[med-svn] r8792 - in trunk/packages/mothur/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Dec 6 16:34:23 UTC 2011
Author: tille
Date: 2011-12-06 16:34:23 +0000 (Tue, 06 Dec 2011)
New Revision: 8792
Added:
trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch
Modified:
trunk/packages/mothur/trunk/debian/changelog
trunk/packages/mothur/trunk/debian/control
trunk/packages/mothur/trunk/debian/patches/series
trunk/packages/mothur/trunk/debian/rules
Log:
Patch to build on any UNIX (incl. BSD)
Modified: trunk/packages/mothur/trunk/debian/changelog
===================================================================
--- trunk/packages/mothur/trunk/debian/changelog 2011-12-06 16:27:39 UTC (rev 8791)
+++ trunk/packages/mothur/trunk/debian/changelog 2011-12-06 16:34:23 UTC (rev 8792)
@@ -1,3 +1,15 @@
+mothur (1.22.2-2) unstable; urgency=low
+
+ * debian/patches/kfreebsd.patch: Enable build on BSD machines
+ (thanks to Christoph Egger <christoph at debian.org> and Robert
+ Millan <rmh at debian.org>)
+ Closes: #650683
+ * debian/control: Fixed Vcs fields
+ * debian/{control,rules}: drop explicite quilt dependency which is
+ just given by source format 3.0 (quilt)
+
+ -- Andreas Tille <tille at debian.org> Tue, 06 Dec 2011 17:14:49 +0100
+
mothur (1.22.2~repack-ubuntu1) lucid; urgency=low
* Backport for Ubuntu
Modified: trunk/packages/mothur/trunk/debian/control
===================================================================
--- trunk/packages/mothur/trunk/debian/control 2011-12-06 16:27:39 UTC (rev 8791)
+++ trunk/packages/mothur/trunk/debian/control 2011-12-06 16:34:23 UTC (rev 8792)
@@ -5,11 +5,11 @@
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Tim Booth <tbooth at ceh.ac.uk>
-Build-Depends: debhelper (>= 8), libreadline-dev, quilt
+Build-Depends: debhelper (>= 8), libreadline-dev
Standards-Version: 3.9.2
Homepage: http://www.mothur.org
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mothur/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mothur/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mothur/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mothur/trunk/
Package: mothur
Architecture: any
Added: trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch (rev 0)
+++ trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch 2011-12-06 16:34:23 UTC (rev 8792)
@@ -0,0 +1,1393 @@
+Authors: Christoph Egger <christoph at debian.org>, Robert Millan <rmh at debian.org>, Andreas Tille <tille at debian.org>
+Date: Tue, 29 Nov 2011 22:50:55 +0100
+Closes: #650683
+Description: Enable build on BSD machines
+--- mothur-1.22.2.orig/classifyseqscommand.h
++++ mothur-1.22.2/classifyseqscommand.h
+@@ -128,7 +128,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
+ classifyData* pDataArray;
+--- mothur-1.22.2.orig/parsimony.cpp
++++ mothur-1.22.2/parsimony.cpp
+@@ -54,7 +54,7 @@
+ }
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ }else{
+@@ -91,7 +91,7 @@
+
+ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDS;
+
+--- mothur-1.22.2.orig/classifyseqscommand.cpp
++++ mothur-1.22.2/classifyseqscommand.cpp
+@@ -383,7 +383,7 @@
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ //this is so the threads can quickly load the reference data
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ if ((processors != 1) && (rdb->referenceSeqs.size() == 0)) { save = true; }
+ #endif
+@@ -599,7 +599,7 @@
+ #else
+
+ vector<unsigned long long> positions;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ positions = m->divideFile(fastaFileNames[s], processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
+ #else
+@@ -796,7 +796,7 @@
+ int num = 0;
+ processIDS.clear();
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ //loop through and create all the processes you want
+@@ -965,7 +965,7 @@
+ }
+ delete candidateSeq;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+--- mothur-1.22.2.orig/chimerauchimecommand.cpp
++++ mothur-1.22.2/chimerauchimecommand.cpp
+@@ -461,7 +461,7 @@
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+ string uchimeCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ uchimeCommand = path + "uchime"; // format the database, -o option gives us the ability
+ #else
+ uchimeCommand = path + "uchime.exe";
+@@ -543,7 +543,7 @@
