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/r-bioc-rtracklayer-1.50.0/src/IRanges_stubs.c
Examining data/r-bioc-rtracklayer-1.50.0/src/R_init_rtracklayer.c
Examining data/r-bioc-rtracklayer-1.50.0/src/S4Vectors_stubs.c
Examining data/r-bioc-rtracklayer-1.50.0/src/XVector_stubs.c
Examining data/r-bioc-rtracklayer-1.50.0/src/bbiHelper.c
Examining data/r-bioc-rtracklayer-1.50.0/src/bbiHelper.h
Examining data/r-bioc-rtracklayer-1.50.0/src/bigBed.c
Examining data/r-bioc-rtracklayer-1.50.0/src/bigBed.h
Examining data/r-bioc-rtracklayer-1.50.0/src/bigBedHelper.c
Examining data/r-bioc-rtracklayer-1.50.0/src/bigBedHelper.h
Examining data/r-bioc-rtracklayer-1.50.0/src/bigWig.c
Examining data/r-bioc-rtracklayer-1.50.0/src/bigWig.h
Examining data/r-bioc-rtracklayer-1.50.0/src/chain_io.c
Examining data/r-bioc-rtracklayer-1.50.0/src/handlers.c
Examining data/r-bioc-rtracklayer-1.50.0/src/handlers.h
Examining data/r-bioc-rtracklayer-1.50.0/src/readGFF.c
Examining data/r-bioc-rtracklayer-1.50.0/src/readGFF.h
Examining data/r-bioc-rtracklayer-1.50.0/src/rtracklayer.h
Examining data/r-bioc-rtracklayer-1.50.0/src/twoBit.c
Examining data/r-bioc-rtracklayer-1.50.0/src/twoBit.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/_cheapcgi.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/_portimpl.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/_portimpl.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/aliType.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/aliType.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/asParse.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/asParse.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/base64.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/base64.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiFile.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiRead.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigWig.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/binRange.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/binRange.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bits.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bits.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgInternal.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgQuery.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/cheapcgi.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/cirTree.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/cirTree.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dlist.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dlist.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnaseq.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnaseq.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/errCatch.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/hash.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/hash.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/hmmstats.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/hmmstats.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/htmlColor.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/htmlColor.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/htmshell.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/memgfx.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/memgfx.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/options.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/os.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/oswin9x.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/portable.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/portimpl.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/rangeTree.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/rangeTree.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/rbTree.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/rbTree.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/sig.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/sqlList.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/sqlList.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/sqlNum.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/sqlNum.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/tokenizer.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/tokenizer.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/verbose.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/verbose.h
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/wildcmp.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/zlibFace.c
Examining data/r-bioc-rtracklayer-1.50.0/src/ucsc/zlibFace.h
Examining data/r-bioc-rtracklayer-1.50.0/src/utils.c
Examining data/r-bioc-rtracklayer-1.50.0/src/utils.h
FINAL RESULTS:
data/r-bioc-rtracklayer-1.50.0/src/handlers.c:9:3: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf(warn_buf, WARN_BUF_SIZE, format, args);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/_portimpl.c:21:3: [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(pathCopy, pathName);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/_portimpl.c:56:3: [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(fi->name, name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/asParse.c:124:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(leftParen, rightParen+1);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:376:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ret->strand, row[5]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:109:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(keyBuf, a->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:634:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(sn->name, name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:878:2: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(s, el->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:880:3: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(s, del);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1198:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"\"%s\"=",pair->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1202:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"%s=",pair->name); // warn but still make string
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1206:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"%s=",pair->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1211:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"\"%s\"",(char *)(pair->val));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1215:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"%s",(char *)(pair->val)); // warn but still make string
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1219:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"%s",(char *)(pair->val));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1252:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"\"%s\"",pair->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1258:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"%s",pair->name); // warn but still make string
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1262:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(strPtr,"%s",pair->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1634:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(resultPtr, string);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1638:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(resultPtr, new);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1643:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(resultPtr, string);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2824:14: [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.
int status = system(cmd);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3224:10: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
int sz = vsnprintf(buffer, bufSize, format, args);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3252:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(buf, src);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3277:1: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(buf, src);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3348:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stdout, label, args);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3361:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(pathBuf, path);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:174:15: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define uglyf printf /* debugging printf */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:261:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:268:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:278:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:285:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:294:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:306:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1352:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 3, 4)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1424:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c:157:10: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
sz = vsnprintf(ds->string + ds->stringSize, avail, format, argscp);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.h:62:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:55:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, args);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:138:1: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(fbuf, "%s\n%s", strerror(errno), format);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:222:1: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(fbuf, "%s\n%s", strerror(errno), format);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.h:29:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.h:39:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.h:64:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.h:71:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.h:154:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.c:197:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(n->name, name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:486:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(buf, url);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:2069:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(npu->file, dyQ->string);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:213:6: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(pathName+fileNameOffset, fileName);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:313:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(host, getHost());
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:403:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(excessStart, excessEnd);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:450:1: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(newPath+newLen, s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:586:1: [4] (shell) execvp:
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.
