[med-svn] r22758 - in trunk/packages/bowtie/tags: . 1.1.2-5/debian 1.1.2-5/debian/patches
Sascha Steinbiss
satta at moszumanska.debian.org
Wed Sep 7 11:07:34 UTC 2016
Author: satta
Date: 2016-09-07 11:07:33 +0000 (Wed, 07 Sep 2016)
New Revision: 22758
Added:
trunk/packages/bowtie/tags/1.1.2-5/
trunk/packages/bowtie/tags/1.1.2-5/debian/changelog
trunk/packages/bowtie/tags/1.1.2-5/debian/patches/reproducible.patch
Removed:
trunk/packages/bowtie/tags/1.1.2-5/debian/changelog
trunk/packages/bowtie/tags/1.1.2-5/debian/patches/reproducible.patch
Log:
[svn-buildpackage] Tagging bowtie 1.1.2-5
Deleted: trunk/packages/bowtie/tags/1.1.2-5/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog 2016-09-06 16:50:33 UTC (rev 22756)
+++ trunk/packages/bowtie/tags/1.1.2-5/debian/changelog 2016-09-07 11:07:33 UTC (rev 22758)
@@ -1,180 +0,0 @@
-bowtie (1.1.2-4) unstable; urgency=medium
-
- * Team upload.
- * Make build reproducible.
- - Use fixed build hostname and compiler version.
- * Fix autopkgtest by adjusting directory.
- * Enable full hardening.
- * Bump Standards-Version.
- * Use secure Vcs-Browser.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 25 May 2016 22:25:27 +0000
-
-bowtie (1.1.2-3) unstable; urgency=medium
-
- * Enable building arch independent packages separately
- Closes: #806220
- * Fix clean target
-
- -- Andreas Tille <tille at debian.org> Wed, 25 Nov 2015 22:38:02 +0100
-
-bowtie (1.1.2-2) unstable; urgency=medium
-
- * Enable building on arm64 (Thanks for the patch to Edmund Grimley Evans)
- Closes: #800548
- * Remove inactive Uploader
- * Fix spelling
-
- -- Andreas Tille <tille at debian.org> Thu, 01 Oct 2015 09:47:23 +0200
-
-bowtie (1.1.2-1) unstable; urgency=medium
-
- * New upstream version
- * remove strange byte-compyled Python code bowtie-buildc (no idea how and
- why it was created)
- * Enabling ppc64el on Makefile and debian/control (Thanks for the patch to
- Fernando Seiti Furusato <ferseiti at br.ibm.com>)
- Closes: #788537
-
- -- Andreas Tille <tille at debian.org> Sun, 05 Jul 2015 21:24:20 +0200
-
-bowtie (1.1.1-2) unstable; urgency=high
-
- * Team upload.
- * Install missing commands. Closes: #776881.
-
- -- Charles Plessy <plessy at debian.org> Tue, 03 Feb 2015 10:44:39 +0900
-
-bowtie (1.1.1-1) unstable; urgency=medium
-
- * New upstream release
- * cme fix dpkg-control
- * Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny)
- * Add Depends: python (also Build-Depends since it is used in tests)
-
- -- Andreas Tille <tille at debian.org> Thu, 02 Oct 2014 14:32:50 +0200
-
-bowtie (1.0.1-3) unstable; urgency=medium
-
- * Drop all architectures except amd64 since there was no success
- in trying to port the code to other architectures. The portability
- patch introduced in the last revision was droped again
- * debian/copyright: Drop unneeded copyright statements about code that
- was removed from upstream source
-
- -- Andreas Tille <tille at debian.org> Mon, 15 Sep 2014 11:00:25 +0200
-
-bowtie (1.0.1-2) unstable; urgency=medium
-
- * Do not use copy of outdated gcc header file which destroys portability
- to other architectures
- Closes: #756780
- * Add README.Debian informing users about the fact that we ignore copy
- of cpuid.h
- * Add unit tests for build time and autopkgtest
- * Add debian/README.test to explain how to test the package
- Attention: Please take notice of /usr/share/bowtie/README.Debian about
- "Test suite for bowtie created and potential issue with sorting"
-
- -- Andreas Tille <tille at debian.org> Wed, 03 Sep 2014 09:50:22 +0200
-
-bowtie (1.0.1-1) unstable; urgency=medium
-
- * New upstream version (adapted patches)
- * drop debian/get-orig-source but rather remove the SeqAn-1.1 code
- copy via Files-Excluded
- * debian/control: Priority: optional
-
- -- Andreas Tille <tille at debian.org> Wed, 30 Jul 2014 13:38:25 +0200
-
-bowtie (1.0.0-6) unstable; urgency=low
-
- * debian/patches/seqan-popcount.patch: New patch. (Closes: #733398)
- * Version 1.4 of seqan-dev is required now.