+ if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); }
+ int totalSeqs = 0;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1) { totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); }
+ else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups); }
+ #else
+@@ -563,7 +563,7 @@
+
+ int numSeqs = 0;
+ int numChimeras = 0;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
+ else{ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
+ #else
+@@ -990,7 +990,7 @@
+ vector<char*> cPara;
+
+ char* tempUchime;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ tempUchime= new char[10];
+ *tempUchime = '\0';
+ strncat(tempUchime, "./uchime ", 9);
+@@ -1286,7 +1286,7 @@
+ processIDS.clear();
+ int process = 1;
+ int num = 0;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //break up file into multiple files
+ vector<string> files;
+ m->divideFile(filename, processors, files);
+@@ -1389,7 +1389,7 @@
+ lines.push_back(linePair(startIndex, endIndex));
+ }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+--- mothur-1.22.2.orig/trimseqscommand.cpp
++++ mothur-1.22.2/trimseqscommand.cpp
+@@ -363,7 +363,7 @@
+ }
+ if(qFileName == "") { qLines = lines; } //files with duds
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
+ }else{
+@@ -723,7 +723,7 @@
+ count++;
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= line->end)) { break; }
+
+@@ -758,7 +758,7 @@
+
+ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ int exitCommand = 1;
+ processIDS.clear();
+@@ -942,7 +942,7 @@
+
+ int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos) {
+ try {
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //set file positions for fasta file
+ fastaFilePos = m->divideFile(filename, processors);
+
+--- mothur-1.22.2.orig/mothurout.cpp
++++ mothur-1.22.2/mothurout.cpp
+@@ -143,7 +143,7 @@
+
+ //add / to name if needed
+ string lastChar = pathname.substr(pathname.length()-1);
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (lastChar != "/") { pathname += "/"; }
+ #else
+ if (lastChar != "\\") { pathname += "\\"; }
+@@ -332,7 +332,7 @@
+ //
+ // On failure, returns 0.0, 0.0
+ int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ vm_usage = 0.0;
+ resident_set = 0.0;
+@@ -504,7 +504,7 @@
+ }
+ /***********************************************************************/
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #ifdef USE_COMPRESSION
+ inline bool endsWith(string s, const char * suffix){
+ size_t suffixLength = strlen(suffix);
+@@ -518,7 +518,7 @@
+
+ string rootName = longName;
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #ifdef USE_COMPRESSION
+ if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
+ int pos = rootName.find_last_of('.');
+@@ -673,7 +673,7 @@
+
+ string cwd;
+ //get current working directory
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ if (path.find("~") != -1) { //go to home directory
+ string homeDir;
+@@ -796,7 +796,7 @@
+ try {
+ //get full path name
+ string completeFileName = getFullPathName(fileName);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #ifdef USE_COMPRESSION
+ // check for gzipped or bzipped file
+ if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+@@ -842,7 +842,7 @@
+
+ //get full path name
+ string completeFileName = getFullPathName(fileName);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #ifdef USE_COMPRESSION
+ // check for gzipped or bzipped file
+ if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+@@ -893,7 +893,7 @@
+ int exist = openInputFile(newName, inTest, "");
+ inTest.close();
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (exist == 0) { //you could open it so you want to delete it
+ string command = "rm " + newName;
+ system(command.c_str());
+@@ -920,7 +920,7 @@
+ try {
+
+ string completeFileName = getFullPathName(fileName);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #ifdef USE_COMPRESSION
+ // check for gzipped file
+ if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+@@ -996,7 +996,7 @@
+
+
+ //if you can, use the unix sort since its been optimized for years
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ string command = "sort -n -k +3 " + distFile + " -o " + outfile;
+ system(command.c_str());
+ #else //you are stuck with my best attempt...