execvp(cmd[0], cmd);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:604:1: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, args);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/oswin9x.c:189:11: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(pathName+fileNameOffset, fileName);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.c:207:1: [4] (shell) execvp:
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.
execvp(proc->cmd[0], proc->cmd);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/tokenizer.h:55:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/verbose.c:26:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(logFile, format, args);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/verbose.h:12:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/verbose.h:27:23: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/r-bioc-rtracklayer-1.50.0/src/utils.c:21:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest, src);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3414:8: [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.
tz=getenv("TZ");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:177:6: [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("ERRASSERT") != NULL) || (getenv("ERRABORT") != NULL))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:177:39: [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("ERRASSERT") != NULL) || (getenv("ERRABORT") != NULL))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1145:18: [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.
char *proxyUrl = getenv("http_proxy");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:262:16: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
hostName = getenv("HTTP_HOST");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:265:13: [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.
hostName = getenv("HOST");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:299:17: [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.
return (host = getenv("MYSQLHOST"));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:432:21: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
char *homeDir = getenv("HOME");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/verbose.c:81:23: [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.
char *emacs = getenv("emacs");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/verbose.c:82:22: [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.
char *term = getenv("TERM");
data/r-bioc-rtracklayer-1.50.0/src/bigBed.c:83:34: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
bigBedIntervalQuery(file, (char *)CHAR(STRING_ELT(r_seqnames, i)),
data/r-bioc-rtracklayer-1.50.0/src/bigBed.c:181:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char startBuf[16], endBuf[16], *row[fieldCount], rgbBuf[8];
data/r-bioc-rtracklayer-1.50.0/src/bigBed.c:282:23: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
hashAddInt(hash, (char *)CHAR(STRING_ELT(names, i)), INTEGER(v)[i]);
data/r-bioc-rtracklayer-1.50.0/src/bigBedHelper.c:53:5: [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 *row[3];
data/r-bioc-rtracklayer-1.50.0/src/bigBedHelper.c:291:1: [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 *line, *row[fieldCount+1];
data/r-bioc-rtracklayer-1.50.0/src/bigWig.c:177:23: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
hashAddInt(hash, (char *)CHAR(STRING_ELT(names, i)), INTEGER(v)[i]);
data/r-bioc-rtracklayer-1.50.0/src/bigWig.c:251:31: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
bigWigIntervalQuery(file, (char *)CHAR(STRING_ELT(r_seqnames, i)),
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:31:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char linebuf[LINEBUF_SIZE];
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:32:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *header[HEADER_SIZE];
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:33:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *data[DATA_SIZE];
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:73:9: [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(block->name, header[2], name_size);
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:82:23: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
atoi(header[1]));
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:89:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
tstart = atoi(header[5]) + 1; /* 0-based -> 1-based */
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:91:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
tstart = atoi(header[3]) - tstart + 2; /* start one too high */
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:92:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
qstart = atoi(header[10]) + 1;
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:94:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
qstart = atoi(header[8]) - qstart + 2;
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:99:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
width = atoi(data[0]);
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:107:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int dt = atoi(data[1]), dq = atoi(data[2]);
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:107:38: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int dt = atoi(data[1]), dq = atoi(data[2]);
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:148:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((stream = fopen(path, "r")) == NULL)
data/r-bioc-rtracklayer-1.50.0/src/handlers.c:8:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char warn_buf[WARN_BUF_SIZE];
data/r-bioc-rtracklayer-1.50.0/src/readGFF.c:31:8: [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 con_buf[25000];
data/r-bioc-rtracklayer-1.50.0/src/readGFF.c:199:2: [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(ae->elts, tag, tag_len);
data/r-bioc-rtracklayer-1.50.0/src/readGFF.c:425:8: [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 errmsg_buf[256];
data/r-bioc-rtracklayer-1.50.0/src/readGFF.c:942:2: [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[IOBUF_SIZE], c;
data/r-bioc-rtracklayer-1.50.0/src/readGFF.c:995:2: [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[IOBUF_SIZE], c;
data/r-bioc-rtracklayer-1.50.0/src/twoBit.c:104:34: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
twoBitReadSeqFrag(file, (char *)CHAR(STRING_ELT(r_seqnames, i)),
data/r-bioc-rtracklayer-1.50.0/src/ucsc/_cheapcgi.c:67:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[4];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/_portimpl.c:20:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char pathCopy[len+1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/asParse.c:105:8: [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 buf[1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/asParse.c:123:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
arraySize = atoi(leftParen+1);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/asParse.c:202:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
col->fixedSize = atoi(tkz->string);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.c:248:1: [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 keyBuf[bpt->keySize], valBuf[bpt->valSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.c:293:5: [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 keyBuf[bpt->keySize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.c:347:1: [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 keyBuf[bpt->keySize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.c:350:5: [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(keyBuf, key, keySize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.c:460:1: [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 keyBuf[keySize+1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bPlusTree.c:512:1: [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 keyBuf[keySize+1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:219:22: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
bl->chromStart = atoi(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:434:1: [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 *row[numFields];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:462:1: [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 *line, *row[bedKnownFields];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:484:1: [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 *line, *row[bedKnownFields];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:727:2: [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 name[50];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:813:5: [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(newBed->blockSizes, bed->blockSizes,
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:816:5: [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(newBed->chromStarts, bed->chromStarts,
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:823:5: [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(newBed->expIds, bed->expIds,
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:826:5: [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(newBed->expScores, bed->expScores,
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:950:1: [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 *chromRow[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:951:1: [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 *row[3] ;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:993:1: [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 dupe[64];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:995:1: [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 *row[4];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1004:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return ( ((atoi(row[0]) & 0xff) << 16) |
