[med-svn] [mothur] 04/07: Upstream applied most of the patches
Andreas Tille
tille at debian.org
Sat May 7 21:40:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mothur.
commit 0f316cd8e1322fd66b772de922ed6cab9fba134a
Author: Andreas Tille <tille at debian.org>
Date: Sat May 7 17:49:12 2016 +0200
Upstream applied most of the patches
---
...link-uchime-statically-and-don-t-strip-it.patch | 33 ----
.../patches/0002-Some-spelling-corrections.patch | 174 ---------------------
...link-against-lncurses-no-symbols-are-used.patch | 22 ---
...FS-cc1plus-error-unrecognized-command-lin.patch | 25 ---
.../0005-Don-t-redirect-anything-to-dev-tty.patch | 22 ---
...-off-unportable-optimizations-in-makefile.patch | 42 -----
debian/patches/0008-Fix-catchall-command.patch | 4 +-
.../patches/0009-Fix-boost_iostreams-flags.patch | 30 ----
...0010-Pass-hardening-flags-to-uchime-build.patch | 55 -------
.../0011-Don-t-hardcode-mpic-as-the-compiler.patch | 24 ---
debian/patches/series | 9 --
11 files changed, 1 insertion(+), 439 deletions(-)
diff --git a/debian/patches/0001-Don-t-link-uchime-statically-and-don-t-strip-it.patch b/debian/patches/0001-Don-t-link-uchime-statically-and-don-t-strip-it.patch
deleted file mode 100644
index 729755f..0000000
--- a/debian/patches/0001-Don-t-link-uchime-statically-and-don-t-strip-it.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-From: Tomasz Buchert <tomasz at debian.org>
-Date: Thu, 3 Sep 2015 23:39:00 +0200
-Subject: Don't link uchime statically and don't strip it
-
----
- source/uchime_src/mk | 10 +++++-----
- 1 file changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/source/uchime_src/mk b/source/uchime_src/mk
-index 24aeba0..4a73330 100755
---- a/source/uchime_src/mk
-+++ b/source/uchime_src/mk
-@@ -13,15 +13,15 @@ do
- rm -f tmp.stderr
- done
-
--LINK_OPTS=
--if [ `uname -s` == Linux ] ; then
-- LINK_OPTS=-static
--fi
-+LINK_OPTS=
-+# if [ `uname -s` == Linux ] ; then
-+# LINK_OPTS=-static
-+# fi
- g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr
- cat tmp.stderr
- cat tmp.stderr >> mk.stderr
- rm -f tmp.stderr
-
--strip uchime
-+# strip uchime
- ls -lh uchime
- sum uchime
diff --git a/debian/patches/0002-Some-spelling-corrections.patch b/debian/patches/0002-Some-spelling-corrections.patch
deleted file mode 100644
index 09cab48..0000000
--- a/debian/patches/0002-Some-spelling-corrections.patch
+++ /dev/null
@@ -1,174 +0,0 @@
-From: Andreas Tille <tille at debian.org>
-Date: Thu, 3 Sep 2015 23:48:01 +0200
-Subject: Some spelling corrections
-
-There are similar spelling problems in comments inside
-the code that are not fixed by this patch
----
- source/commands/degapseqscommand.cpp | 2 +-
- source/commands/getcurrentcommand.cpp | 2 +-
- source/commands/getmetacommunitycommand.cpp | 4 ++--
- source/commands/matrixoutputcommand.cpp | 2 +-
- source/commands/mgclustercommand.cpp | 4 ++--
- source/commands/phylotypecommand.cpp | 2 +-
- source/commands/screenseqscommand.cpp | 2 +-
- source/commands/setcurrentcommand.cpp | 2 +-
- source/commands/sffmultiplecommand.cpp | 2 +-
- source/commands/treegroupscommand.cpp | 2 +-
- source/commands/trimseqscommand.cpp | 2 +-
- 11 files changed, 13 insertions(+), 13 deletions(-)
-
-diff --git a/source/commands/degapseqscommand.cpp b/source/commands/degapseqscommand.cpp
-index 6352d7c..b987708 100644
---- a/source/commands/degapseqscommand.cpp
-+++ b/source/commands/degapseqscommand.cpp
-@@ -36,7 +36,7 @@ string DegapSeqsCommand::getHelpString(){
- helpString += "The degap.seqs command parameter are fasta and processors.\n";
- helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required unless you have a valid current fasta file. \n";
- helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
-- helpString += "The processors paramter allows you to enter the number of processors you would like to use. \n";
-+ helpString += "The processors parameter allows you to enter the number of processors you would like to use. \n";
- helpString += "The degap.seqs command should be in the following format: \n";
- helpString += "degap.seqs(fasta=yourFastaFile) \n";
- helpString += "Example: degap.seqs(fasta=abrecovery.align) \n";
