[med-svn] r12395 - in trunk/packages/mothur/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Fri Oct 12 11:47:01 UTC 2012
Author: tbooth-guest
Date: 2012-10-12 11:47:01 +0000 (Fri, 12 Oct 2012)
New Revision: 12395
Added:
trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch
trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch
trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically
Modified:
trunk/packages/mothur/trunk/debian/changelog
trunk/packages/mothur/trunk/debian/control
trunk/packages/mothur/trunk/debian/patches/makefile.patch
Log:
Committing various tweaks made for Bio-Linux but relevant for Debian.
The most important change is that the makefile definitely shouldn't
have "-march=native" as it enables optimisations specific to the build
machine and potentially incompatible with other CPUs.
Modified: trunk/packages/mothur/trunk/debian/changelog
===================================================================
--- trunk/packages/mothur/trunk/debian/changelog 2012-10-12 05:09:37 UTC (rev 12394)
+++ trunk/packages/mothur/trunk/debian/changelog 2012-10-12 11:47:01 UTC (rev 12395)
@@ -9,10 +9,19 @@
mothur (1.27.0+repack-precise1) precise; urgency=low
+ * Remove -march=native from makefile as this makes the result
+ depend on the build machine - so a package built on a Core3
+ CPU won't work on a Xeon.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 12 Oct 2012 11:41:04 +0100
+
+mothur (1.27.0+repack-precise2) precise; urgency=low
+
* New minor release from upstream
* Build MPI version alongside regular version
+ * ...but only for 64-bit
- -- Tim Booth <tbooth at ceh.ac.uk> Tue, 14 Aug 2012 18:46:58 +0100
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 10 Oct 2012 11:20:43 +0100
mothur (1.25.0~repack-lucid3) lucid; urgency=low
Modified: trunk/packages/mothur/trunk/debian/control
===================================================================
--- trunk/packages/mothur/trunk/debian/control 2012-10-12 05:09:37 UTC (rev 12394)
+++ trunk/packages/mothur/trunk/debian/control 2012-10-12 11:47:01 UTC (rev 12395)
@@ -25,9 +25,9 @@
calculators and visualization tools were added.
Package: mothur-mpi
-Architecture: any
+Architecture: amd64
Depends: ${shlibs:Depends}, ${misc:Depends}, mothur, openmpi-bin
Description: mpi-enabled binary for mothur
Provides the MPI-enabled binary for Mothur
According to the docs this is of limited usefulness but is provided
- for completeness
+ for completeness.
Added: trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch (rev 0)
+++ trunk/packages/mothur/trunk/debian/patches/build_without_tty.patch 2012-10-12 11:47:01 UTC (rev 12395)
@@ -0,0 +1,11 @@
+--- a/uchime_src/mk
++++ b/uchime_src/mk
+@@ -6,7 +6,7 @@
+
+ for CPPName in $CPPNames
+ do
+- echo $CPPName >> /dev/tty
++ echo $CPPName >&2
+ g++ $ENV_GCC_OPTS -c -O2 -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
Added: trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch (rev 0)
+++ trunk/packages/mothur/trunk/debian/patches/catchall_fix.patch 2012-10-12 11:47:01 UTC (rev 12395)
@@ -0,0 +1,26 @@
+This removes a workaround that is better fixed in Catchall than in
+Mothur, so I did that (packaged in bio-linux-catchall just now as I
+don't have the source compiling yet.)
+
+--- a/catchallcommand.cpp
++++ b/catchallcommand.cpp
+@@ -190,6 +190,7 @@
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
++ /* TB for Bio-Linux: Don't need this...
+ //get location of catchall
+ path = m->argv;
+ path = path.substr(0, (path.find_last_of("othur")-5));
+@@ -238,6 +239,11 @@
+
+ //prepare full output directory
+ outputDir = m->getFullPathName(outputDir);
++ */
++
++ /* TB for Bio-Linux: We just need this, assuming catchall is properly wrapped to avoid
++ * the bug described above - see the bio-linux-catchall package */
++ string catchAllCommandExe = "catchall ";
+
+ if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); }
+
Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-10-12 05:09:37 UTC (rev 12394)
+++ trunk/packages/mothur/trunk/debian/patches/makefile.patch 2012-10-12 11:47:01 UTC (rev 12395)
@@ -1,8 +1,18 @@
-Author: Steffen Moeller <moeller at debian.org>
+Author: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
Purpose: Comment MAC specific option
+ Set -m64 but not -march=native for 64-bit build
--- a/makefile
+++ b/makefile
-@@ -28,7 +28,7 @@
+@@ -21,14 +21,15 @@
+ FORTRAN_FLAGS =
+
+ # Optimize to level 3:
+-CXXFLAGS += -O3
++# Nope, let debuild set this.
++# CXXFLAGS += -O3
+
+ ifeq ($(strip $(64BIT_VERSION)),yes)
+ #if you are using centos uncomment the following lines
#CXX = g++44
#if you are a mac user use the following line
@@ -11,12 +21,19 @@
#if you using cygwin to build Windows the following line
#CXX = x86_64-w64-mingw32-g++
-@@ -37,7 +37,7 @@
- #TARGET_ARCH += -m64 -static
+@@ -38,6 +39,10 @@
#if you are a linux user use the following line
-- #CXXFLAGS += -mtune=native -march=native -m64
-+ CXXFLAGS += -mtune=native -march=native -m64
+ #CXXFLAGS += -mtune=native -march=native -m64
++ # But not if you are trying to make a generic build for
++ # packaging, because your binary will end up being specific
++ # to your processor.
++ CXXFLAGS += -m64
CXXFLAGS += -DBIT_VERSION
FORTRAN_FLAGS = -m64
+@@ -120,4 +125,3 @@
+ clean :
+ @rm -f $(OBJECTS)
+ @rm -f uchime
+-
Added: trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically (rev 0)
+++ trunk/packages/mothur/trunk/debian/patches/uchime_link_dynamically 2012-10-12 11:47:01 UTC (rev 12395)
@@ -0,0 +1,18 @@
+Unfortunately there is no explanation for why the upstream does not build
+this dynamically. I'm therefore commenting it out until someone shouts.
+
+--- a/uchime_src/mk
++++ b/uchime_src/mk
+@@ -14,9 +14,9 @@
+ done
+
+ LINK_OPTS=
+-if [ `uname -s` == Linux ] ; then
+- LINK_OPTS=-static
+-fi
++#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
More information about the debian-med-commit
mailing list