf + offset, p, copy);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/md5.c:382:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pms->buf, p, left);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:134:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char md5_hash[TNG_MD5_HASH_LEN];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:602:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[TNG_MAX_STR_LEN], *temp_alloc;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:889:32: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
tng_data->input_file = fopen(tng_data->input_file_path, "rb");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:926:33: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
tng_data->output_file = fopen(tng_data->output_file_path, "wb+");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2258:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hash[TNG_MD5_HASH_LEN];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2422:5: [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(block->name, "GENERAL INFO");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2933:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hash[TNG_MD5_HASH_LEN];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:3342:5: [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(block->name, "MOLECULES");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:3564:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hash[TNG_MD5_HASH_LEN];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:3777:5: [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(block->name, "TRAJECTORY FRAME SET");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:3932:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hash[TNG_MD5_HASH_LEN];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:4095:5: [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(block->name, "PARTICLE MAPPING");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5607:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((char *)data->values + n_frames_div * size * n_values *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5612:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data->values, contents, full_data_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6037:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(contents, data->values, full_data_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6417:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hash[TNG_MD5_HASH_LEN];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9541:29: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
tng_data->output_file = fopen(tng_data->output_file_path, "rb+");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:11699:9: [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(block->name, "GENERAL INFO");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:11704:9: [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(block->name, "MOLECULES");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12771:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data->values, new_data, size * n_frames_div *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12776:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data->values, new_data, size * n_frames_div *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:13585:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(copy, values, write_n_particles * n_values_per_frame * size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:13604:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(copy, values, write_n_particles * n_values_per_frame * size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14337:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*values, data->values, full_data_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14347:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(((char *)*values) + size * (i * i_step + mapping *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14900:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*values, current_values, size * (*n_particles) *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14905:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*values, current_values, size * (*n_values_per_frame));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14927:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*values, (char *)current_values + n_frames_div * frame_size,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14971:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(((char *)*values) + n_frames_div * frame_size,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15782:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*values, (char *)data->values + i * full_data_len, full_data_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15941:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*values, (char *)data->values + i * full_data_len, full_data_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16655:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((char *)data->values + sizeof(float) * frame_pos * n_particles *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16661:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data->values, values, sizeof(float) * n_particles *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16725:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((char *)data->values + sizeof(float) * frame_pos *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16731:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data->values, values, sizeof(float) * n_values_per_frame);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16893:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((char *)data->values + sizeof(double) * frame_pos * n_particles *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16899:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data->values, values, sizeof(double) * n_particles *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16963:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((char *)data->values + sizeof(double) * frame_pos *
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:16969:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(data->values, values, sizeof(double) * n_values_per_frame);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/include/xdrfile.h:101:9: [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.
extern char *exdr_message[exdrNR];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:63:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *exdr_message[exdrNR] = {
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:194:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char newmode[5];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:201:3: [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(newmode,"wb+");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:205:3: [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(newmode,"ab+");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:209:3: [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(newmode,"rb");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:216:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((xfp->fp=fopen(path,newmode))==NULL)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:1781:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cfilename[512];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:1782:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cmode[5];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:2126:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char xdr_zero[BYTES_PER_XDR_UNIT] = {0, 0, 0, 0};
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:2300:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char crud[BYTES_PER_XDR_UNIT];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile_trr.c:95:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[BUFSIZE];
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:57:11: [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).
int len=strlen(filename);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:405:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fio_size_t rc = read(fd, (void*) (((char *) ptr) + (cnt * size)), size);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:423:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fio_size_t rc = read(fd, iov[i].iov_base, iov[i].iov_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/include/fastio.h:475:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(str);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dcd/src/dcdplugin.c:734:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(title_string, remarks, 80);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:537:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&v, sizeof(v));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:565:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&keys[0], keys.size()*sizeof(keys[0]));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:897:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t rc = read(fd, mapping, framesize);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:2009:49: [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).
meta_t( "FORMAT", "char", sizeof(char), strlen(format), format ));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:2011:48: [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).
meta_t( "TITLE", "char", sizeof(char), strlen(title), title ));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/dtr/src/dtrplugin.cxx:2111:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&meta.invmass[0], sz*sizeof(meta.invmass[0]));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:607:13: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(tng_data->input_file);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:633:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*str, temp, count);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:661:24: [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).
len = tng_min_size(strlen(str) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2004:29: [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).
name_len = tng_min_size(strlen(block->name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2201:43: [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).
first_program_name_len = tng_min_size(strlen(tng_data->first_program_name) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2203:42: [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).
last_program_name_len = tng_min_size(strlen(tng_data->last_program_name) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2205:40: [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).
