[med-svn] r14592 - in trunk/packages/mothur/tags: . 1.31.2+dfsg-2/debian 1.31.2+dfsg-2/debian/patches
Aaron M. Ucko
ucko at alioth.debian.org
Thu Sep 5 03:06:02 UTC 2013
Author: ucko
Date: 2013-09-05 03:06:01 +0000 (Thu, 05 Sep 2013)
New Revision: 14592
Added:
trunk/packages/mothur/tags/1.31.2+dfsg-2/
trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/changelog
trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/patches/makefile.patch
Removed:
trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/changelog
trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/patches/makefile.patch
Log:
[svn-buildpackage] Tagging mothur 1.31.2+dfsg-2
Deleted: trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/changelog
===================================================================
--- trunk/packages/mothur/trunk/debian/changelog 2013-09-04 13:26:42 UTC (rev 14588)
+++ trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/changelog 2013-09-05 03:06:01 UTC (rev 14592)
@@ -1,177 +0,0 @@
-mothur (1.31.2+dfsg-1) unstable; urgency=low
-
- * New upstream version
- * debian/watch: use dversionmangle to properly detect new upstream
- versions
- * debian/copyright: Add Files-Excluded to document what was removed from
- original source
- * debian/rules: Use enhanced uscan
- * debian/control:
- - cme fix dpkg-control
- - debhelper 9
- - use anonscm for Vcs fields
- * debian/patches/uchime_hardening.patch: Hardening for uchime
- * debian/uchime.1
- * debian/patches/spelling.patch: Some spelling corrections
-
- -- Andreas Tille <tille at debian.org> Tue, 30 Jul 2013 14:32:44 +0200
-
-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> Wed, 10 Oct 2012 11:20:43 +0100
-
-mothur (1.25.0~repack-lucid3) lucid; urgency=low
-
- * Removed dependency on catchall - this belongs in the
- bio-linux-mothur package. Not sure what I was thinking there.
-
- -- Tim Booth <tbooth at ceh.ac.uk> Mon, 14 May 2012 10:57:22 +0100
-
-mothur (1.25.0~repack-lucid2) lucid; urgency=low
-
- * Fix 32-bit build and add uchime (which should be packaged
- separately, but I've no time for that just now)
-
- -- Tim Booth <tbooth at ceh.ac.uk> Thu, 10 May 2012 10:43:04 +0100
-
-mothur (1.25.0~repack-lucid1) lucid; urgency=low
-
- * Rebuild for Lucid with repack fudge again
-
- -- Tim Booth <tbooth at ceh.ac.uk> Wed, 09 May 2012 11:20:15 +0100
-
-mothur (1.25.0-1) UNRELEASED; urgency=low
-
- * New upstream release
- * debian/upstream: more complete authors information in proper BibTeX
- format
-
- -- Andreas Tille <tille at debian.org> Tue, 08 May 2012 18:00:19 +0200
-
-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)
- * debian/upstream:
- - fixed typo: s/TITILE/TITLE/
- - Moved DOI+PMID to references
- * debian/control:
- - Standards-Version: 3.9.3 (no changes needed)
- - Build-Depends: gfortran
- * debian/get-orig-source:
- - be not that verbose
- - more reproducible creation of tarball
- - Strip some useless files from tarball (.*; *.o)
- * debhelper 9 (control+compat)
- * debian/copyright: DEP5 changes and verified using
- cme fix dpkg-copyright
-
- -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 14:52:47 +0100
-
-mothur (1.22.2-2) unstable; urgency=low
-
- * debian/patches/kfreebsd.patch: Enable build on BSD machines