+--- mothur-1.22.2.orig/setdircommand.cpp
++++ mothur-1.22.2/setdircommand.cpp
+@@ -114,7 +114,7 @@
+ }else {
+ //add / to name if needed
+ string lastChar = output.substr(output.length()-1);
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (lastChar != "/") { output += "/"; }
+ #else
+ if (lastChar != "\\") { output += "\\"; }
+@@ -146,7 +146,7 @@
+ }else {
+ //add / to name if needed
+ string lastChar = input.substr(input.length()-1);
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (lastChar != "/") { input += "/"; }
+ #else
+ if (lastChar != "\\") { input += "\\"; }
+@@ -188,7 +188,7 @@
+ }else {
+ //add / to name if needed
+ string lastChar = tempdefault.substr(tempdefault.length()-1);
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (lastChar != "/") { tempdefault += "/"; }
+ #else
+ if (lastChar != "\\") { tempdefault += "\\"; }
+--- mothur-1.22.2.orig/pintail.cpp
++++ mothur-1.22.2/pintail.cpp
+@@ -74,7 +74,7 @@
+ #ifdef USE_MPI
+ //do nothing
+ #else
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //find breakup of templatefile for quantiles
+ if (processors == 1) { templateLines.push_back(new linePair(0, templateSeqs.size())); }
+ else {
+@@ -529,7 +529,7 @@
+ //**************************************************************************************************
+ void Pintail::createProcessesQuan() {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDS;
+
+--- mothur-1.22.2.orig/chimeraccodecommand.cpp
++++ mothur-1.22.2/chimeraccodecommand.cpp
+@@ -397,7 +397,7 @@
+ }
+
+ //break up file
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+
+ numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
+@@ -521,7 +521,7 @@
+ }
+ delete candidateSeq;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -608,7 +608,7 @@
+
+ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int num = 0;
+
+--- mothur-1.22.2.orig/seqerrorcommand.cpp
++++ mothur-1.22.2/seqerrorcommand.cpp
+@@ -293,7 +293,7 @@
+ if(qualFileName == "") { qLines = lines; rLines = lines; } //fills with duds
+
+ int numSeqs = 0;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
+ }else{
+@@ -361,7 +361,7 @@
+ processIDS.clear();
+ map<char, vector<int> >::iterator it;
+ int num = 0;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+@@ -734,7 +734,7 @@
+
+ index++;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = queryFile.tellg();
+ if ((pos == -1) || (pos >= line.end)) { break; }
+ #else
+@@ -1210,7 +1210,7 @@
+
+ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos, vector<unsigned long long>& rfileFilePos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //set file positions for fasta file
+ fastaFilePos = m->divideFile(filename, processors);
+
+--- mothur-1.22.2.orig/filterseqscommand.cpp
++++ mothur-1.22.2/filterseqscommand.cpp
+@@ -425,7 +425,7 @@
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
+ numSeqs += numFastaSeqs;
+@@ -567,7 +567,7 @@
+ count++;
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -595,7 +595,7 @@
+
+ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int num = 0;
+ processIDS.clear();
+@@ -741,7 +741,7 @@
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
+ numSeqs += numFastaSeqs;
+@@ -876,7 +876,7 @@
+ count++;
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -948,7 +948,7 @@
+
+ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ int num = 0;
+ processIDS.clear();
+--- mothur-1.22.2.orig/trimflowscommand.h
++++ mothur-1.22.2/trimflowscommand.h
+@@ -130,7 +130,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
+ trimFlowData* pDataArray;
+--- mothur-1.22.2.orig/distancecommand.h
++++ mothur-1.22.2/distancecommand.h
+@@ -53,7 +53,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
+ distanceData* pDataArray;
+--- mothur-1.22.2.orig/indicatorcommand.cpp
++++ mothur-1.22.2/indicatorcommand.cpp
+@@ -1120,7 +1120,7 @@
+ try {
+ vector<float> pvalues;
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+@@ -1234,7 +1234,7 @@
+ try {
+ vector<float> pvalues;
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+--- mothur-1.22.2.orig/seqsummarycommand.cpp
++++ mothur-1.22.2/seqsummarycommand.cpp
+@@ -282,7 +282,7 @@
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ #else