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1005:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
((atoi(row[1]) & 0xff) << 8) |
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1006:10: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
(atoi(row[2]) & 0xff) );
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1434:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char colors[4];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1682:1: [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 *row[3];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.h:26:5: [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 strand[2]; /* + or -. */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:97:1: [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 *row[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:176:1: [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 *row[maxRowSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:501:1: [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 uncBuf[uncBufSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:503:1: [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 compBuf[compBufSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:624:2: [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 compBuf[compBufSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:142:1: [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(startBuf, "%u", interval->start);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:143:1: [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(endBuf, "%u", interval->end);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:342:1: [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 fieldString[fieldSize+1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:343:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fieldString, field, fieldSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:463:1: [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 chromName[bbi->chromBpt->keySize+1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bits.c:70:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(bits, orig, byteCount);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bits.c:103:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(bits, orig, byteCount);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:74:1: [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 buf[bufSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:131:5: [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 compBuf[maxCompSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:198:1: [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 *words[1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:277:1: [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 *words[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:399:5: [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 *wordPairs[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:494:5: [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 *words[5];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:1156:2: [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 *words[5];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:18:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newPt, pt, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:27:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(d, s, copySize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:61:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newBuf, a, aLen);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:62:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(newBuf+aLen, b, bLen);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:648:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sn->name, name, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:864:1: [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 del[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1066:1: [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 name[1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1067:1: [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 val[1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1068:1: [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 buf[1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1336:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return (atoi((char *)(a->val)) - atoi((char *)(b->val)));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1336:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return (atoi((char *)(a->val)) - atoi((char *)(b->val)));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1663:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(p,newStr,strlen(newStr));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1854:19: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int diff = atoi(a) - atoi(b);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1854:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int diff = atoi(a) - atoi(b);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2379:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new, line, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2454:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((f = fopen(fileName, mode)) == NULL)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2538:33: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean fastReadString(FILE *f, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2601:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(fileName, flags, mode);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3358:1: [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 pathBuf[PATH_LEN];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3413:5: [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 save_tz[100];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:252:39: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
#define CopyArray(source, dest,count) memcpy(dest,source,(count)*sizeof(dest[0]))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:509:5: [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 name[1]; /* Allocated at run time to length of string. */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1062:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN],
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1062:28: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN],
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1062:48: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN],
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1063:9: [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 extension[FILEEXT_LEN]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1154:33: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean fastReadString(FILE *f, char buf[256]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1235:1: [2] (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, *pPt, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1242:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*pPt, buf, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1433:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
|| atoi(setting) != 0) )
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnaseq.c:34:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(seq->dna, orig->dna, seq->size+1);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:332:1: [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 ntChars[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:352:1: [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 ntMixedCaseChars[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:499:1: [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 choppyCopy[len+1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:501:1: [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 *alleles[len];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:599:26: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
long dnaOrAaFilteredSize(char *raw, char filter[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:599:37: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
long dnaOrAaFilteredSize(char *raw, char filter[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:612:20: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void dnaOrAaFilter(char *in, char *out, char filter[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:612:30: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void dnaOrAaFilter(char *in, char *out, char filter[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:612:41: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void dnaOrAaFilter(char *in, char *out, char filter[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:1088:5: [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 abbreviation[3];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c:87:1: [2] (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+oldSize, string, stringSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:135:1: [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 fbuf[512];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:219:1: [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 fbuf[512];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:355:1: [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 pidStr[64];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/hash.c:92:1: [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 s[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/hash.c:128:5: [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(el->name, name, nameSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.c:96:1: [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 hostnameProto[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.c:156:2: [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 s[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.c:195:2: [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 s[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.c:215:1: [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 sbuf[32768]; // socket buffer sv[1] to user