- (thanks to Christoph Egger <christoph at debian.org> and Robert
- Millan <rmh at debian.org>)
- Closes: #650683
- * debian/control: Fixed Vcs fields
- * debian/{control,rules}: drop explicite quilt dependency which is
- just given by source format 3.0 (quilt)
-
- -- Andreas Tille <tille at debian.org> Tue, 06 Dec 2011 17:14:49 +0100
-
-mothur (1.22.2~repack-ubuntu1) lucid; urgency=low
-
- * Backport for Ubuntu
- * Need to fudge version as upstream was repacked by Andreas'
- script
-
- -- Tim Booth <tbooth at ceh.ac.uk> Mon, 05 Dec 2011 17:37:16 +0000
-
-mothur (1.22.2-1) unstable; urgency=low
-
- * New upstream version
- * debian/patches/drop_sse_option.patch: Fix for FTBFS: unrecognized
- command line option '-msse2' (Thanks for the patch to
- Nobuhiro Iwamatsu <iwamatsu at nigauri.org>)
- Closes: #648255
-
- -- Andreas Tille <tille at debian.org> Thu, 10 Nov 2011 08:38:32 +0100
-
-mothur (1.22.1-1) unstable; urgency=low
-
- [ Thorsten Alteholz ]
- * new upstream version
- * adapted patches to this version
- * debian/control: no dependency on quilt needed
- * debian/control + debian/compat: dh version set to >= 8
-
- [ Andreas Tille ]
- * debian/control: readd quilt dependency because build fails otherwise
- * debian/copyright: fix spelling error
-
- -- Andreas Tille <tille at debian.org> Mon, 07 Nov 2011 11:14:17 +0100
-
-mothur (1.18.1-1) unstable; urgency=low
-
- * New upstream version (adapted patches to new location of
- makefile)
- * debian/rules: No need to specify SOURCEDIR any more
- * Added Tim Booth <tbooth at ceh.ac.uk> as Uploader,
- removed Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
- from uploaders
- * Standards-Version: 3.9.2 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Tue, 26 Apr 2011 19:58:45 +0200
-
-mothur (1.18.0-1ubuntu1) lucid; urgency=low
-
- * Rebuild for PPA
- * Source now comes in subdirectory Mothur.source - modify rules file
- to handle this
-
- -- Tim Booth <tbooth at ceh.ac.uk> Thu, 14 Apr 2011 14:50:24 +0100
-
-mothur (1.17.3-1) unstable; urgency=low
-
- * New upstream version, which specifically solves some copyright
- questions of ftpmaster (Charles, thanks for reviewing
- debian/copyright)
- Closes: #589675
- * Updated patches
- * debian/copyright:
- Clarified license issues
-
- -- Andreas Tille <tille at debian.org> Wed, 30 Mar 2011 09:01:52 +0200
-
-mothur (1.15.0-1ubuntu1) lucid; urgency=low
-
- * Rebuild for upload to PPA, license or not.
-
- -- Tim Booth <tbooth at ceh.ac.uk> Sun, 30 Jan 2011 12:14:18 +0000
-
-mothur (1.15.0-1) unstable; urgency=low
-
- * Initial release (Closes: #589675)
-
- -- Andreas Tille <tille at debian.org> Wed, 02 Feb 2011 08:59:45 +0100
Copied: trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/changelog (from rev 14591, trunk/packages/mothur/trunk/debian/changelog)
===================================================================
--- trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/changelog (rev 0)
+++ trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/changelog 2013-09-05 03:06:01 UTC (rev 14592)
@@ -0,0 +1,185 @@
+mothur (1.31.2+dfsg-2) unstable; urgency=low
+
+ * Team upload.
+ * debian/patches/makefile.patch: Leave off -m64, which ia64 doesn't
+ support and other 64-bit architectures don't need. (Closes: #721770.)