- * Standards-Version: 3.9.5 (no changes needed).
- * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy.
-
- -- Ognyan Kulev <ogi at debian.org> Sat, 08 Mar 2014 15:13:16 +0200
-
-bowtie (1.0.0-5) unstable; urgency=low
-
- * Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target
- instead of override_dh_fixperms in debian/rules.
-
- -- Ognyan Kulev <ogi at debian.org> Thu, 30 May 2013 09:41:25 +0300
-
-bowtie (1.0.0-4) unstable; urgency=low
-
- * Lintian fixes:
- - Removed DM-Upload-Allowed field.
- - Standards Version 3.9.4 (no changes needed).
- - Remove execute bits on some files in bowtie-examples.
- * Don't compress *.ebwt index files in bowtie-examples package.
- * Package description now starts with a capital letter.
-
- -- Ognyan Kulev <ogi at debian.org> Wed, 29 May 2013 22:53:13 +0300
-
-bowtie (1.0.0-3) unstable; urgency=low
-
- * New patch no_hash_style_both_for_mips.patch.
- This fixes build errors on mips and mipsel.
-
- -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 15:15:37 +0300
-
-bowtie (1.0.0-2) unstable; urgency=low
-
- * Requires version 1.3 of SeqAn.
- * Updated README.source about using Debian's SeqAn library.
- * Removed machine_bits_detection.patch and added disable_bits_flag.patch.
-
- -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 10:49:47 +0300
-
-bowtie (1.0.0-1) unstable; urgency=low
-
- * New upstream version. (Closes: #705616)
- * Refreshed patches: use_debian_seqan.patch, use-dpkg-buildflags.patch.
- * Removed patch gcc-4.7.patch (fixed upstream).
- * New patch machine_bits_detection.patch.
- * Added build dependancy on seqan-dev.
- * Activated use_debian_seqan.patch and added the following patches:
- - seqan-fix-setBegin-call.patch
- - seqan-rename-ChunkPool.patch
- - seqan-rename-fill-to-resize.patch
- * Added myself to Uploaders control field.
-
- -- Ognyan Kulev <ogi at debian.org> Tue, 23 Apr 2013 16:43:49 +0300
-
-bowtie (0.12.7-3) unstable; urgency=low
-
- * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
- hardening flags (thanks for the patch to Simon Ruderich
- <simon at ruderich.org>)
- Closes: #670230
-
- -- Andreas Tille <tille at debian.org> Tue, 24 Apr 2012 13:21:32 +0200
-
-bowtie (0.12.7-2) unstable; urgency=low
-
- * Do not give a pointer to non existing info pages in manpages
- * debian/control:
- - fixed Vcs fields
- - Standards-Version: 3.9.3 (no changes needed)
- * debian/upstream: Add citation information
- * debian/rules: calculate pkg name instead of setting it
- * debian/copyright: DEP5 verified using
- cme fix dpkg-copyright
- * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
- the function is used
- Thanks to Rodolfo García Peñas <kix at kix.es> and
- gregor herrmann <gregoa at debian.org>
- Closes: #667120
- * debhelper 9 (control+compat)
- Hardening flags were explicitly tested but not enforced in debian/rules
-
- -- Andreas Tille <tille at debian.org> Sun, 22 Apr 2012 21:09:05 +0200
-
-bowtie (0.12.7-1) unstable; urgency=low
-
- * Initial release (Closes: #604940)
-
- -- Andreas Tille <tille at debian.org> Wed, 02 Feb 2011 13:47:12 +0100
Copied: trunk/packages/bowtie/tags/1.1.2-5/debian/changelog (from rev 22757, trunk/packages/bowtie/trunk/debian/changelog)
===================================================================
--- trunk/packages/bowtie/tags/1.1.2-5/debian/changelog (rev 0)
+++ trunk/packages/bowtie/tags/1.1.2-5/debian/changelog 2016-09-07 11:07:33 UTC (rev 22758)
@@ -0,0 +1,188 @@
+bowtie (1.1.2-5) unstable; urgency=medium
+
+ * Team upload.
+ * Make build reproducible again.
+ - Remove build directory from recorded CFLAGS.
+
+ -- Sascha Steinbiss <satta at debian.org> Wed, 07 Sep 2016 10:13:36 +0000
+
+bowtie (1.1.2-4) unstable; urgency=medium
+
+ * Team upload.
+ * Make build reproducible.
+ - Use fixed build hostname and compiler version.
+ * Fix autopkgtest by adjusting directory.
+ * Enable full hardening.
+ * Bump Standards-Version.