+ vector<unsigned long long> positions;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ positions = m->divideFile(fastafile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
+ #else
+@@ -429,7 +429,7 @@
+ outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -525,7 +525,7 @@
+ int num = 0;
+ processIDS.clear();
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+--- mothur-1.22.2.orig/clustersplitcommand.cpp
++++ mothur-1.22.2/clustersplitcommand.cpp
+@@ -559,7 +559,7 @@
+ //sanity check
+ if (processors > distName.size()) { processors = distName.size(); }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
+ }else{
+@@ -907,7 +907,7 @@
+ int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> > > dividedNames){
+ try {
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int exitCommand = 1;
+ processIDS.clear();
+--- mothur-1.22.2.orig/formatphylip.cpp
++++ mothur-1.22.2/formatphylip.cpp
+@@ -96,7 +96,7 @@
+ string outfile = m->getRootName(tempFile) + "sorted.dist.temp";
+
+ //use the unix sort
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ string command = "sort -n " + tempFile + " -o " + outfile;
+ system(command.c_str());
+ #else //sort using windows sort
+--- mothur-1.22.2.orig/mothur.h
++++ mothur-1.22.2/mothur.h
+@@ -53,7 +53,7 @@
+ #endif
+ /***********************************************************************/
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #include <sys/wait.h>
+ #include <sys/time.h>
+ #include <sys/resource.h>
+--- mothur-1.22.2.orig/engine.cpp
++++ mothur-1.22.2/engine.cpp
+@@ -34,7 +34,7 @@
+
+ //delimiting path char
+ char delim;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ delim = ':';
+ #else
+ delim = ';';
+@@ -56,7 +56,7 @@
+
+ if (mothurPath != "") {
+ //add mothur so it looks like what argv would look like
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ mothurPath += "/mothur";
+ #else
+ mothurPath += "\\mothur";
+@@ -71,7 +71,7 @@
+ //is this mothurs path?
+ ifstream in;
+ string tempIn = dirs[i];
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ tempIn += "/mothur";
+ #else
+ tempIn += "\\mothur";
+@@ -217,7 +217,7 @@
+ string Engine::getCommand() {
+ try {
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #ifdef USE_READLINE
+ char* nextCommand = NULL;
+ nextCommand = readline("mothur > ");
+--- mothur-1.22.2.orig/bellerophon.cpp
++++ mothur-1.22.2/bellerophon.cpp
+@@ -314,7 +314,7 @@
+ #else
+
+ //divide breakpoints between processors
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ lines.push_back(linePair(0, iters));
+
+@@ -356,7 +356,7 @@
+
+ int Bellerophon::createProcesses(vector<int> mid) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int exitCommand = 1;
+ vector<int> processIDS;
+--- mothur-1.22.2.orig/aligncommand.h
++++ mothur-1.22.2/aligncommand.h
+@@ -118,7 +118,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
+ alignData* pDataArray;
+--- mothur-1.22.2.orig/catchallcommand.cpp
++++ mothur-1.22.2/catchallcommand.cpp
+@@ -176,7 +176,7 @@
+
+ savedOutputDir = outputDir;
+ string catchAllCommandExe = "";
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
+ if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
+ #else
+@@ -224,7 +224,7 @@
+
+ //create system command
+ string catchAllCommand = "";
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+@@ -269,7 +269,7 @@
+
+ //create system command
+ string catchAllCommand = "";
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+@@ -334,7 +334,7 @@
+
+ //create system command
+ string catchAllCommand = "";
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
+ #else
+ if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
+--- mothur-1.22.2.orig/shhhercommand.cpp
++++ mothur-1.22.2/shhhercommand.cpp
+@@ -1211,7 +1211,7 @@
+ string ShhherCommand::createDistFile(int processors){
+ try{
+ //////////////////////// until I figure out the shared memory issue //////////////////////
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ processors=1;
+ #endif
+@@ -1239,7 +1239,7 @@
+ end[i] = int(sqrt(float(i+1)/float(processors)) * numUniques);
+ }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+@@ -1556,7 +1556,7 @@
+ void ShhherCommand::calcCentroids(){
+ try{
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ if(processors == 1) {
+ calcCentroidsDriver(0, numOTUs);
