[med-svn] r10269 - in trunk/packages/mothur/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Apr 3 09:13:59 UTC 2012
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 <tille at debian.org> 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 <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
- 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 <tille at debian.org>
---- 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 <moeller at debian.org>
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 <tille at debian.org>
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
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