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-bitseq-1.34.0+dfsg/src/ArgumentParser.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/ArgumentParser.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/CollapsedSampler.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/CollapsedSampler.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/FileHeader.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/FileHeader.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/GibbsParameters.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/GibbsParameters.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/GibbsSampler.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/GibbsSampler.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/MyTimer.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/MyTimer.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/R_init_BitSeq.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/Rhtslib_bam_plbuf.c
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/Rhtslib_sam.c
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/Sampler.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/Sampler.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/SimpleSparse.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/SimpleSparse.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TagAlignments.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TagAlignments.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptExpression.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptExpression.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptInfo.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptInfo.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptSequence.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptSequence.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/asa103/asa103.hpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/common.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/common.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/estimateExpression.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/estimateHyperPar.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/estimateVBExpression.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/getGeneExpression.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/getVariance.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/getWithinGeneExpression.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/lowess.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/lowess.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/misc.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/misc.h
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/parseAlignment.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/transposeFiles.cpp
Examining data/r-bioc-bitseq-1.34.0+dfsg/src/transposeFiles.h

FINAL RESULTS:

data/r-bioc-bitseq-1.34.0+dfsg/src/common.h:29:22:  [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 message(...) printf(__VA_ARGS__)
data/r-bioc-bitseq-1.34.0+dfsg/src/common.h:30:24:  [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 messageF(...) {printf(__VA_ARGS__);fflush(stdout);}
data/r-bioc-bitseq-1.34.0+dfsg/src/common.h:32:51:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define warning(...) {fprintf(stderr,"WARNING: ");fprintf(stderr, __VA_ARGS__);}
data/r-bioc-bitseq-1.34.0+dfsg/src/common.h:33:47:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define error(...) {fprintf(stderr,"ERROR: ");fprintf(stderr, __VA_ARGS__);}
data/r-bioc-bitseq-1.34.0+dfsg/src/Sampler.h:27:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::mt11213b rng_mt;
data/r-bioc-bitseq-1.34.0+dfsg/src/Sampler.h:28:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::gamma_distribution<double> gammaDistribution;
data/r-bioc-bitseq-1.34.0+dfsg/src/Sampler.h:29:19:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   typedef boost::random::gamma_distribution<double>::param_type gDP;
data/r-bioc-bitseq-1.34.0+dfsg/src/Sampler.h:31:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::uniform_01<double> uniformDistribution;
data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.cpp:19:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
typedef boost::random::gamma_distribution<double>::param_type gDP;
data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.cpp:56:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::normal_distribution<long double> normalD;
data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.cpp:346:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::gamma_distribution<double> gammaDistribution;
data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.h:27:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::mt11213b rng_mt;
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:91:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::mt11213b rng_mt(ns_misc::getSeed(args));
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:92:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::gamma_distribution<long double> gammaDistribution;
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:93:19:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   typedef boost::random::gamma_distribution<long double>::param_type gDP;
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:94:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   boost::random::normal_distribution<long double> normalDistribution;
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:95:19:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   typedef boost::random::normal_distribution<long double>::param_type nDP;
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateHyperPar.cpp:115:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::mt11213b rng_mt(ns_misc::getSeed(args));
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateHyperPar.cpp:116:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::uniform_01<long double> uniformDistribution;
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateHyperPar.cpp:117:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::normal_distribution<long double> normalDistributionA,normalDistributionB;
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateHyperPar.cpp:118:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      typedef boost::random::normal_distribution<long double>::param_type nDP;
data/r-bioc-bitseq-1.34.0+dfsg/src/ArgumentParser.cpp:120:33:  [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).
               mapL[names[opt]]=atoi(val.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/GibbsParameters.cpp:42:4:  [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 tmp[256];
data/r-bioc-bitseq-1.34.0+dfsg/src/GibbsParameters.cpp:43:10:  [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).
   pFile.open(paramFileName.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.cpp:29:24:  [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).