+@@ -1829,7 +1829,7 @@
+ void ShhherCommand::calcNewDistances(){
+ try{
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ if(processors == 1) {
+ calcNewDistancesParent(0, numSeqs);
+--- mothur-1.22.2.orig/seqsummarycommand.h
++++ mothur-1.22.2/seqsummarycommand.h
+@@ -96,7 +96,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
+ seqSumData* pDataArray;
+--- mothur-1.22.2.orig/metastatscommand.cpp
++++ mothur-1.22.2/metastatscommand.cpp
+@@ -233,7 +233,7 @@
+ if (numGroups == 2) { processors = 1; }
+ else if (numGroups < 2) { m->mothurOut("Not enough sets, I need at least 2 valid sets. Unable to complete command."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors != 1){
+ int numPairs = namesOfGroupCombos.size();
+ int numPairsPerProcessor = numPairs / processors;
+@@ -339,7 +339,7 @@
+ int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
+ try {
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ driver(0, namesOfGroupCombos.size(), thisLookUp);
+ }else{
+--- mothur-1.22.2.orig/distancecommand.cpp
++++ mothur-1.22.2/distancecommand.cpp
+@@ -380,7 +380,7 @@
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ #else
+
+- //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ //#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //if you don't need to fork anything
+ if(processors == 1){
+ if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
+@@ -507,7 +507,7 @@
+ /**************************************************************************************************/
+ void DistanceCommand::createProcesses(string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ processIDS.clear();
+
+@@ -1014,7 +1014,7 @@
+ string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
+
+ //use the unix sort
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ string command = "sort -n " + outputFile + " -o " + outfile;
+ system(command.c_str());
+ #else //sort using windows sort
+@@ -1102,7 +1102,7 @@
+ string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
+
+ //use the unix sort
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ string command = "sort -n " + outputFile + " -o " + outfile;
+ system(command.c_str());
+ #else //sort using windows sort
+--- mothur-1.22.2.orig/aligncommand.cpp
++++ mothur-1.22.2/aligncommand.cpp
+@@ -248,7 +248,7 @@
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ //this is so the threads can quickly load the reference data
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ if (processors != 1) { save = true; }
+ #endif
+@@ -427,7 +427,7 @@
+ #else
+
+ vector<unsigned long long> positions;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ positions = m->divideFile(candidateFileNames[s], processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
+ #else
+@@ -622,7 +622,7 @@
+ }
+ delete candidateSeq;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -831,7 +831,7 @@
+ try {
+ int num = 0;
+ processIDS.resize(0);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ //loop through and create all the processes you want
+--- mothur-1.22.2.orig/pairwiseseqscommand.cpp
++++ mothur-1.22.2/pairwiseseqscommand.cpp
+@@ -444,7 +444,7 @@
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ #else
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //if you don't need to fork anything
+ if(processors == 1){
+ if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
+@@ -535,7 +535,7 @@
+ /**************************************************************************************************/
+ void PairwiseSeqsCommand::createProcesses(string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ processIDS.clear();
+
+--- mothur-1.22.2.orig/rarefact.cpp
++++ mothur-1.22.2/rarefact.cpp
+@@ -24,7 +24,7 @@
+ if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
+ else { increment = percentFreq; }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ driver(rcd, increment, nIters);
+ }else{
+@@ -114,7 +114,7 @@
+
+ int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ vector<int> processIDS;
+--- mothur-1.22.2.orig/matrixoutputcommand.cpp
++++ mothur-1.22.2/matrixoutputcommand.cpp
+@@ -459,7 +459,7 @@
+ vector<SharedRAbundVector*> subset;
+ vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size()); //one for each calc, this will be used to make .dist files