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 04 Sep 2013 22:37:31 -0400
+
+mothur (1.31.2+dfsg-1) unstable; urgency=low
+
+ * New upstream version
+ * debian/watch: use dversionmangle to properly detect new upstream
+ versions
+ * debian/copyright: Add Files-Excluded to document what was removed from
+ original source
+ * debian/rules: Use enhanced uscan
+ * debian/control:
+ - cme fix dpkg-control
+ - debhelper 9
+ - use anonscm for Vcs fields
+ * debian/patches/uchime_hardening.patch: Hardening for uchime
+ * debian/uchime.1
+ * debian/patches/spelling.patch: Some spelling corrections
+
+ -- Andreas Tille <tille at debian.org> Tue, 30 Jul 2013 14:32:44 +0200
+
+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> Wed, 10 Oct 2012 11:20:43 +0100
+
+mothur (1.25.0~repack-lucid3) lucid; urgency=low
+
+ * Removed dependency on catchall - this belongs in the
+ bio-linux-mothur package. Not sure what I was thinking there.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 14 May 2012 10:57:22 +0100
+
+mothur (1.25.0~repack-lucid2) lucid; urgency=low
+
+ * Fix 32-bit build and add uchime (which should be packaged
+ separately, but I've no time for that just now)
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 10 May 2012 10:43:04 +0100
+
+mothur (1.25.0~repack-lucid1) lucid; urgency=low
+
+ * Rebuild for Lucid with repack fudge again
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 09 May 2012 11:20:15 +0100
+
+mothur (1.25.0-1) UNRELEASED; urgency=low
+
+ * New upstream release
+ * debian/upstream: more complete authors information in proper BibTeX
+ format
+
+ -- Andreas Tille <tille at debian.org> Tue, 08 May 2012 18:00:19 +0200
+
+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)
+ * debian/upstream:
+ - fixed typo: s/TITILE/TITLE/
+ - Moved DOI+PMID to references
+ * debian/control:
+ - Standards-Version: 3.9.3 (no changes needed)
+ - Build-Depends: gfortran
+ * debian/get-orig-source:
+ - be not that verbose
+ - more reproducible creation of tarball
+ - Strip some useless files from tarball (.*; *.o)
+ * debhelper 9 (control+compat)
+ * debian/copyright: DEP5 changes and verified using
+ cme fix dpkg-copyright
+
+ -- Andreas Tille <tille at debian.org> Thu, 08 Mar 2012 14:52:47 +0100
+
+mothur (1.22.2-2) unstable; urgency=low
+
+ * debian/patches/kfreebsd.patch: Enable build on BSD machines
+ (thanks to Christoph Egger <christoph at debian.org> and Robert
+ Millan <rmh at debian.org>)
+ Closes: #650683
+ * debian/control: Fixed Vcs fields
+ * debian/{control,rules}: drop explicite quilt dependency which is
+ just given by source format 3.0 (quilt)
+
+ -- Andreas Tille <tille at debian.org> Tue, 06 Dec 2011 17:14:49 +0100
+
+mothur (1.22.2~repack-ubuntu1) lucid; urgency=low
+
+ * Backport for Ubuntu
+ * Need to fudge version as upstream was repacked by Andreas'
+ script
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 05 Dec 2011 17:37:16 +0000
+
+mothur (1.22.2-1) unstable; urgency=low
+
+ * New upstream version
+ * debian/patches/drop_sse_option.patch: Fix for FTBFS: unrecognized
+ command line option '-msse2' (Thanks for the patch to
+ Nobuhiro Iwamatsu <iwamatsu at nigauri.org>)
+ Closes: #648255
+
+ -- Andreas Tille <tille at debian.org> Thu, 10 Nov 2011 08:38:32 +0100
+
+mothur (1.22.1-1) unstable; urgency=low
+
+ [ Thorsten Alteholz ]
+ * new upstream version
+ * adapted patches to this version
+ * debian/control: no dependency on quilt needed
+ * debian/control + debian/compat: dh version set to >= 8
+
+ [ Andreas Tille ]
+ * debian/control: readd quilt dependency because build fails otherwise
+ * debian/copyright: fix spelling error
+
+ -- Andreas Tille <tille at debian.org> Mon, 07 Nov 2011 11:14:17 +0100
+
+mothur (1.18.1-1) unstable; urgency=low
+
+ * New upstream version (adapted patches to new location of
+ makefile)
+ * debian/rules: No need to specify SOURCEDIR any more