bool PosteriorSamples::open(string fileName){//{{{
data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.cpp:31:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
   samplesF.open(fileName.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.cpp:41:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
   if(! open(fileName))return false;
data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.h:21:12:  [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).
      bool open(string fileName);
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:426:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
   outF.open(logFileName.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptInfo.cpp:19:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
   trF.open(fileName.c_str(),ios::out | ios::trunc);
data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptInfo.cpp:29:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
   geF.open(fileName.c_str(),ios::out | ios::trunc);
data/r-bioc-bitseq-1.34.0+dfsg/src/TranscriptSequence.cpp:27:11:  [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).
   fastaF.open(fileName.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.cpp:83:28:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      if(vals!=phi_sm->val)memcpy(phi_sm->val,vals,T*sizeof(double));
data/r-bioc-bitseq-1.34.0+dfsg/src/VariationalBayes.cpp:231:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(phiOld,phi_sm->val,T*sizeof(double)); // memcpy(phiOld,pack(),T*sizeof(double));
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:215:22:  [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).
         outFiles[c].open(fileName.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:231:19:  [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).
      outFiles[C].open(varFileName.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateDE.cpp:244:10:  [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).
   outF->open(outFileName.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateExpression.cpp:51:11:  [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).
   inFile.open(args.args()[0].c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateExpression.cpp:426:28:  [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).
            samplesFile[j].open(samplesFileNames[j].c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateExpression.cpp:442:14:  [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).
   meansFile.open((args.getS("outFilePrefix")+".thetaMeans").c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/estimateVBExpression.cpp:28:11:  [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).
   inFile.open(args.args()[0].c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/misc.cpp:51:10:  [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).
   outF->open(args.getS("outFileName").c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/misc.cpp:59:10:  [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).
   outF->open(name.c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/misc.cpp:153:15:  [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).
      mapFile.open(args.getS("trMapFile").c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/misc.cpp:156:15:  [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).
      mapFile.open(args.getS("geneListFile").c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/parseAlignment.cpp:443:12:  [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).
      outF.open(args.getS("failed").c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/transposeFiles.cpp:30:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      inFile[i].open(inFileNames[i].c_str());
data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.cpp:51:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
   return read();
data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.cpp:53:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool PosteriorSamples::read(){//{{{
data/r-bioc-bitseq-1.34.0+dfsg/src/PosteriorSamples.h:22:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bool read();
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:750:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
double ReadDistribution::getPosBias(long start, long end, readT read, long trLen) const { //{{{
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:771:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
double ReadDistribution::getSeqBias(long pos, readT read, long tid) const{ //{{{
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:802:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
double ReadDistribution::getSeqBias(long start, long end, readT read, const string &fSeq) const{ //{{{
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:830:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
double ReadDistribution::getWeightNorm(long len, readT read, long tid){ //{{{
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:832:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
   if(weightNorms[read][tid].count(len) == 0){
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:842:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
         w = getPosBias(pos, pos + len, read, trLen) *
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:843:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
             getSeqBias(pos, pos + len, read, trS);
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:846:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      weightNorms[read][tid][len] = norm;
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.cpp:850:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
   return weightNorms[read][tid][len];
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.h:108:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      double getPosBias(long start, long end, ns_rD::readT read,
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.h:110:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      double getSeqBias(long pos, ns_rD::readT read, long tid) const;
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.h:112:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      double getSeqBias(long start, long end, ns_rD::readT read,
data/r-bioc-bitseq-1.34.0+dfsg/src/ReadDistribution.h:115:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      double getWeightNorm(long len, ns_rD::readT read, long tid);

ANALYSIS SUMMARY:

Hits = 63
Lines analyzed = 8342 in approximately 0.26 seconds (32237 lines/second)
Physical Source Lines of Code (SLOC) = 6499
Hits@level = [0]   2 [1]  16 [2]  26 [3]  17 [4]   4 [5]   0
Hits@level+ = [0+]  65 [1+]  63 [2+]  47 [3+]  21 [4+]   4 [5+]   0
Hits/KSLOC@level+ = [0+] 10.0015 [1+] 9.6938 [2+] 7.23188 [3+] 3.23127 [4+] 0.615479 [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.