diff options
Diffstat (limited to 'sci-biology/mothur/files/mothur-1.27.0-overflows.patch')
-rw-r--r-- | sci-biology/mothur/files/mothur-1.27.0-overflows.patch | 93 |
1 files changed, 93 insertions, 0 deletions
diff --git a/sci-biology/mothur/files/mothur-1.27.0-overflows.patch b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch new file mode 100644 index 000000000000..0b612cf7b529 --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch @@ -0,0 +1,93 @@ + chimerauchimecommand.cpp | 2 +- + clearcutcommand.cpp | 32 ++++++++++++++++---------------- + 2 files changed, 17 insertions(+), 17 deletions(-) + +diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp +index bd31c19..2070840 100644 +--- a/chimerauchimecommand.cpp ++++ b/chimerauchimecommand.cpp +@@ -1264,7 +1264,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc + } + + if (ucl) { +- char* tempucl = new char[5]; ++ char* tempucl = new char[6]; + strcpy(tempucl, "--ucl"); + cPara.push_back(tempucl); + } +diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp +index 6a0eb25..2e8164e 100644 +--- a/clearcutcommand.cpp ++++ b/clearcutcommand.cpp +@@ -269,35 +269,35 @@ int ClearcutCommand::execute() { + + vector<char*> cPara; + +- char* tempClearcut = new char[8]; ++ char* tempClearcut = new char[16]; + strcpy(tempClearcut, "clearcut"); + cPara.push_back(tempClearcut); + + //you gave us a distance matrix +- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); } ++ if (phylipfile != "") { char* temp = new char[16]; strcpy(temp, "--distance"); cPara.push_back(temp); } + + //you gave us a fastafile +- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); } ++ if (fastafile != "") { char* temp = new char[16]; strcpy(temp, "--alignment"); cPara.push_back(temp); } + +- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); } +- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); } +- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); } ++ if (version) { char* temp = new char[16]; strcpy(temp, "--version"); cPara.push_back(temp); } ++ if (verbose) { char* temp = new char[16]; strcpy(temp, "--verbose"); cPara.push_back(temp); } ++ if (quiet) { char* temp = new char[16]; strcpy(temp, "--quiet"); cPara.push_back(temp); } + if (seed != "*") { + string tempSeed = "--seed=" + seed; + char* temp = new char[tempSeed.length()]; + strcpy(temp, tempSeed.c_str()); + cPara.push_back(temp); + } +- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); } +- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } +- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } ++ if (norandom) { char* temp = new char[16]; strcpy(temp, "--norandom"); cPara.push_back(temp); } ++ if (shuffle) { char* temp = new char[16]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } ++ if (neighbor) { char* temp = new char[16]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } + + string tempIn = "--in=" + inputFile; + char* tempI = new char[tempIn.length()]; + strcpy(tempI, tempIn.c_str()); + cPara.push_back(tempI); + +- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); } ++ if (stdoutWanted) { char* temp = new char[16]; strcpy(temp, "--stdout"); cPara.push_back(temp); } + else{ + string tempOut = "--out=" + outputName; + +@@ -306,10 +306,10 @@ int ClearcutCommand::execute() { + cPara.push_back(temp); + } + +- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); } +- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); } +- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); } +- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); } ++ if (DNA) { char* temp = new char[16]; strcpy(temp, "--DNA"); cPara.push_back(temp); } ++ if (protein) { char* temp = new char[16]; strcpy(temp, "--protein"); cPara.push_back(temp); } ++ if (jukes) { char* temp = new char[16]; strcpy(temp, "--jukes"); cPara.push_back(temp); } ++ if (kimura) { char* temp = new char[16]; strcpy(temp, "--kimura"); cPara.push_back(temp); } + if (matrixout != "") { + string tempMatrix = "--matrixout=" + outputDir + matrixout; + char* temp = new char[tempMatrix.length()]; +@@ -326,8 +326,8 @@ int ClearcutCommand::execute() { + cPara.push_back(temp); + } + +- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); } +- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); } ++ if (expblen) { char* temp = new char[16]; strcpy(temp, "--expblen"); cPara.push_back(temp); } ++ if (expdist) { char* temp = new char[16]; strcpy(temp, "--expdist"); cPara.push_back(temp); } + + char** clearcutParameters; + clearcutParameters = new char*[cPara.size()]; |