data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.c:216:1: [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 bbuf[32768]; // bio buffer
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c:81:43: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean internetIpToDottedQuad(bits32 ip, char dottedQuad[17])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c:124:30: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void internetParseDottedQuad(char *dottedQuad, unsigned char quad[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c:124:57: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void internetParseDottedQuad(char *dottedQuad, unsigned char quad[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c:133:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
quad[i] = atoi(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c:138:47: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void internetUnpackIp(bits32 packed, unsigned char unpacked[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c:150:37: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean internetIpInSubnet(unsigned char unpackedIp[4], unsigned char subnet[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.c:150:66: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean internetIpInSubnet(unsigned char unpackedIp[4], unsigned char subnet[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.h:19:43: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean internetIpToDottedQuad(bits32 ip, char dottedQuad[17]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.h:32:30: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void internetParseDottedQuad(char *dottedQuad, unsigned char quad[4]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.h:32:57: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void internetParseDottedQuad(char *dottedQuad, unsigned char quad[4]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.h:35:47: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void internetUnpackIp(bits32 packed, unsigned char unpacked[4]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.h:39:37: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean internetIpInSubnet(unsigned char unpackedIp[4],
data/r-bioc-rtracklayer-1.50.0/src/ucsc/internet.h:40:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char subnet[4]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:23:1: [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 buf[20];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:118:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fd = open(fileName, O_RDONLY)) >= 0)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:228:1: [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 tbiName[tbiNameSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:339:14: [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(fileName, O_RDONLY);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:1014:8: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return atoi(ascii);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:1161:1: [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 errMsg[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:1176:1: [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 errMsg[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:1308:24: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
*contentLength = atoi(code);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.c:126:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(new, pt, oldSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.c:134:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(d, pt, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.c:146:5: [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(s, string, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.c:256:1: [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 cmbEndCookie[4] = {0x44, 0x33, 0x7F, 0x42};
data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.c:291:5: [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 maxAlloc[32];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.c:292:5: [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 allocRequest[32];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.c:306:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pEndCookie, cmbEndCookie, sizeof(cmbEndCookie));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.c:348:5: [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(newBlk, vpt, cmb->size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/memalloc.c:363:1: [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 errMsg[1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:248:33: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return netMustConnect(hostName, atoi(portName));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:292:42: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int netAcceptFrom(int acceptor, unsigned char subnet[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:311:15: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (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 unpacked[4];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:390:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void netParseSubnet(char *in, unsigned char out[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:390:40: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void netParseSubnet(char *in, unsigned char out[4])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:398:5: [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 *words[5];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:409:6: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
x = atoi(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:481:1: [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 buf[1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:494:5: [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(parsed->protocol, "http");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:549:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(parsed->user, "anonymous");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:550:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(parsed->password, "x@genome.ucsc.edu");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:581:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(parsed->port, "80");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:583:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(parsed->port, "443");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:585:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(parsed->port, "21");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:707:2: [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[4*1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:743:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int reply = atoi(startLastLine);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:770:1: [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 *words[7];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:780:10: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
result = atoi(words[4])*256+atoi(words[5]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:780:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
result = atoi(words[4])*256+atoi(words[5]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:788:1: [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 *words[3];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:804:1: [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 *words[3];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:861:1: [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 cmd[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:907:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int sd = openFtpControlSocket(npu.host, atoi(npu.port), npu.user, npu.password);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:910:1: [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 cmd[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:956:1: [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 buf[32768];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:994:1: [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 cmd[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1001:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int sd = openFtpControlSocket(npu.host, atoi(npu.port), npu.user, npu.password);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1100:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
sd = netConnect(npu.host, atoi(npu.port));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1104:36: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
sd = netConnectHttps(npu.host, atoi(npu.port));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1119:5: [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 up[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1241:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
status = atoi(word);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1278:1: [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 rangeUrl[2048];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1309:12: [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).