+ * Use secure Vcs-Browser.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 25 May 2016 22:25:27 +0000
+
+bowtie (1.1.2-3) unstable; urgency=medium
+
+ * Enable building arch independent packages separately
+ Closes: #806220
+ * Fix clean target
+
+ -- Andreas Tille <tille at debian.org> Wed, 25 Nov 2015 22:38:02 +0100
+
+bowtie (1.1.2-2) unstable; urgency=medium
+
+ * Enable building on arm64 (Thanks for the patch to Edmund Grimley Evans)
+ Closes: #800548
+ * Remove inactive Uploader
+ * Fix spelling
+
+ -- Andreas Tille <tille at debian.org> Thu, 01 Oct 2015 09:47:23 +0200
+
+bowtie (1.1.2-1) unstable; urgency=medium
+
+ * New upstream version
+ * remove strange byte-compyled Python code bowtie-buildc (no idea how and
+ why it was created)
+ * Enabling ppc64el on Makefile and debian/control (Thanks for the patch to
+ Fernando Seiti Furusato <ferseiti at br.ibm.com>)
+ Closes: #788537
+
+ -- Andreas Tille <tille at debian.org> Sun, 05 Jul 2015 21:24:20 +0200
+
+bowtie (1.1.1-2) unstable; urgency=high
+
+ * Team upload.
+ * Install missing commands. Closes: #776881.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 03 Feb 2015 10:44:39 +0900
+
+bowtie (1.1.1-1) unstable; urgency=medium
+
+ * New upstream release
+ * cme fix dpkg-control
+ * Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny)
+ * Add Depends: python (also Build-Depends since it is used in tests)
+
+ -- Andreas Tille <tille at debian.org> Thu, 02 Oct 2014 14:32:50 +0200
+
+bowtie (1.0.1-3) unstable; urgency=medium
+
+ * Drop all architectures except amd64 since there was no success
+ in trying to port the code to other architectures. The portability
+ patch introduced in the last revision was droped again
+ * debian/copyright: Drop unneeded copyright statements about code that
+ was removed from upstream source
+
+ -- Andreas Tille <tille at debian.org> Mon, 15 Sep 2014 11:00:25 +0200
+
+bowtie (1.0.1-2) unstable; urgency=medium
+
+ * Do not use copy of outdated gcc header file which destroys portability
+ to other architectures
+ Closes: #756780
+ * Add README.Debian informing users about the fact that we ignore copy
+ of cpuid.h
+ * Add unit tests for build time and autopkgtest
+ * Add debian/README.test to explain how to test the package
+ Attention: Please take notice of /usr/share/bowtie/README.Debian about
+ "Test suite for bowtie created and potential issue with sorting"
+
+ -- Andreas Tille <tille at debian.org> Wed, 03 Sep 2014 09:50:22 +0200
+
+bowtie (1.0.1-1) unstable; urgency=medium
+
+ * New upstream version (adapted patches)
+ * drop debian/get-orig-source but rather remove the SeqAn-1.1 code
+ copy via Files-Excluded
+ * debian/control: Priority: optional
+
+ -- Andreas Tille <tille at debian.org> Wed, 30 Jul 2014 13:38:25 +0200
+
+bowtie (1.0.0-6) unstable; urgency=low
+
+ * debian/patches/seqan-popcount.patch: New patch. (Closes: #733398)
+ * Version 1.4 of seqan-dev is required now.
+ * Standards-Version: 3.9.5 (no changes needed).
+ * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy.
+
+ -- Ognyan Kulev <ogi at debian.org> Sat, 08 Mar 2014 15:13:16 +0200
+
+bowtie (1.0.0-5) unstable; urgency=low
+
+ * Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target
+ instead of override_dh_fixperms in debian/rules.
+
+ -- Ognyan Kulev <ogi at debian.org> Thu, 30 May 2013 09:41:25 +0300
+
+bowtie (1.0.0-4) unstable; urgency=low
+
+ * Lintian fixes:
+ - Removed DM-Upload-Allowed field.
+ - Standards Version 3.9.4 (no changes needed).
+ - Remove execute bits on some files in bowtie-examples.
+ * Don't compress *.ebwt index files in bowtie-examples package.
+ * Package description now starts with a capital letter.
+
+ -- Ognyan Kulev <ogi at debian.org> Wed, 29 May 2013 22:53:13 +0300
+
+bowtie (1.0.0-3) unstable; urgency=low
+
+ * New patch no_hash_style_both_for_mips.patch.
+ This fixes build errors on mips and mipsel.
+
+ -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 15:15:37 +0300
+
+bowtie (1.0.0-2) unstable; urgency=low
+
+ * Requires version 1.3 of SeqAn.
+ * Updated README.source about using Debian's SeqAn library.