-diff --git a/source/commands/getcurrentcommand.cpp b/source/commands/getcurrentcommand.cpp
-index d221e83..91ccc4d 100644
---- a/source/commands/getcurrentcommand.cpp
-+++ b/source/commands/getcurrentcommand.cpp
-@@ -32,7 +32,7 @@ string GetCurrentCommand::getHelpString(){
- string helpString = "";
- helpString += "The get.current command outputs the current files saved by mothur.\n";
- helpString += "The get.current command has one parameter: clear.\n";
-- helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
-+ helpString += "The clear parameter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
- helpString += "The get.current command should be in the following format: \n";
- helpString += "get.current() or get.current(clear=fasta-name-accnos)\n";
- return helpString;
-diff --git a/source/commands/getmetacommunitycommand.cpp b/source/commands/getmetacommunitycommand.cpp
-index 15356d8..a9e3d97 100644
---- a/source/commands/getmetacommunitycommand.cpp
-+++ b/source/commands/getmetacommunitycommand.cpp
-@@ -46,8 +46,8 @@ string GetMetaCommunityCommand::getHelpString(){
- helpString += "The get.communitytype command parameters are shared, method, label, groups, minpartitions, maxpartitions, optimizegap and processors. The shared file is required. \n";
- helpString += "The label parameter is used to analyze specific labels in your input. labels are separated by dashes.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your shared file you would like analyzed. Group names are separated by dashes.\n";
-- helpString += "The method parameter allows to select the method you would like to use. Options are dmm, kmeans and pam. Default=dmm.\n";
-- helpString += "The calc parameter allows to select the calculator you would like to use to calculate the distance matrix used by the pam and kmeans method. By default the rjsd calculator is used.\n";
-+ helpString += "The method parameter allows you to select the method you would like to use. Options are dmm, kmeans and pam. Default=dmm.\n";
-+ helpString += "The calc parameter allows you to select the calculator you would like to use to calculate the distance matrix used by the pam and kmeans method. By default the rjsd calculator is used.\n";
- helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample while calculating the distance matrix for the pam and kmeans method.\n";
- helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group while calculating the distance matrix for the pam and kmeans methods.\n";
- helpString += "The minpartitions parameter is used to .... Default=5.\n";
-diff --git a/source/commands/matrixoutputcommand.cpp b/source/commands/matrixoutputcommand.cpp
-index 6cb1846..ba1364f 100644
---- a/source/commands/matrixoutputcommand.cpp
-+++ b/source/commands/matrixoutputcommand.cpp
-@@ -840,7 +840,7 @@ int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int star
-
- for (int l = 0; l < k; l++) {
-
-- if (k != l) { //we dont need to similiarity of a groups to itself
-+ if (k != l) { //we dont need to similarity of a groups to itself
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
-diff --git a/source/commands/mgclustercommand.cpp b/source/commands/mgclustercommand.cpp
-index 6512eb6..ef83eca 100644
---- a/source/commands/mgclustercommand.cpp
-+++ b/source/commands/mgclustercommand.cpp
-@@ -43,7 +43,7 @@ string MGClusterCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The mgcluster command parameter options are blast, name, cutoff, precision, hard, method, merge, min, length, penalty, adjust and hcluster. The blast parameter is required.\n";
-- helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similiar to the OTUs.\n";
-+ helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similar to the OTUs.\n";
- helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n";
- helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n";
- helpString += "The precision parameter's default value is 100. \n";
-@@ -53,7 +53,7 @@ string MGClusterCommand::getHelpString(){
- helpString += "The adjust parameter is used to handle missing distances. If you set a cutoff, adjust=f by default. If not, adjust=t by default. Adjust=f, means ignore missing distances and adjust cutoff as needed with the average neighbor method. Adjust=t, will treat missing distances as 1.0. You can also set the value the missing distances should be set to, adjust=0.5 would give missing distances a value of 0.5.\n";