return open(url, O_RDONLY);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1332:1: [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 buf[4*1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1388:1: [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 buf[2000];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1520:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bre[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1543:5: [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 bre[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1837:1: [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 *netGetString(int sd, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1837:28: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *netGetString(int sd, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.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 sbuf[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1930:1: [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 *netRecieveString(int sd, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1930:32: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *netRecieveString(int sd, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1972:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
sd = netConnect((*npu)->host, atoi((*npu)->port));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1994:5: [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 up[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:42:36: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int netAcceptFrom(int sd, unsigned char subnet[4]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:75:1: [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 *netRecieveString(int sd, char buf[256]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:75:32: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *netRecieveString(int sd, char buf[256]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:87:1: [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 *netGetString(int sd, char buf[256]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:87:28: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *netGetString(int sd, char buf[256]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:111:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void netParseSubnet(char *in, unsigned char out[4]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:111:40: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void netParseSubnet(char *in, unsigned char out[4]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:118:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char protocol[16]; /* Protocol - http or ftp, etc. */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:119:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char user[128]; /* User name (optional) */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:120:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char password[128]; /* Password (optional) */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:121:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char host[128]; /* Name of host computer - www.yahoo.com, etc. */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:122:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char port[16]; /* Port, usually 80 or 8080. */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.h:123:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char file[1024]; /* Remote file name/query string, starts with '/' */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:20:11: [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).
FILE *f = fopen(fileName, "r+b");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:28:9: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of 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(fileName, "wb");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:144:1: [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 *row[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:156:1: [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 *row[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:193:5: [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).
s = open(source, O_RDONLY);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:547:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%lld,%03lld,%03lld,%03lld,%03lld", trillions, billions, millions, thousands, l);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:557:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%lld,%03lld,%03lld,%03lld", billions, millions, thousands, l);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:565:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%lld,%03lld,%03lld", millions, thousands, l);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:571:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%lld,%03lld", thousands, l);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:574:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%lld", l);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:580:1: [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 ascii[32];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:779:1: [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 temp[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:87:8: [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 dir[PATH_LEN];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:196:1: [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 pathName[512];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:200:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pathName, dir, dirNameSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:259:8: [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 buf[128];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:292:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char hostBuf[128];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:312:1: [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 host[512];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:319:8: [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 name[PATH_LEN];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:329:8: [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 fileName[PATH_LEN];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:427:1: [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 newPath[PATH_LEN];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:576:1: [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 *cmd[3], pidStr[32];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:662:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f = fopen(fileName, "w");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/oswin9x.c:79:8: [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 dir[_MAX_PATH];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/oswin9x.c:165:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char pathName[512];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/oswin9x.c:181:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pathName, dir, dirNameSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.c:468:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(fname, O_RDONLY);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.c:482:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(fname, flags, 0666);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.c:575:1: [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 **cmds[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.c:585:1: [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 **cmds[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/pipeline.c:596:1: [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 **cmds[2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/portable.h:31:5: [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 name[1]; /* Allocated at run time. */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/portable.h:92:2: [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 forCgi[128];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/portable.h:93:2: [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 forHtml[128];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/tokenizer.c:174:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(tkz->string, start, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c:50:47: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (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 boolean udcFastReadStringWrap(void *f, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c:81:44: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (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 boolean fastReadStringWrap(void *f, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c:246:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(last4, dna+i, seq->size-i);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c:453:5: [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 name[256];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c:688:5: [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 buf[256*2];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.h:53:43: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean (*ourFastReadString)(void *f, char buf[256]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:174:5: [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 rangeUrl[2048];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:461:46: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean udcFastReadString(struct udcFile *f, char buf[256])
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:484:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(path, file->cacheDir, dirLen);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:486:1: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(path+dirLen+1, fileName, nameLen);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:536:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int fd = open(fileName, O_RDWR);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:740:2: [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(d, "Q%02X", (unsigned)c);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:772:2: [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 auth[1024];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:898:2: [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(&(file->connInfo), &(info.ci), sizeof(struct connInfo));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1013:1: [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 protocol[16];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1024:1: [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 afterProtocol[4096];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1289:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cbuf, file->sparseReadAheadBuf + (start-raStart), sizeInBuf);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1425:1: [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 shortBuf[2], *longBuf = NULL, *buf = shortBuf;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1435:2: [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(newBuf, buf, bufSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1460:1: [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 shortBuf[2], *longBuf = NULL, *buf = shortBuf;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1470:2: [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(newBuf, buf, bufSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.h:152:46: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
boolean udcFastReadString(struct udcFile *f, char buf[256]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/zlibFace.c:34:9: [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 msg[128];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/zlibFace.c:86:1: [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 compBuf[compBufSize];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/zlibFace.c:88:1: [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 uncBuf[uncSize];
data/r-bioc-rtracklayer-1.50.0/src/bigBed.c:323:24: [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).