first_user_name_len = tng_min_size(strlen(tng_data->first_user_name) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2207:39: [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).
last_user_name_len = tng_min_size(strlen(tng_data->last_user_name) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2209:44: [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).
first_computer_name_len = tng_min_size(strlen(tng_data->first_computer_name) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2211:43: [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).
last_computer_name_len = tng_min_size(strlen(tng_data->last_computer_name) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2213:44: [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).
first_pgp_signature_len = tng_min_size(strlen(tng_data->first_pgp_signature) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2215:43: [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).
last_pgp_signature_len = tng_min_size(strlen(tng_data->last_pgp_signature) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2217:40: [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).
forcefield_name_len = tng_min_size(strlen(tng_data->forcefield_name) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2411:16: [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).
name_len = strlen("GENERAL INFO");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2809:30: [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).
*len += tng_min_size(strlen(molecule->name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2827:34: [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).
*len += tng_min_size(strlen(chain->name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2850:34: [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).
*len += tng_min_size(strlen(residue->name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2872:34: [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).
*len += tng_min_size(strlen(atom->name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:2885:34: [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).
*len += tng_min_size(strlen(atom->atom_type) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:3331:30: [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).
name_len = (unsigned int)strlen("MOLECULES");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:3762:30: [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).
name_len = (unsigned int)strlen("TRAJECTORY FRAME SET");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:3764:24: [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).
if(!block->name || strlen(block->name) < name_len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:4080:30: [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).
name_len = (unsigned int)strlen("PARTICLE MAPPING");
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:4082:24: [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).
if(!block->name || strlen(block->name) < name_len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5050:33: [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).
*len += strlen(second_dim_values[k]) + 1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5062:29: [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).
*len += strlen(second_dim_values[j]) + 1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5398:35: [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).
data->block_name = malloc(strlen(block->name) + 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5402:34: [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).
(unsigned int)strlen(block->name)+1, __FILE__, __LINE__);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5557:44: [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).
len = tng_min_size(strlen(contents+offset) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5571:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(second_dim_values[k], contents+offset, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5583:40: [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).
len = tng_min_size(strlen(contents+offset) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5597:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(data->strings[0][i][j], contents+offset, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5773:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(data->block_name) + 1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5775:24: [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).
if(!block->name || strlen(block->name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:5788:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(block->name, data->block_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6713:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, atom->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6716:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(atom->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6734:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6738:22: [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(atom->name && strlen(atom->name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6754:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(atom->name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6769:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(type, atom->atom_type, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6772:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(atom->atom_type) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6790:24: [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).
len = tng_min_size(strlen(new_type) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6794:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(atom->atom_type && strlen(atom->atom_type) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:6810:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(atom->atom_type, new_type, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7082:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, molecule->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7085:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(molecule->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7103:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7107:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(molecule->name && strlen(molecule->name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7123:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(molecule->name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7656:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, chain->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7659:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(chain->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7676:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7680:23: [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(chain->name && strlen(chain->name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7696:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(chain->name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7881:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, residue->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7884:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(residue->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7901:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7905:25: [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(residue->name && strlen(residue->name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:7921:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(residue->name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8200:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, mol->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8203:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(mol->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8367:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, atom->residue->chain->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8370:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(atom->residue->chain->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8419:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, atom->residue->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8422:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(atom->residue->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8562:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, atom->name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8565:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(atom->name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8610:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(type, atom->atom_type, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:8613:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(atom->atom_type) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9279:40: [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).
dest->input_file_path = malloc(strlen(src->input_file_path) + 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9283:34: [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).
(unsigned int)strlen(src->input_file_path) + 1, __FILE__, __LINE__);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9296:41: [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).
dest->output_file_path = malloc(strlen(src->output_file_path) + 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9300:34: [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).
(unsigned int)strlen(src->output_file_path) + 1, __FILE__, __LINE__);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9401:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(file_name, tng_data->input_file_path, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9404:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->input_file_path) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9433:24: [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).
len = tng_min_size(strlen(file_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9445:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->input_file_path, file_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9458:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(file_name, tng_data->output_file_path, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9461:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->output_file_path) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9489:24: [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).
len = tng_min_size(strlen(file_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9501:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->output_file_path, file_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9527:24: [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).
len = tng_min_size(strlen(file_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9539:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->output_file_path, file_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9701:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, tng_data->first_program_name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9704:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->first_program_name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9720:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9722:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(tng_data->first_program_name && strlen(tng_data->first_program_name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9738:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->first_program_name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9750:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, tng_data->last_program_name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9753:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->last_program_name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9769:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9771:39: [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).