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ driver(thisLookup, 0, numGroups, calcDists);
+ }else{
+--- mothur-1.22.2.orig/unifracweightedcommand.cpp
++++ mothur-1.22.2/unifracweightedcommand.cpp
+@@ -337,7 +337,7 @@
+
+ lines.clear();
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors != 1){
+ int numPairs = namesOfGroupCombos.size();
+ int numPairsPerProcessor = numPairs / processors;
+@@ -356,7 +356,7 @@
+ //get scores for random trees
+ for (int j = 0; j < iters; j++) {
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
+ }else{
+@@ -454,7 +454,7 @@
+
+ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector< vector<double> >& scores) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDS;
+
+--- mothur-1.22.2.orig/summarysharedcommand.cpp
++++ mothur-1.22.2/summarysharedcommand.cpp
+@@ -511,7 +511,7 @@
+ vector< vector<seqDist> > calcDists; //vector containing vectors that contains the summary results for each group compare
+ calcDists.resize(sumCalculators.size()); //one for each calc, this will be used to make .dist files
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
+ m->appendFiles((sumFileName + ".temp"), sumFileName);
+--- mothur-1.22.2.orig/chimeraslayercommand.cpp
++++ mothur-1.22.2/chimeraslayercommand.cpp
+@@ -495,14 +495,14 @@
+ else {
+ //add / to name if needed
+ string lastChar = blastlocation.substr(blastlocation.length()-1);
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (lastChar != "/") { blastlocation += "/"; }
+ #else
+ if (lastChar != "\\") { blastlocation += "\\"; }
+ #endif
+ blastlocation = m->getFullPathName(blastlocation);
+ string formatdbCommand = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ formatdbCommand = blastlocation + "formatdb";
+ #else
+ formatdbCommand = blastlocation + "formatdb.exe";
+@@ -515,7 +515,7 @@
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
+
+ string blastCommand = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ blastCommand = blastlocation + "megablast";
+ #else
+ blastCommand = blastlocation + "megablast.exe";
+@@ -533,7 +533,7 @@
+ if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+
+ //until we resolve the issue 10-18-11
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ processors=1;
+ #endif
+@@ -644,7 +644,7 @@
+ //create chimera here if you are mac or linux because fork will copy for you. Create in create processes instead if you are windows.
+ if (processors == 1) { templateSeqsLength = setupChimera(thisFastaName, thisPriority); }
+ else {
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
++ #if defined (__APPLE__) || (__MACH__) || (__unix__) || USE_MPI
+ templateSeqsLength = setupChimera(thisFastaName, thisPriority);
+ #endif
+ }
+@@ -657,7 +657,7 @@
+ #else
+ //break up file
+ vector<unsigned long long> positions;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ positions = m->divideFile(thisFastaName, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
+ #else
+@@ -687,7 +687,7 @@
+
+ #endif
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || USE_MPI
++ #if defined (__APPLE__) || (__MACH__) || (__unix__) || USE_MPI
+ delete chimera;
+ #endif
+
+@@ -1197,7 +1197,7 @@
+ count++;
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -1358,7 +1358,7 @@
+ int numNoParents = 0;
+ processIDS.clear();
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+--- mothur-1.22.2.orig/screenseqscommand.cpp
++++ mothur-1.22.2/screenseqscommand.cpp
+@@ -390,7 +390,7 @@
+
+ #else
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
+
+@@ -645,7 +645,7 @@
+ }
+
+ int numSeqs = 0;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ }else{
+@@ -723,7 +723,7 @@
+ count++;
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -744,7 +744,7 @@
+ /**************************************************************************************************/
+ int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ int num = 0;
+ processIDS.clear();
+@@ -1049,7 +1049,7 @@
+ count++;
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -1156,7 +1156,7 @@
+
+ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int num = 0;
+
+--- mothur-1.22.2.orig/chimeraslayercommand.h
++++ mothur-1.22.2/chimeraslayercommand.h