mustWrite(f, asText, strlen(asText) + 1);
data/r-bioc-rtracklayer-1.50.0/src/bigBedHelper.c:15:44: [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).
if (strncmp(asCol->name, bedCol->name, strlen(asCol->name)) == 0)
data/r-bioc-rtracklayer-1.50.0/src/bigBedHelper.c:148:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(keyBuf,item->name, maxBedNameSize);
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:42:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(linebuf) == LINEBUF_SIZE - 1) {
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:50:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (!strlen(linebuf)) {
data/r-bioc-rtracklayer-1.50.0/src/chain_io.c:69:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int name_size = strlen(header[2])+1;
data/r-bioc-rtracklayer-1.50.0/src/twoBit.c:13:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
struct dnaSeq *seq = newDnaSeq((DNA *)dna, strlen(dna),
data/r-bioc-rtracklayer-1.50.0/src/ucsc/_portimpl.c:19:13: [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(pathName);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/_portimpl.c:50:13: [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(name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/asParse.c:136:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int typeLen = strlen(buf);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/base64.c:64:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
l = strlen(p);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/base64.c:92:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t inplen = strlen(input);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:769:1: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:805:1: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(newBed->strand, bed->strand, sizeof(bed->strand));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:997:1: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(dupe, itemRgb, sizeof(dupe));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1369:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(bed->chrom) >= BB_MAX_CHROM_STRING) // must leave room for 0 terminator
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1371:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(bed->chrom) < 1)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1384:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(bed->name) > 255)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1398:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (!isCt && strlen(row[5]) > 1)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1618:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(row[i]) > 255)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/basicBed.c:1619:117: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
lineFileAbort(lf, "expecting length (%llu) of string (%s) not to exceed 255 in field %s", (unsigned long long)strlen(row[i]), row[i], asCol->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiRead.c:185:40: [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 (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiRead.c:230:40: [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 (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiRead.c:503:40: [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 (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:64:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(chromName);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bbiWrite.c:164:16: [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).
int size = strlen(row[rowIx]);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:95:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int restLen = strlen(blockPt);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:271:8: [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).
name, strlen(name), sizeof(struct offsetSize));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:289:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
name, strlen(name), sizeof(struct offsetSize));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:321:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
end = line + strlen(line);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bigBed.c:333:8: [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).
return strlen(name) == fieldSize && memcmp(name, field, fieldSize) == 0;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:606:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(chromName);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:656:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(el->name) > maxChromNameSize)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/bwgCreate.c:657:22: [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).
maxChromNameSize = strlen(el->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:35:27: [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).
return cloneStringZExt(s, strlen(s), size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:44:8: [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).
size = strlen(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:51:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t size = strlen(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:58:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int aLen = strlen(a), bLen = strlen(b);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:58:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int aLen = strlen(a), bLen = strlen(b);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:632:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:871:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len += strlen(el->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1115:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(name)<1)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1174:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
count += strlen(pair->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1175:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
count += strlen((char *)(pair->val));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1191:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (pair = list; pair != NULL; pair = pair->next, strPtr += strlen(strPtr))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1207:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strPtr += strlen(strPtr);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1234:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
count += strlen(pair->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1245:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (pair = list; pair != NULL; pair = pair->next, strPtr += strlen(strPtr))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1405:11: [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(firstWord);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1422:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char c = line[strlen(firstWord)];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1437:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (ix == strlen(word))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1458:13: [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 nSize = strlen(needle);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1460:23: [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).
for (pos = haystack + strlen(haystack) - nSize; pos >= haystack; pos -= 1)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1477:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pos = p + strlen(start);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1493:8: [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).
sLen = strlen(string);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1494:8: [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).
eLen = strlen(end);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1506:10: [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).
return s[strlen(s)-1];
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1512:11: [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(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1523:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char *sPos = s + (strlen(s) - 1);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1613:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int oldLen = strlen(old);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1614:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int newLen = strlen(new);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1626:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strLen = max(strlen(string) + (numTimes * (newLen - oldLen)), strlen(string));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1626:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strLen = max(strlen(string) + (numTimes * (newLen - oldLen)), strlen(string));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1654:48: [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).
for(p=strstr(string,oldStr);p!=NULL;p=strstr(p+strlen(oldStr),oldStr))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1658:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if((strlen(string)+(count*(strlen(newStr) - strlen(oldStr))))>=sz)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1658:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if((strlen(string)+(count*(strlen(newStr) - strlen(oldStr))))>=sz)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1658:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if((strlen(string)+(count*(strlen(newStr) - strlen(oldStr))))>=sz)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1660:48: [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).
for(p=strstr(string,oldStr);p!=NULL;p=strstr(p+strlen(newStr),oldStr))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1662:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memmove(p+strlen(newStr),p+strlen(oldStr),strlen(p+strlen(oldStr))+1); // NULL at end is also moved!