- helpString += "The penalty parameter is used to adjust the error rate. The default is 0.10.\n";
- helpString += "The merge parameter allows you to shut off merging based on overlaps and just cluster. By default merge is true, meaning you want to merge.\n";
-- helpString += "The hcluster parameter allows you to use the hcluster algorithm when clustering. This may be neccessary if your file is too large to fit into RAM. The default is false.\n";
-+ helpString += "The hcluster parameter allows you to use the hcluster algorithm when clustering. This may be necessary if your file is too large to fit into RAM. The default is false.\n";
- helpString += "The mgcluster command should be in the following format: \n";
- helpString += "mgcluster(blast=yourBlastfile, name=yourNameFile, cutoff=yourCutOff).\n";
- helpString += "Note: No spaces between parameter labels (i.e. balst), '=' and parameters (i.e.yourBlastfile).\n";
-diff --git a/source/commands/phylotypecommand.cpp b/source/commands/phylotypecommand.cpp
-index f22a50b..4ffcc42 100644
---- a/source/commands/phylotypecommand.cpp
-+++ b/source/commands/phylotypecommand.cpp
-@@ -45,7 +45,7 @@ string PhylotypeCommand::getHelpString(){
- helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
- helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
- helpString += "The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n";
-- helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
-+ helpString += "For the label parameter, levels count down from the root to keep the output similar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
- helpString += "The phylotype command should be in the following format: \n";
- helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
- helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
-diff --git a/source/commands/screenseqscommand.cpp b/source/commands/screenseqscommand.cpp
-index 36ddace..01a86c7 100644
---- a/source/commands/screenseqscommand.cpp
-+++ b/source/commands/screenseqscommand.cpp
-@@ -70,7 +70,7 @@ string ScreenSeqsCommand::getHelpString(){
- helpString += "The taxonomy parameter allows you to remove bad seqs from taxonomy files.\n";
- helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1.\n";
- helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n";
-- helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
-+ helpString += "The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.\n";
- helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
- helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
- helpString += "The maxn parameter allows you to set and maximum number of N's allowed in a sequence. \n";
-diff --git a/source/commands/setcurrentcommand.cpp b/source/commands/setcurrentcommand.cpp
-index 32d2a25..6e8b6c1 100644
---- a/source/commands/setcurrentcommand.cpp
-+++ b/source/commands/setcurrentcommand.cpp
-@@ -58,7 +58,7 @@ string SetCurrentCommand::getHelpString(){
- string helpString = "";
- helpString += "The set.current command allows you to set the current files saved by mothur.\n";
- helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary, file and taxonomy.\n";
-- helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
-+ helpString += "The clear parameter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
- helpString += "The set.current command should be in the following format: \n";
- helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
- return helpString;
-diff --git a/source/commands/sffmultiplecommand.cpp b/source/commands/sffmultiplecommand.cpp
-index 7d3733c..abd012d 100644
---- a/source/commands/sffmultiplecommand.cpp
-+++ b/source/commands/sffmultiplecommand.cpp
-@@ -76,7 +76,7 @@ string SffMultipleCommand::getHelpString(){
- helpString += parameters[parameters.size()-1] + ".\n";
- helpString += "The file parameter allows you to enter the a file containing the list of sff files and optional oligos files.\n";
- helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores generated by sffinfo trimmed to the clipQualLeft and clipQualRight values. Default=True. \n";
-- helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
-+ helpString += "The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.\n";
- helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
- helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
- helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
-diff --git a/source/commands/treegroupscommand.cpp b/source/commands/treegroupscommand.cpp
-index 7f5ae66..3b8cc00 100644
---- a/source/commands/treegroupscommand.cpp
-+++ b/source/commands/treegroupscommand.cpp
-@@ -47,7 +47,7 @@ string TreeGroupCommand::getHelpString(){
- try {
- string helpString = "";
- ValidCalculators validCalculator;
-- helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
-+ helpString += "The tree.shared command creates a .tre to represent the similarity between groups or sequences.\n";
- helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
- helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
-diff --git a/source/commands/trimseqscommand.cpp b/source/commands/trimseqscommand.cpp
-index 28e01e8..1d18071 100644
---- a/source/commands/trimseqscommand.cpp
-+++ b/source/commands/trimseqscommand.cpp
-@@ -70,7 +70,7 @@ string TrimSeqsCommand::getHelpString(){
- helpString += "The oligos parameter allows you to provide an oligos file.\n";
- helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
- helpString += "The count parameter allows you to provide a count file with your fasta file.\n";
-- helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
-+ helpString += "The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.\n";
- helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
- helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
- helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
diff --git a/debian/patches/0003-Don-t-link-against-lncurses-no-symbols-are-used.patch b/debian/patches/0003-Don-t-link-against-lncurses-no-symbols-are-used.patch
deleted file mode 100644
index 605a1f6..0000000
--- a/debian/patches/0003-Don-t-link-against-lncurses-no-symbols-are-used.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From: Andreas Tille <tille at debian.org>
-Date: Thu, 3 Sep 2015 23:50:12 +0200
-Subject: Don't link against lncurses (no symbols are used)
-
----
- makefile | 3 +--
- 1 file changed, 1 insertion(+), 2 deletions(-)
-
-diff --git a/makefile b/makefile
-index f03fd3d..708bc20 100644
---- a/makefile
-+++ b/makefile
-@@ -52,8 +52,7 @@ endif
- ifeq ($(strip $(USEREADLINE)),yes)
- CXXFLAGS += -DUSE_READLINE
- LIBS = \
-- -lreadline\
-- -lncurses
-+ -lreadline
- endif
-
-
diff --git a/debian/patches/0004-Fix-for-FTBFS-cc1plus-error-unrecognized-command-lin.patch b/debian/patches/0004-Fix-for-FTBFS-cc1plus-error-unrecognized-command-lin.patch
deleted file mode 100644
index 74023bf..0000000
--- a/debian/patches/0004-Fix-for-FTBFS-cc1plus-error-unrecognized-command-lin.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From: Nobuhiro Iwamatsu <iwamatsu at nigauri.org>
-Date: Thu, 3 Sep 2015 23:53:41 +0200
-Subject: Fix for FTBFS: cc1plus: error: unrecognized command line option
- '-msse2'
-
-Also -O3 is removed.
-
-This closes bug #648255.
----
- source/uchime_src/mk | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/uchime_src/mk b/source/uchime_src/mk
-index 4a73330..7332a46 100755
---- a/source/uchime_src/mk
-+++ b/source/uchime_src/mk
-@@ -7,7 +7,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr
- for CPPName in $CPPNames
- do
- echo $CPPName >> /dev/tty
-- g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr
-+ g++ $ENV_GCC_OPTS -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr
- cat tmp.stderr
- cat tmp.stderr >> mk.stderr
- rm -f tmp.stderr
diff --git a/debian/patches/0005-Don-t-redirect-anything-to-dev-tty.patch b/debian/patches/0005-Don-t-redirect-anything-to-dev-tty.patch
deleted file mode 100644
index 4e65cfb..0000000
--- a/debian/patches/0005-Don-t-redirect-anything-to-dev-tty.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From: Tomasz Buchert <tomasz at debian.org>
-Date: Thu, 3 Sep 2015 23:56:06 +0200
-Subject: Don't redirect anything to /dev/tty
-
-The tty device may not exist.
