Author: tille Date: 2012-04-03 09:13:59 +0000 (Tue, 03 Apr 2012) New Revision: 10269
Removed: trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch Modified: trunk/packages/mothur/trunk/debian/changelog trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch trunk/packages/mothur/trunk/debian/patches/makefile.patch trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch trunk/packages/mothur/trunk/debian/patches/series Log: Upload new upstream version with adapted patches Modified: trunk/packages/mothur/trunk/debian/changelog =================================================================== --- trunk/packages/mothur/trunk/debian/changelog 2012-04-03 09:00:32 UTC (rev 10268) +++ trunk/packages/mothur/trunk/debian/changelog 2012-04-03 09:13:59 UTC (rev 10269) @@ -1,3 +1,12 @@ +mothur (1.24.1-1) unstable; urgency=low + + * New upstream version + - adpated patches + - droped debian/patches/kfreebsd.patch because it was applied + upstream + + -- Andreas Tille <[email protected]> Tue, 03 Apr 2012 09:05:44 +0200 + mothur (1.23.1-1) unstable; urgency=low * New upstream version (including updating patches) Modified: trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch =================================================================== --- trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch 2012-04-03 09:00:32 UTC (rev 10268) +++ trunk/packages/mothur/trunk/debian/patches/drop_sse_option.patch 2012-04-03 09:13:59 UTC (rev 10269) @@ -2,8 +2,8 @@ Date: Thu, 10 Nov 2011 00:39:01 UTC Closes: #648255 Description: Fix for FTBFS: cc1plus: error: unrecognized command line option '-msse2' ---- mothur-1.23.1.orig/uchime_src/mk -+++ mothur-1.23.1/uchime_src/mk +--- mothur-1.24.1.orig/uchime_src/mk ++++ mothur-1.24.1/uchime_src/mk @@ -7,7 +7,7 @@ for CPPName in $CPPNames do Deleted: trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch =================================================================== --- trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch 2012-04-03 09:00:32 UTC (rev 10268) +++ trunk/packages/mothur/trunk/debian/patches/kfreebsd.patch 2012-04-03 09:13:59 UTC (rev 10269) @@ -1,910 +0,0 @@ -Authors: Christoph Egger <[email protected]>, Robert Millan <[email protected]>, Andreas Tille <[email protected]> -Date: Tue, 29 Nov 2011 22:50:55 +0100 -Closes: #650683 -Description: Enable build on BSD machines - Remark: This patch can be recreated by doing the following - cp -a mothur-<version> mothur-<version>.orig - cd mothur-<version> - sed -i 's/^\(#if defined.*\)(linux) || (__linux)\(.*\)$/\1(__unix__)\2/' *.h *.cpp - cd .. - diff -ubrN mothur-<version>.orig mothur-<version> > kfreebsd.patch - Andreas Tille <[email protected]> ---- mothur-1.23.1.orig/aligncommand.cpp -+++ mothur-1.23.1/aligncommand.cpp -@@ -826,7 +826,7 @@ - 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-1.23.1.orig/aligncommand.h -+++ mothur-1.23.1/aligncommand.h -@@ -120,7 +120,7 @@ - }; - - /**************************************************************************************************/ --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){ - alignData* pDataArray; ---- mothur-1.23.1.orig/bellerophon.cpp -+++ mothur-1.23.1/bellerophon.cpp -@@ -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-1.23.1.orig/blastdb.cpp -+++ mothur-1.23.1/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"; ---- mothur-1.23.1.orig/chimeraccodecommand.cpp -+++ mothur-1.23.1/chimeraccodecommand.cpp -@@ -611,7 +611,7 @@ - - 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-1.23.1.orig/chimeracheckcommand.cpp -+++ mothur-1.23.1/chimeracheckcommand.cpp -@@ -599,7 +599,7 @@ - - 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-1.23.1.orig/chimeraperseuscommand.cpp -+++ mothur-1.23.1/chimeraperseuscommand.cpp -@@ -762,7 +762,7 @@ - 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-1.23.1.orig/chimeraperseuscommand.h -+++ mothur-1.23.1/chimeraperseuscommand.h -@@ -98,7 +98,7 @@ - } - }; - /**************************************************************************************************/ --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){ - perseusData* pDataArray; ---- mothur-1.23.1.orig/chimerapintailcommand.cpp -+++ mothur-1.23.1/chimerapintailcommand.cpp -@@ -697,7 +697,7 @@ - - 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-1.23.1.orig/chimeraslayercommand.cpp -+++ mothur-1.23.1/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 -@@ -594,7 +594,7 @@ - #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(linePair(positions[i], positions[(i+1)])); } - #else -@@ -1187,7 +1187,7 @@ - m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine(); - - lines.clear(); --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - int proc = 1; - vector<unsigned long long> positions = m->divideFile(thisFastaName, proc); - lines.push_back(linePair(positions[0], positions[1])); -@@ -1244,7 +1244,7 @@ - breakUp.push_back(thisFileToPriority); - } - --#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(); -@@ -1628,7 +1628,7 @@ - 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) { - int pid = fork(); ---- mothur-1.23.1.orig/chimeraslayercommand.h -+++ mothur-1.23.1/chimeraslayercommand.h -@@ -172,7 +172,7 @@ - }; - - /**************************************************************************************************/ --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){ - slayerData* pDataArray; ---- mothur-1.23.1.orig/chimerauchimecommand.cpp -+++ mothur-1.23.1/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"; -@@ -1005,7 +1005,7 @@ - path = path.substr(0, (tempPath.find_last_of('m'))); - - string uchimeCommand = path; --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - uchimeCommand += "uchime "; - #else - uchimeCommand += "uchime"; -@@ -1243,7 +1243,7 @@ - - //uchime_main(numArgs, uchimeParameters); - //cout << "commandString = " << commandString << endl; --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - commandString = "\"" + commandString + "\""; - #endif -@@ -1309,7 +1309,7 @@ - int num = 0; - vector<string> files; - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - //break up file into multiple files - m->divideFile(filename, processors, files); - -@@ -1492,7 +1492,7 @@ - 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-1.23.1.orig/chimerauchimecommand.h -+++ mothur-1.23.1/chimerauchimecommand.h -@@ -141,7 +141,7 @@ - }; - - /**************************************************************************************************/ --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){ - uchimeData* pDataArray; -@@ -189,7 +189,7 @@ - path = path.substr(0, (tempPath.find_last_of('m'))); - - string uchimeCommand = path; --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - uchimeCommand += "uchime "; - #else - uchimeCommand += "uchime"; -@@ -403,7 +403,7 @@ - - //uchime_main(numArgs, uchimeParameters); - //cout << "commandString = " << commandString << endl; --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - commandString = "\"" + commandString + "\""; - #endif ---- mothur-1.23.1.orig/classifyseqscommand.cpp -+++ mothur-1.23.1/classifyseqscommand.cpp -@@ -594,7 +594,7 @@ - #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 -@@ -791,7 +791,7 @@ - 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 ---- mothur-1.23.1.orig/classifyseqscommand.h -+++ mothur-1.23.1/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-1.23.1.orig/distancecommand.cpp -+++ mothur-1.23.1/distancecommand.cpp -@@ -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(); - ---- mothur-1.23.1.orig/distancecommand.h -+++ mothur-1.23.1/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-1.23.1.orig/filterseqscommand.cpp -+++ mothur-1.23.1/filterseqscommand.cpp -@@ -598,7 +598,7 @@ - - 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(); -@@ -954,7 +954,7 @@ - - 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-1.23.1.orig/indicatorcommand.cpp -+++ mothur-1.23.1/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-1.23.1.orig/mothur.h -+++ mothur-1.23.1/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-1.23.1.orig/mothurout.cpp -+++ mothur-1.23.1/mothurout.cpp -@@ -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('.'); -@@ -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")) { -@@ -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")) { ---- mothur-1.23.1.orig/myseqdist.cpp -+++ mothur-1.23.1/myseqdist.cpp -@@ -46,7 +46,7 @@ - /**************************************************************************************************/ - int correctDist::execute(string distanceFileName){ - try { --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - processors = 1; - #endif -@@ -146,7 +146,7 @@ - - int correctDist::createProcess(string distanceFileName){ - try { --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - int process = 1; - vector<int> processIDs; - ---- mothur-1.23.1.orig/myutils.cpp -+++ mothur-1.23.1/myutils.cpp -@@ -11,7 +11,7 @@ - #include <signal.h> - #include <float.h> - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #include <sys/time.h> - #include <sys/resource.h> - #include <unistd.h> -@@ -139,7 +139,7 @@ - return isatty(fd) != 0; - } - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - //#ifdef BIT_VERSION - //#include <io.h> -@@ -176,7 +176,7 @@ - Log("fpos %ld (retval %d)\n", (long) fpos, fgetpos_retval); - // Log("eof %d\n", _eof(fd)); - #endif --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - #ifdef BIT_VERSION - __int64 pos64 = _ftelli64(f); -@@ -612,7 +612,7 @@ - fprintf(stderr, "\n---Fatal error---\n%s\n", szStr); - Log("\n---Fatal error---\n%s\n", szStr); - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - //if (IsDebuggerPresent()) - // __debugbreak(); -@@ -1205,7 +1205,7 @@ - g_Opts.insert(Opt); - } - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - #pragma warning(disable: 4505) // unreferenced local function - #endif ---- mothur-1.23.1.orig/pairwiseseqscommand.cpp -+++ mothur-1.23.1/pairwiseseqscommand.cpp -@@ -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-1.23.1.orig/parsimony.cpp -+++ mothur-1.23.1/parsimony.cpp -@@ -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-1.23.1.orig/pintail.cpp -+++ mothur-1.23.1/pintail.cpp -@@ -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-1.23.1.orig/preclustercommand.cpp -+++ mothur-1.23.1/preclustercommand.cpp -@@ -299,7 +299,7 @@ - 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-1.23.1.orig/preclustercommand.h -+++ mothur-1.23.1/preclustercommand.h -@@ -113,7 +113,7 @@ - }; - - /**************************************************************************************************/ --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){ - preClusterData* pDataArray; ---- mothur-1.23.1.orig/rarefact.cpp -+++ mothur-1.23.1/rarefact.cpp -@@ -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-1.23.1.orig/screenseqscommand.cpp -+++ mothur-1.23.1/screenseqscommand.cpp -@@ -664,7 +664,7 @@ - vector<int> ambigBases; - vector<int> longHomoPolymer; - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - vector<unsigned long long> positions = m->divideFile(fastafile, processors); - - for (int i = 0; i < (positions.size()-1); i++) { -@@ -808,7 +808,7 @@ - /**************************************************************************************************/ - 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(); -@@ -1270,7 +1270,7 @@ - - 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-1.23.1.orig/seqerrorcommand.cpp -+++ mothur-1.23.1/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) { -@@ -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-1.23.1.orig/seqsummarycommand.cpp -+++ mothur-1.23.1/seqsummarycommand.cpp -@@ -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-1.23.1.orig/seqsummarycommand.h -+++ mothur-1.23.1/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-1.23.1.orig/shhhercommand.cpp -+++ mothur-1.23.1/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) { -@@ -1555,7 +1555,7 @@ - void ShhherCommand::calcCentroids(){ - try{ - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - - if(processors == 1) { - calcCentroidsDriver(0, numOTUs); -@@ -1828,7 +1828,7 @@ - void ShhherCommand::calcNewDistances(){ - try{ - --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - - if(processors == 1) { - calcNewDistancesParent(0, numSeqs); ---- mothur-1.23.1.orig/shhhercommand.h -+++ mothur-1.23.1/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-1.23.1.orig/shhhseqscommand.cpp -+++ mothur-1.23.1/shhhseqscommand.cpp -@@ -358,7 +358,7 @@ - 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-1.23.1.orig/shhhseqscommand.h -+++ mothur-1.23.1/shhhseqscommand.h -@@ -97,7 +97,7 @@ - }; - - /**************************************************************************************************/ --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){ - shhhseqsData* pDataArray; ---- mothur-1.23.1.orig/summaryqualcommand.cpp -+++ mothur-1.23.1/summaryqualcommand.cpp -@@ -157,7 +157,7 @@ - if (namefile != "") { nameMap = m->readNames(namefile); } - - vector<unsigned long long> positions; --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - positions = m->divideFile(qualfile, processors); - for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); } - #else -@@ -262,7 +262,7 @@ - count += num; - } - --#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 -@@ -286,7 +286,7 @@ - int numSeqs = 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-1.23.1.orig/summaryqualcommand.h -+++ mothur-1.23.1/summaryqualcommand.h -@@ -84,7 +84,7 @@ - }; - - /**************************************************************************************************/ --#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) -+#if defined (__APPLE__) || (__MACH__) || (__unix__) - #else - static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){ - seqSumQualData* pDataArray; ---- mothur-1.23.1.orig/trimflowscommand.cpp -+++ mothur-1.23.1/trimflowscommand.cpp -@@ -447,7 +447,7 @@ - //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; } -@@ -688,7 +688,7 @@ - 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-1.23.1.orig/trimflowscommand.h -+++ mothur-1.23.1/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-1.23.1.orig/trimseqscommand.cpp -+++ mothur-1.23.1/trimseqscommand.cpp -@@ -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(); ---- mothur-1.23.1.orig/unifracweightedcommand.cpp -+++ mothur-1.23.1/unifracweightedcommand.cpp -@@ -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-1.23.1.orig/unweighted.cpp -+++ mothur-1.23.1/unweighted.cpp -@@ -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; - -@@ -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-1.23.1.orig/weighted.cpp -+++ mothur-1.23.1/weighted.cpp -@@ -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; - Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch =================================================================== --- trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-04-03 09:00:32 UTC (rev 10268) +++ trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-04-03 09:13:59 UTC (rev 10269) @@ -1,8 +1,8 @@ Author: Steffen Moeller <[email protected]> Purpose: Comment MAC specific option ---- mothur-1.23.1.orig/makefile -+++ mothur-1.23.1/makefile -@@ -27,7 +27,7 @@ +--- mothur-1.24.1.orig/makefile ++++ mothur-1.24.1/makefile +@@ -28,7 +28,7 @@ #CXX = g++44 #if you are a mac user use the following line Modified: trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch =================================================================== --- trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch 2012-04-03 09:00:32 UTC (rev 10268) +++ trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch 2012-04-03 09:13:59 UTC (rev 10269) @@ -1,9 +1,9 @@ Author: Andreas Tille <[email protected]> Date: 2011-01-30 Dscription: There is no need to link against lncurses because its symbols are not used ---- mothur-1.23.1.orig/makefile -+++ mothur-1.23.1/makefile -@@ -60,8 +60,7 @@ +--- mothur-1.24.1.orig/makefile ++++ mothur-1.24.1/makefile +@@ -63,8 +63,7 @@ ifeq ($(strip $(USEREADLINE)),yes) CXXFLAGS += -DUSE_READLINE LIBS = \ Modified: trunk/packages/mothur/trunk/debian/patches/series =================================================================== --- trunk/packages/mothur/trunk/debian/patches/series 2012-04-03 09:00:32 UTC (rev 10268) +++ trunk/packages/mothur/trunk/debian/patches/series 2012-04-03 09:13:59 UTC (rev 10269) @@ -1,4 +1,3 @@ makefile.patch no_lcurses.patch drop_sse_option.patch -kfreebsd.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