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1662:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memmove(p+strlen(newStr),p+strlen(oldStr),strlen(p+strlen(oldStr))+1); // NULL at end is also moved!
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1662:47: [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).
memmove(p+strlen(newStr),p+strlen(oldStr),strlen(p+strlen(oldStr))+1); // NULL at end is also moved!
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1662:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memmove(p+strlen(newStr),p+strlen(oldStr),strlen(p+strlen(oldStr))+1); // NULL at end is also moved!
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1663:21: [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).
memcpy(p,newStr,strlen(newStr));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1713:22: [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 (inout == NULL || strlen(inout) < 2 || *inout != encloser)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1716:22: [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).
char *end = inout + (strlen(inout) - 1);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1728:30: [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).
return memmove(inout,inout+1,strlen(inout)); // use memmove to safely copy in place
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:1735:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int stripSize = strlen(strip);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2150:11: [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(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2390:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*line += strlen(new);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2404:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*pStrings += strlen(p)+1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2499:11: [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(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2628:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
actualSize = read(fd, cbuf, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2680:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int size = strlen(head) + strlen(suffix) +1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:2680:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int size = strlen(head) + strlen(suffix) +1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3123:15: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (((ch = getc(fh)) != EOF) && (ch != '\n'))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3191:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
haystackLen = strlen(haystack);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3192:13: [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).
needleLen = strlen(needle);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3249:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t slen = strlen(src);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3266:1: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, src, n);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3273:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t blen = strlen(buf);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3274:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t slen = strlen(src);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3283:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t blen = strlen(buf);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3286:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t slen = strlen(src);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.c:3289:1: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(buf, src, n);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:884:50: [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).
#define strSwapChar(s,old,new) memSwapChar((s),strlen(s),(old),(new))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:885:50: [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).
#define subChar(s,old,new) (void)memSwapChar((s),strlen(s),(old),(new))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/common.h:1132:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
#define readOneFd(fd, var) (read((fd), &(var), sizeof(var)) == sizeof(var))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:319:11: [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).
dnaSize = strlen(dna);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:498:11: [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(alleleStr);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dnautil.c:508:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int alLen = strlen(allele);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c:122:29: [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).
dyStringAppendN(ds, string, strlen(string));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c:183:11: [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(format) * 3;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c:196:13: [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 inLen = strlen(in), outLen = strlen(out), origLen = strlen(orig);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c:196:34: [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).
int inLen = strlen(in), outLen = strlen(out), origLen = strlen(orig);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/dystring.c:196:57: [1] (buffer) strlen:
Does not handle 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 inLen = strlen(in), outLen = strlen(out), origLen = strlen(orig);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:116:23: [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).
strings[1] += strlen(strings[1]) + 1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/errAbort.c:331:34: [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).
write(STDERR_FILENO, errMsg, strlen(errMsg));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/hash.c:151:29: [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).
return hashAddN(hash, name, strlen(name), val);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/htmlColor.c:75:21: [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 (*code != '#' || strlen(code) != 7)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/https.c:267:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
srd = read(params->sv[1], sbuf, 32768);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:49:42: [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).
cgiDecode(fileName, fileNameDecoded, strlen(fileName));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:121:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((bytesread=read(fd,result,numbytes)) < numbytes)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:205:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
lf->bufSize = lf->bytesInBuf = strlen(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:227:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int tbiNameSize = strlen(fileOrUrl) + strlen(".tbi") + 1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:227:39: [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).
int tbiNameSize = strlen(fileOrUrl) + strlen(".tbi") + 1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:270:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tabixSeqId = ti_get_tid(lf->tabix->idx, seqName+strlen("chr"));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:404:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
oneSize = read(fd, buf, size);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:467:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int lineSize = strlen(line);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/linefile.c:813:23: [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).
end = start + strlen(start);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.c:157:39: [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).
return lmCloneStringZ(lm, string, strlen(string));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/localmem.c:195:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int size = sizeof(*n) + strlen(name) + 1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:363:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
oneRead = read(sd, buf + totalRead, size - totalRead);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:484:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(url) >= sizeof(buf))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:510:5: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(parsed->file, "/");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:532:31: [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).