+@@ -135,7 +135,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
+ slayerData* pDataArray;
+--- mothur-1.22.2.orig/weighted.cpp
++++ mothur-1.22.2/weighted.cpp
+@@ -34,7 +34,7 @@
+ }
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ }else{
+@@ -69,7 +69,7 @@
+
+ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDS;
+
+--- mothur-1.22.2.orig/chimeracheckcommand.cpp
++++ mothur-1.22.2/chimeracheckcommand.cpp
+@@ -431,7 +431,7 @@
+ }
+
+ //break up file
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
+
+@@ -519,7 +519,7 @@
+ }
+ delete candidateSeq;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -596,7 +596,7 @@
+
+ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int num = 0;
+
+--- mothur-1.22.2.orig/blastdb.cpp
++++ mothur-1.22.2/blastdb.cpp
+@@ -24,7 +24,7 @@
+ int randNumber = rand();
+ //int randNumber = 12345;
+ string pid = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ pid += getpid();
+ #else
+ pid += toString(threadID);
+@@ -42,7 +42,7 @@
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ path += "blast/bin/";
+ #else
+ path += "blast\\bin\\";
+@@ -51,7 +51,7 @@
+
+
+ string formatdbCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
+ #else
+ formatdbCommand = path + "formatdb.exe";
+@@ -64,7 +64,7 @@
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
+ #else
+ blastCommand = path + "blastall.exe";
+@@ -80,7 +80,7 @@
+
+
+ string megablastCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+ #else
+ megablastCommand = path + "megablast.exe";
+@@ -114,7 +114,7 @@
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ path += "blast/bin/";
+ #else
+ path += "blast\\bin\\";
+@@ -123,7 +123,7 @@
+
+ int randNumber = rand();
+ string pid = "";
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ pid += getpid();
+ #else
+ pid += toString(threadID);
+@@ -134,7 +134,7 @@
+ blastFileName = pid + toString(randNumber) + ".blast";
+
+ string formatdbCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
+ #else
+ formatdbCommand = path + "formatdb.exe";
+@@ -149,7 +149,7 @@
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
+ #else
+ blastCommand = path + "blastall.exe";
+@@ -165,7 +165,7 @@
+
+
+ string megablastCommand;
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+ #else
+ megablastCommand = path + "megablast.exe";
+@@ -226,7 +226,7 @@
+ // long. With this setting, it seems comparable in speed to the suffix tree approach.
+
+ string blastCommand;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+
+ blastCommand = path + "blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
+@@ -289,7 +289,7 @@
+ // long. With this setting, it seems comparable in speed to the suffix tree approach.
+ //7000004128189528left 0 100 66 0 0 1 66 61 126 1e-31 131
+ string blastCommand;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ blastCommand = path + "megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
+ #else
+@@ -363,7 +363,7 @@
+
+ string formatdbCommand;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ formatdbCommand = path + "formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ #else
+ //formatdbCommand = path + "blast\\bin\\formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+--- mothur-1.22.2.orig/unweighted.cpp
++++ mothur-1.22.2/unweighted.cpp
+@@ -48,7 +48,7 @@
+ }
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ }else{
+@@ -83,7 +83,7 @@
+
+ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDS;
+
+@@ -291,7 +291,7 @@
+ }
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+ }else{
+@@ -326,7 +326,7 @@
+
+ EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+ vector<int> processIDS;
+
+--- mothur-1.22.2.orig/chimerapintailcommand.cpp
++++ mothur-1.22.2/chimerapintailcommand.cpp
+@@ -493,7 +493,7 @@
+ }
+
+ //break up file
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+
+ numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
+@@ -609,7 +609,7 @@
+ }
+ delete candidateSeq;
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+@@ -695,7 +695,7 @@
+
+ int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ try {
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 0;
+ int num = 0;
+
+--- mothur-1.22.2.orig/formatcolumn.cpp
++++ mothur-1.22.2/formatcolumn.cpp
+@@ -82,7 +82,7 @@