+ * Removed machine_bits_detection.patch and added disable_bits_flag.patch.
+
+ -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 10:49:47 +0300
+
+bowtie (1.0.0-1) unstable; urgency=low
+
+ * New upstream version. (Closes: #705616)
+ * Refreshed patches: use_debian_seqan.patch, use-dpkg-buildflags.patch.
+ * Removed patch gcc-4.7.patch (fixed upstream).
+ * New patch machine_bits_detection.patch.
+ * Added build dependancy on seqan-dev.
+ * Activated use_debian_seqan.patch and added the following patches:
+ - seqan-fix-setBegin-call.patch
+ - seqan-rename-ChunkPool.patch
+ - seqan-rename-fill-to-resize.patch
+ * Added myself to Uploaders control field.
+
+ -- Ognyan Kulev <ogi at debian.org> Tue, 23 Apr 2013 16:43:49 +0300
+
+bowtie (0.12.7-3) unstable; urgency=low
+
+ * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
+ hardening flags (thanks for the patch to Simon Ruderich
+ <simon at ruderich.org>)
+ Closes: #670230
+
+ -- Andreas Tille <tille at debian.org> Tue, 24 Apr 2012 13:21:32 +0200
+
+bowtie (0.12.7-2) unstable; urgency=low
+
+ * Do not give a pointer to non existing info pages in manpages
+ * debian/control:
+ - fixed Vcs fields
+ - Standards-Version: 3.9.3 (no changes needed)
+ * debian/upstream: Add citation information
+ * debian/rules: calculate pkg name instead of setting it
+ * debian/copyright: DEP5 verified using
+ cme fix dpkg-copyright
+ * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
+ the function is used
+ Thanks to Rodolfo García Peñas <kix at kix.es> and
+ gregor herrmann <gregoa at debian.org>
+ Closes: #667120
+ * debhelper 9 (control+compat)
+ Hardening flags were explicitly tested but not enforced in debian/rules
+
+ -- Andreas Tille <tille at debian.org> Sun, 22 Apr 2012 21:09:05 +0200
+
+bowtie (0.12.7-1) unstable; urgency=low
+
+ * Initial release (Closes: #604940)
+
+ -- Andreas Tille <tille at debian.org> Wed, 02 Feb 2011 13:47:12 +0100
Deleted: trunk/packages/bowtie/tags/1.1.2-5/debian/patches/reproducible.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/reproducible.patch 2016-09-06 16:50:33 UTC (rev 22756)
+++ trunk/packages/bowtie/tags/1.1.2-5/debian/patches/reproducible.patch 2016-09-07 11:07:33 UTC (rev 22758)
@@ -1,17 +0,0 @@
-Description: make build reproducible
-Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/Makefile
-+++ b/Makefile
-@@ -207,9 +207,9 @@
-
- DEFS=-fno-strict-aliasing \
- -DBOWTIE_VERSION="\"`cat VERSION`\"" \
-- -DBUILD_HOST="\"`hostname`\"" \
-- -DBUILD_TIME="\"`date`\"" \
-- -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
-+ -DBUILD_HOST="\"Debian-reproducible\"" \
-+ -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
-+ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
- $(FILE_FLAGS) \
- $(PTHREAD_DEF) \
- $(PREF_DEF) \
Copied: trunk/packages/bowtie/tags/1.1.2-5/debian/patches/reproducible.patch (from rev 22757, trunk/packages/bowtie/trunk/debian/patches/reproducible.patch)
===================================================================
--- trunk/packages/bowtie/tags/1.1.2-5/debian/patches/reproducible.patch (rev 0)
+++ trunk/packages/bowtie/tags/1.1.2-5/debian/patches/reproducible.patch 2016-09-07 11:07:33 UTC (rev 22758)
@@ -0,0 +1,28 @@
+Description: make build reproducible
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/Makefile
++++ b/Makefile
+@@ -207,9 +207,9 @@
+
+ DEFS=-fno-strict-aliasing \
+ -DBOWTIE_VERSION="\"`cat VERSION`\"" \
+- -DBUILD_HOST="\"`hostname`\"" \
+- -DBUILD_TIME="\"`date`\"" \
+- -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
++ -DBUILD_HOST="\"Debian-reproducible\"" \
++ -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" \
++ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" \
+ $(FILE_FLAGS) \
+ $(PTHREAD_DEF) \
+ $(PREF_DEF) \
+@@ -217,8 +217,8 @@
+ $(SHMEM_DEF)
+
+ ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
+-DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
+-RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
++DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(subst $(shell pwd),.,$(ALL_FLAGS))\""
++RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(subst $(shell pwd),.,$(ALL_FLAGS))\""
+
+ #
+ # bowtie-build targets
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