+ * Added Tim Booth <tbooth at ceh.ac.uk> as Uploader,
+ removed Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+ from uploaders
+ * Standards-Version: 3.9.2 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Tue, 26 Apr 2011 19:58:45 +0200
+
+mothur (1.18.0-1ubuntu1) lucid; urgency=low
+
+ * Rebuild for PPA
+ * Source now comes in subdirectory Mothur.source - modify rules file
+ to handle this
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 14 Apr 2011 14:50:24 +0100
+
+mothur (1.17.3-1) unstable; urgency=low
+
+ * New upstream version, which specifically solves some copyright
+ questions of ftpmaster (Charles, thanks for reviewing
+ debian/copyright)
+ Closes: #589675
+ * Updated patches
+ * debian/copyright:
+ Clarified license issues
+
+ -- Andreas Tille <tille at debian.org> Wed, 30 Mar 2011 09:01:52 +0200
+
+mothur (1.15.0-1ubuntu1) lucid; urgency=low
+
+ * Rebuild for upload to PPA, license or not.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Sun, 30 Jan 2011 12:14:18 +0000
+
+mothur (1.15.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #589675)
+
+ -- Andreas Tille <tille at debian.org> Wed, 02 Feb 2011 08:59:45 +0100
Deleted: trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/patches/makefile.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/makefile.patch 2013-09-04 13:26:42 UTC (rev 14588)
+++ trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/patches/makefile.patch 2013-09-05 03:06:01 UTC (rev 14592)
@@ -1,39 +0,0 @@
-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
-@@ -21,14 +21,15 @@ FORTAN_COMPILER = gfortran
- FORTRAN_FLAGS =
-
- # Optimize to level 3:
--CXXFLAGS += -O3
-+# Nope, let debuild set this.
-+# CXXFLAGS += -O3
-
- ifeq ($(strip $(64BIT_VERSION)),yes)
- #if you are using centos uncomment the following lines
- #CXX = g++44
-
- #if you are a mac user use the following line
-- TARGET_ARCH += -arch x86_64
-+ #TARGET_ARCH += -arch x86_64
-
- #if you using cygwin to build Windows the following line
- #CXX = x86_64-w64-mingw32-g++
-@@ -38,6 +39,10 @@ ifeq ($(strip $(64BIT_VERSION)),yes)
-
- #if you are a linux user use the following line
- #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 @@ install : mothur
- clean :
- @rm -f $(OBJECTS)
- @rm -f uchime
--
Copied: trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/patches/makefile.patch (from rev 14590, trunk/packages/mothur/trunk/debian/patches/makefile.patch)
===================================================================
--- trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/patches/makefile.patch (rev 0)
+++ trunk/packages/mothur/tags/1.31.2+dfsg-2/debian/patches/makefile.patch 2013-09-05 03:06:01 UTC (rev 14592)
@@ -0,0 +1,42 @@
+Author: Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
+Purpose: Comment MAC specific option
+ Don't bother with any compilation flags, as the defaults are already sane
+ on all architectures (and trying to set -m64 explicitly fails on ia64).
+--- a/makefile
++++ b/makefile
+@@ -21,14 +21,15 @@ FORTAN_COMPILER = gfortran
+ FORTRAN_FLAGS =
+
+ # Optimize to level 3:
+-CXXFLAGS += -O3
++# Nope, let debuild set this.
++# CXXFLAGS += -O3
+
+ ifeq ($(strip $(64BIT_VERSION)),yes)
+ #if you are using centos uncomment the following lines
+ #CXX = g++44
+
+ #if you are a mac user use the following line
+- TARGET_ARCH += -arch x86_64
++ #TARGET_ARCH += -arch x86_64
+
+ #if you using cygwin to build Windows the following line
+ #CXX = x86_64-w64-mingw32-g++
+@@ -38,9 +39,11 @@ ifeq ($(strip $(64BIT_VERSION)),yes)
+
+ #if you are a linux user use the following line
+ #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 += -DBIT_VERSION
+- FORTRAN_FLAGS = -m64
+ endif
+
+
+@@ -120,4 +123,3 @@ install : mothur
+ clean :
+ @rm -f $(OBJECTS)
+ @rm -f uchime
+-
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