+ string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
+
+ //use the unix sort
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ string command = "sort -n " + squareFile + " -o " + outfile;
+ system(command.c_str());
+ #else //sort using windows sort
+--- mothur-1.22.2.orig/shhhercommand.h
++++ mothur-1.22.2/shhhercommand.h
+@@ -160,7 +160,7 @@
+ };
+
+ /**************************************************************************************************/
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #else
+ static DWORD WINAPI MyflowDistParentForkThreadFunction(LPVOID lpParam){
+ flowDistParentForkData* pDataArray;
+--- mothur-1.22.2.orig/mothur.cpp
++++ mothur-1.22.2/mothur.cpp
+@@ -46,7 +46,7 @@
+
+ m->setFileName(logFileName);
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ system("clear");
+ #else
+ system("CLS");
+@@ -57,7 +57,7 @@
+
+ //add / to name if needed
+ string lastChar = temp.substr(temp.length()-1);
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if (lastChar != "/") { temp += "/"; }
+ #else
+ if (lastChar != "\\") { temp += "\\"; }
+@@ -88,7 +88,7 @@
+
+ if (outputHeader) {
+ //version
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ #if defined (__APPLE__) || (__MACH__)
+ m->mothurOutJustToLog("Mac version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+--- mothur-1.22.2.orig/phylodiversitycommand.cpp
++++ mothur-1.22.2/phylodiversitycommand.cpp
+@@ -348,7 +348,7 @@
+ if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) { numSampledList.insert(diversity[mGroups[j]].size()-1); }
+ }
+
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ if(processors == 1){
+ driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
+ }else{
+@@ -398,7 +398,7 @@
+ //**********************************************************************************************************************
+ int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum){
+ try {
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ vector<int> processIDS;
+--- mothur-1.22.2.orig/endiannessmacros.h
++++ mothur-1.22.2/endiannessmacros.h
+@@ -125,7 +125,7 @@
+ * out at over 2-times faster than iswap_int4 above.
+ */
+ #if 0
+-#if defined(__linux__)
++#if defined(__GLIBC____)
+ # include <byteswap.h>
+ # undef iswap_int8
+ # undef iswap_int4
+--- mothur-1.22.2.orig/trimflowscommand.cpp
++++ mothur-1.22.2/trimflowscommand.cpp
+@@ -226,7 +226,7 @@
+ }
+
+ vector<unsigned long long> flowFilePos;
+- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++ #if defined (__APPLE__) || (__MACH__) || (__unix__)
+ flowFilePos = getFlowFileBreaks();
+ for (int i = 0; i < (flowFilePos.size()-1); i++) {
+ lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
+@@ -445,7 +445,7 @@
+ //report progress
+ if((count) % 10000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ unsigned long long pos = flowFile.tellg();
+
+ if ((pos == -1) || (pos >= line->end)) { break; }
+@@ -686,7 +686,7 @@
+ processIDS.clear();
+ int exitCommand = 1;
+
+-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
++#if defined (__APPLE__) || (__MACH__) || (__unix__)
+ int process = 1;
+
+ //loop through and create all the processes you want
+--- mothur-1.22.2.orig/uchime_src/myutils.cpp
++++ mothur-1.22.2/uchime_src/myutils.cpp
+@@ -635,7 +635,7 @@
+ g_PeakMemUseBytes = Bytes;
+ return Bytes;
+ }
+-#elif linux || __linux__
++#elif defined(__unix__)
+ double GetMemUseBytes()
+ {
+ static char statm[64];
Modified: trunk/packages/mothur/trunk/debian/patches/series
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/series 2011-12-06 16:27:39 UTC (rev 8791)
+++ trunk/packages/mothur/trunk/debian/patches/series 2011-12-06 16:34:23 UTC (rev 8792)
@@ -1,3 +1,4 @@
makefile.patch
no_lcurses.patch
drop_sse_option.patch
+kfreebsd.patch
Modified: trunk/packages/mothur/trunk/debian/rules
===================================================================
--- trunk/packages/mothur/trunk/debian/rules 2011-12-06 16:27:39 UTC (rev 8791)
+++ trunk/packages/mothur/trunk/debian/rules 2011-12-06 16:34:23 UTC (rev 8792)
@@ -8,7 +8,7 @@
ARCHBITS ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH_BITS)
%:
- dh $@ --with quilt
+ dh $@
override_dh_auto_build:
if [ $(ARCHBITS) -eq 64 ] ; then \
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