----
- source/uchime_src/mk | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/uchime_src/mk b/source/uchime_src/mk
-index 7332a46..a69fc34 100755
---- a/source/uchime_src/mk
-+++ b/source/uchime_src/mk
-@@ -6,7 +6,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr
-
- for CPPName in $CPPNames
- do
-- echo $CPPName >> /dev/tty
-+ echo $CPPName >&2
- g++ $ENV_GCC_OPTS -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr
- cat tmp.stderr
- cat tmp.stderr >> mk.stderr
diff --git a/debian/patches/0006-Turn-off-unportable-optimizations-in-makefile.patch b/debian/patches/0006-Turn-off-unportable-optimizations-in-makefile.patch
deleted file mode 100644
index 9c81588..0000000
--- a/debian/patches/0006-Turn-off-unportable-optimizations-in-makefile.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-From: Tomasz Buchert <tomasz at debian.org>
-Date: Thu, 3 Sep 2015 23:58:54 +0200
-Subject: Turn off unportable optimizations in makefile
-
-Adapted from the original patch of Steffen Moeller <moeller at debian.org>
-and Tim Booth <tbooth at ceh.ac.uk>
----
- makefile | 6 ++----
- 1 file changed, 2 insertions(+), 4 deletions(-)
-
-diff --git a/makefile b/makefile
-index 708bc20..7f37404 100644
---- a/makefile
-+++ b/makefile
-@@ -18,12 +18,12 @@ RELEASE_DATE = "\"7/27/2015\""
- VERSION = "\"1.36.1\""
-
- # Optimize to level 3:
--CXXFLAGS += -O3
-+# CXXFLAGS += -O3
-
-
- ifeq ($(strip $(64BIT_VERSION)),yes)
- #if you are a mac user use the following line
-- TARGET_ARCH += -arch x86_64
-+ # TARGET_ARCH += -arch x86_64
-
- #if you using cygwin to build Windows the following line
- #CXX = x86_64-w64-mingw32-g++
-@@ -107,7 +107,6 @@ endif
-
- mothur : $(OBJECTS) uchime
- $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
-- strip mothur
-
-
- uchime:
-@@ -129,4 +128,3 @@ install : mothur
- clean :
- @rm -f $(OBJECTS)
- @rm -f uchime
--
diff --git a/debian/patches/0008-Fix-catchall-command.patch b/debian/patches/0008-Fix-catchall-command.patch
index fcbf263..a1ab000 100644
--- a/debian/patches/0008-Fix-catchall-command.patch
+++ b/debian/patches/0008-Fix-catchall-command.patch
@@ -12,8 +12,6 @@ information.
source/commands/catchallcommand.cpp | 6 ++++++
1 file changed, 6 insertions(+)
-diff --git a/source/commands/catchallcommand.cpp b/source/commands/catchallcommand.cpp
-index 9e2bcbb..5530c81 100644
--- a/source/commands/catchallcommand.cpp
+++ b/source/commands/catchallcommand.cpp
@@ -199,6 +199,7 @@ int CatchAllCommand::execute() {
@@ -24,7 +22,7 @@ index 9e2bcbb..5530c81 100644
//get location of catchall
path = m->argv;
path = path.substr(0, (path.find_last_of("othur")-5));
-@@ -247,6 +248,11 @@ int CatchAllCommand::execute() {
+@@ -257,6 +258,11 @@ int CatchAllCommand::execute() {
//prepare full output directory
outputDir = m->getFullPathName(outputDir);
diff --git a/debian/patches/0009-Fix-boost_iostreams-flags.patch b/debian/patches/0009-Fix-boost_iostreams-flags.patch
deleted file mode 100644
index 1846007..0000000
--- a/debian/patches/0009-Fix-boost_iostreams-flags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From: Tomasz Buchert <tomasz at debian.org>
-Date: Fri, 4 Sep 2015 00:49:28 +0200
-Subject: Fix boost_iostreams flags
-
----
- makefile | 8 +++-----
- 1 file changed, 3 insertions(+), 5 deletions(-)
-
-diff --git a/makefile b/makefile
-index 7f37404..0de3ef9 100644
---- a/makefile
-+++ b/makefile
-@@ -63,14 +63,12 @@ endif
-
- #The boost libraries allow you to read gz files.
- ifeq ($(strip $(USEBOOST)),yes)
-- BOOST_INCLUDE_DIR="/usr/local/include"
-- BOOST_LIBRARY_DIR="/usr/local/lib"
-+ # BOOST_INCLUDE_DIR="/usr/local/include"
-+ # BOOST_LIBRARY_DIR="/usr/local/lib"
-
- CXXFLAGS += -DUSE_BOOST
-
-- LIBS += \
-- ${BOOST_LIBRARY_DIR}/libboost_iostreams.a \
-- ${BOOST_LIBRARY_DIR}/zlib.a
-+ LIBS += -lboost_iostreams
-
- #if linux or windows then ${BOOST_LIBRARY_DIR}/libz.a
- endif
diff --git a/debian/patches/0010-Pass-hardening-flags-to-uchime-build.patch b/debian/patches/0010-Pass-hardening-flags-to-uchime-build.patch
deleted file mode 100644
index eb71273..0000000
--- a/debian/patches/0010-Pass-hardening-flags-to-uchime-build.patch
+++ /dev/null
@@ -1,55 +0,0 @@
-From: Tomasz Buchert <tomasz at debian.org>
-Date: Fri, 4 Sep 2015 02:04:29 +0200
-Subject: Pass hardening flags to uchime build and use CXX
-
-Also add some debug so that we can see the flags.