if(tng_data->last_program_name && strlen(tng_data->last_program_name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9787:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->last_program_name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9799:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, tng_data->first_user_name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9802:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->first_user_name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9818:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9822:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(tng_data->first_user_name && strlen(tng_data->first_user_name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9838:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->first_user_name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9850:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, tng_data->last_user_name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9853:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->last_user_name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9869:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9873:36: [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(tng_data->last_user_name && strlen(tng_data->last_user_name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9889:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->last_user_name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9901:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, tng_data->first_computer_name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9904:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->first_computer_name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9920:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9924:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(tng_data->first_computer_name && strlen(tng_data->first_computer_name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9940:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->first_computer_name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9952:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, tng_data->last_computer_name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9955:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->last_computer_name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9971:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9975:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(tng_data->last_computer_name && strlen(tng_data->last_computer_name) <
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:9992:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->last_computer_name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10004:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(signature, tng_data->first_pgp_signature, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10007:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->first_pgp_signature) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10023:24: [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).
len = tng_min_size(strlen(signature) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10027:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(tng_data->first_pgp_signature && strlen(tng_data->first_pgp_signature) <
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10044:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->first_pgp_signature, signature, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10056:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(signature, tng_data->last_pgp_signature, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10059:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->last_pgp_signature) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10075:24: [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).
len = tng_min_size(strlen(signature) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10079:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(tng_data->last_pgp_signature && strlen(tng_data->last_pgp_signature) <
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10096:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->last_pgp_signature, signature, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10108:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, tng_data->forcefield_name, max_len - 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10111:8: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(tng_data->forcefield_name) > (unsigned int)max_len - 1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10127:24: [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).
len = tng_min_size(strlen(new_name) + 1, TNG_MAX_STR_LEN);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10131:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(tng_data->forcefield_name && strlen(tng_data->forcefield_name) < len)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:10147:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tng_data->forcefield_name, new_name, len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12606:35: [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).
data->block_name = malloc(strlen(block_name) + 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12610:34: [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).
(unsigned int)strlen(block_name)+1, __FILE__, __LINE__);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12613:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(data->block_name, block_name, strlen(block_name) + 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12613:47: [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).
strncpy(data->block_name, block_name, strlen(block_name) + 1);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12707:48: [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).
len = tng_min_size(strlen(new_data_c) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12720:29: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(second_dim_values[k],
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12734:44: [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).
len = tng_min_size(strlen(new_data_c) + 1,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12747:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(second_dim_values[j],
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12852:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, data->block_name, max_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12862:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, data->block_name, max_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12911:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, data->block_name, max_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:12924:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, data->block_name, max_len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14045:31: [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).
len = strlen(data->strings[i][j][k]) + 1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14047:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((*values)[i][mapping][k].c,
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14124:27: [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).
len = strlen(data->strings[0][i][j]) + 1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14126:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((*values)[0][i][j].c, data->strings[0][i][j], len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14559:31: [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).
len = strlen(data->strings[current_frame_pos][j][k]) + 1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14561:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((*values)[i][mapping][k].c, data->strings[current_frame_pos][j][k], len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14569:27: [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).
len = strlen(data->strings[0][current_frame_pos][j]) + 1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:14571:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((*values)[0][i][j].c, data->strings[0][current_frame_pos][j], len);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15436:30: [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).
(*names)[i] = malloc(strlen(atom->name));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15438:30: [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).
(*types)[i] = malloc(strlen(atom->atom_type));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15440:34: [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).
(*res_names)[i] = malloc(strlen(res->name));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/tng/src/lib/tng_io.c:15442:36: [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).
(*chain_names)[i] = malloc(strlen(chain->name));
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:457:10: [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).
int len=strlen(ptr)+1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile.c:2367:11: [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).
size = strlen (sp);
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile_trr.c:111:21: [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 (slen != strlen(version)+1)
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile_trr.c:118:16: [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).
slen = strlen(version)+1;
data/mdtraj-1.9.4+git20201015.068f29a/mdtraj/formats/xtc/src/xdrfile_trr.c:121:50: [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 (xdrfile_write_string(version,xd) != (strlen(version)+1) )
ANALYSIS SUMMARY:
Hits = 404
Lines analyzed = 53726 in approximately 1.61 seconds (33381 lines/second)
Physical Source Lines of Code (SLOC) = 36374
Hits@level = [0] 730 [1] 169 [2] 205 [3] 5 [4] 22 [5] 3
Hits@level+ = [0+] 1134 [1+] 404 [2+] 235 [3+] 30 [4+] 25 [5+] 3
Hits/KSLOC@level+ = [0+] 31.1761 [1+] 11.1068 [2+] 6.46066 [3+] 0.824765 [4+] 0.687304 [5+] 0.0824765
Dot directories skipped = 2 (--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.