cgiDecodeFull(u,parsed->file,strlen(u)); // decodes %FF but not +
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:544:2: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(parsed->user, "");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:545:2: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(parsed->password, "");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:561:2: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy(parsed->password, "");
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:570:41: [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).
cgiDecode(parsed->user,parsed->user,strlen(parsed->user));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:571:49: [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).
cgiDecode(parsed->password,parsed->password,strlen(parsed->password));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:691:22: [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).
mustWriteFd(sd, cmd, strlen(cmd));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:713:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((readSize = read(sd, buf, sizeof(buf))) == 0)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:722:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
startLastLine = rs->string+strlen(rs->string)-1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:730:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(startLastLine)>4)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:809:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(words[1]) < strlen(EXPECTED_MDTM_FORMAT))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:809:24: [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 (strlen(words[1]) < strlen(EXPECTED_MDTM_FORMAT))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:961:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((rd = read(params->sdata, buf, 32768)) > 0)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1024:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
safef(cmd,sizeof(cmd),"%s %s\r\n",((npu.file[strlen(npu.file)-1]) == '/') ? "LIST" : "RETR", npu.file);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1122:30: [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).
b64up = base64Encode(up, strlen(up));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1337:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((readSize = read(sd, buf, sizeof(buf))) > 0)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1419:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nread = read(sd, &c, 1); /* one char at a time, but http headers are small */
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1685:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cgiDecode(url, urlDecoded, strlen(url));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1766:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int length = strlen(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1788:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned length = strlen(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1814:24: [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).
unsigned long length = strlen(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/net.c:1997:30: [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).
b64up = base64Encode(up, strlen(up));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:202:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((bytesRead = read(s, buf, bufSize)) > 0)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:217:13: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(inFh)) != EOF)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:233:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
readSize = read(s, buf, bufSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:394:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int newSize = strlen(in) + countChars(in, toEscape);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:404:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int newSize = 2 + strlen(in) + countChars(in, quoteChar);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/obscure.c:805:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int nameLen = strlen(name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:194:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int dirNameSize = strlen(dir);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:278:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, hostName, sizeof(buf));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:411:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(path);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:445:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
newLen = strlen(newPath);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:447:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int remainingLen = strlen(s);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:455:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int lastPos = strlen(newPath)-1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/osunix.c:535:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read(STDIN_FILENO,&c,1) != 1)
data/r-bioc-rtracklayer-1.50.0/src/ucsc/oswin9x.c:163:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int dirNameSize = strlen(dir);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/sqlList.c:1204:1: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, sqlGetOptQuoteString(pS), bufSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c:338:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int nameLen = strlen(twoBit->name);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/twoBit.c:511:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (!bptFileFind(tbf->bpt, name, strlen(name), &offset, sizeof(offset)))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:136:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssize_t rd = read(sd, buf, chunkSize);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:354:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((remaining > 0) && ((rd = read(sd, buf, remaining)) > 0))
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:481:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int dirLen = strlen(file->cacheDir);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:482:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int nameLen = strlen(fileName);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:779:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
afterHost = afterProtocol+strlen(afterProtocol);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:803:11: [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(cacheDir) + 1 + strlen(protocol) + 1 + strlen(afterProtocol) + 1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:803:34: [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).
int len = strlen(cacheDir) + 1 + strlen(protocol) + 1 + strlen(afterProtocol) + 1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:803:57: [1] (buffer) strlen:
Does not handle 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(cacheDir) + 1 + strlen(protocol) + 1 + strlen(afterProtocol) + 1;
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1010:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
offset = strlen(cacheDir);
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1014:1: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(protocol, path+offset, sizeof(protocol));
data/r-bioc-rtracklayer-1.50.0/src/ucsc/udc.c:1025:16: [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).
qDecode(path+1+strlen(protocol)+1, afterProtocol, sizeof(afterProtocol));
data/r-bioc-rtracklayer-1.50.0/src/utils.c:14:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len += strlen(CHAR(STRING_ELT(x, i))) + 1;
data/r-bioc-rtracklayer-1.50.0/src/utils.c:20:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int src_len = strlen(src);
ANALYSIS SUMMARY:
Hits = 523
Lines analyzed = 39615 in approximately 1.12 seconds (35500 lines/second)
Physical Source Lines of Code (SLOC) = 28003
Hits@level = [0] 75 [1] 176 [2] 275 [3] 10 [4] 62 [5] 0
Hits@level+ = [0+] 598 [1+] 523 [2+] 347 [3+] 72 [4+] 62 [5+] 0
Hits/KSLOC@level+ = [0+] 21.3549 [1+] 18.6766 [2+] 12.3915 [3+] 2.57115 [4+] 2.21405 [5+] 0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.