----
- makefile | 5 ++++-
- source/uchime_src/mk | 8 ++++++--
- 2 files changed, 10 insertions(+), 3 deletions(-)
-
-diff --git a/makefile b/makefile
-index 0de3ef9..6fc97a1 100644
---- a/makefile
-+++ b/makefile
-@@ -108,7 +108,10 @@ mothur : $(OBJECTS) uchime
-
-
- uchime:
-- cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
-+ echo ENV_CXX="$(CXX)"
-+ echo ENV_GCC_OPTS="$(CPPFLAGS) $(CXXFLAGS)"
-+ echo ENV_LINK_OPTS="$(LDFLAGS)"
-+ cd source/uchime_src && ENV_CXX="$(CXX)" ENV_GCC_OPTS="$(CPPFLAGS) $(CXXFLAGS)" ENV_LINK_OPTS="$(LDFLAGS)" ./mk && mv uchime ../../ && cd ..
-
-
- install : mothur
-diff --git a/source/uchime_src/mk b/source/uchime_src/mk
-index a69fc34..3bfb5bd 100755
---- a/source/uchime_src/mk
-+++ b/source/uchime_src/mk
-@@ -4,10 +4,14 @@ ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o
-
- rm -f *.o mk.stdout mk.stderr tmp.stderr
-
-+CXX=${ENV_CXX:-g++}
-+
- for CPPName in $CPPNames
- do
- echo $CPPName >&2
-- g++ $ENV_GCC_OPTS -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr
-+ set -x
-+ ${CXX} $ENV_GCC_OPTS -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr
-+ set +x
- cat tmp.stderr
- cat tmp.stderr >> mk.stderr
- rm -f tmp.stderr
-@@ -17,7 +21,7 @@ LINK_OPTS=
- # if [ `uname -s` == Linux ] ; then
- # LINK_OPTS=-static
- # fi
--g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr
-+${CXX} $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr
- cat tmp.stderr
- cat tmp.stderr >> mk.stderr
- rm -f tmp.stderr
diff --git a/debian/patches/0011-Don-t-hardcode-mpic-as-the-compiler.patch b/debian/patches/0011-Don-t-hardcode-mpic-as-the-compiler.patch
deleted file mode 100644
index fd07962..0000000
--- a/debian/patches/0011-Don-t-hardcode-mpic-as-the-compiler.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-From: Tomasz Buchert <tomasz at debian.org>
-Date: Fri, 4 Sep 2015 09:37:45 +0200
-Subject: Don't hardcode mpic++ as the compiler
-
----
- makefile | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/makefile b/makefile
-index 6fc97a1..cbe078c 100644
---- a/makefile
-+++ b/makefile
-@@ -55,9 +55,9 @@ ifeq ($(strip $(USEREADLINE)),yes)
- -lreadline
- endif
-
--
-+MPICXX ?= mpic++
- ifeq ($(strip $(USEMPI)),yes)
-- CXX = mpic++
-+ CXX = $(MPICXX)
- CXXFLAGS += -DUSE_MPI
- endif
-
diff --git a/debian/patches/series b/debian/patches/series
index f6ceefa..7b40027 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,10 +1 @@
-0001-Don-t-link-uchime-statically-and-don-t-strip-it.patch
-0002-Some-spelling-corrections.patch
-0003-Don-t-link-against-lncurses-no-symbols-are-used.patch
-0004-Fix-for-FTBFS-cc1plus-error-unrecognized-command-lin.patch
-0005-Don-t-redirect-anything-to-dev-tty.patch
-0006-Turn-off-unportable-optimizations-in-makefile.patch
0008-Fix-catchall-command.patch
-0009-Fix-boost_iostreams-flags.patch
-0010-Pass-hardening-flags-to-uchime-build.patch
-0011-Don-t-hardcode-mpic-as-the-compiler.patch
--
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