[med-svn] r9608 - in trunk/packages/mummer/tags: . 3.23~dfsg-1/debian
Charles Plessy
plessy at alioth.debian.org
Tue Feb 7 06:25:56 UTC 2012
Author: plessy
Date: 2012-02-07 06:25:55 +0000 (Tue, 07 Feb 2012)
New Revision: 9608
Added:
trunk/packages/mummer/tags/3.23~dfsg-1/
trunk/packages/mummer/tags/3.23~dfsg-1/debian/changelog
trunk/packages/mummer/tags/3.23~dfsg-1/debian/control
trunk/packages/mummer/tags/3.23~dfsg-1/debian/rules
trunk/packages/mummer/tags/3.23~dfsg-1/debian/source/
Removed:
trunk/packages/mummer/tags/3.23~dfsg-1/debian/changelog
trunk/packages/mummer/tags/3.23~dfsg-1/debian/control
trunk/packages/mummer/tags/3.23~dfsg-1/debian/rules
Log:
[svn-buildpackage] Tagging mummer 3.23~dfsg-1
Deleted: trunk/packages/mummer/tags/3.23~dfsg-1/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog 2012-02-06 21:30:55 UTC (rev 9603)
+++ trunk/packages/mummer/tags/3.23~dfsg-1/debian/changelog 2012-02-07 06:25:55 UTC (rev 9608)
@@ -1,120 +0,0 @@
-mummer (3.23~dfsg-1) UNRELEASED; urgency=low
-
- * New upstream release adding -D and --banded option to nucmer.
- * Updated debian/patches/02at_docs_web.diff.
- * Corrected VCS URLs (debian/control).
- * Conforms to Policy 3.9.2 (debian/control, no other changes needed).
- * Using Debhelper 8 (debian/control, debian/compat).
- * Support DEB_BUILD_OPTIONS via Debhelper (debian/rules).
-
- -- Charles Plessy <plessy at debian.org> Thu, 02 Feb 2012 12:59:31 +0900
-
-mummer (3.22~dfsg-2) unstable; urgency=low
-
- [ Andreas Tille ]
- * Make sure scripts will use the installation path instead of
- the temporary build path
- Closes: #575105
- * Make real use of debian/sh-replacement-scripts and drop csh
- (build-)dependency
- * incremented Standards-Version to reflect concordance with Debian Policy
- 3.8.4 (no changes needed).
- * install tandem-repeat.awk which was lacking from installation
- previousely
-
- [ Charles Plessy ]
- * Updated upstream-metadata.yaml to use simple key=value form
- instead of BibTeX entry
-
- -- Andreas Tille <tille at debian.org> Wed, 24 Mar 2010 17:10:43 +0000
-
-mummer (3.22~dfsg-1) unstable; urgency=low
-
- * New upstream release:
- 3.22
- - Significant 'dnadiff' bug fixes.
- - Unaligned contig output format switched to match show-diff format.
- - Dynamic memory allocation for run-mummer1.
- - Turned off output of the near useless .cluster files from nucmer and
- promer (let us know if you still want them).
- 3.21
- - gcc compatibility fix.
- * debian/get-orig-source: rename mutilated upstream tarball.
- * debian/control:
- - incremented Standards-Version to reflect concordance with Debian Policy
- 3.8.3 (no changes needed).
- - mummer-docs depends on ${misc:Depends}.
- - dropped versionned dependencies when they are even satisfied in oldstable.
- - dropped dependency on CDBS and patchutils, and added dependency on quilt.
- - using Debhelper 7 (debian/compat).
- - build-depend on csh for correct interpreter path detection.
- * debian/patches:
- - replaces some Makefile patches by environment variables in debian/rules.
- - replaced 02at_scripts.diff by separate files in sh-replacement-scripts.
- - added a series file to use Quilt.
- - dropped the patch ‘01sm_src_tigr.diff’ that allowed to use MUMmer on
- computers with less that 512 Mo of memory and is now obsoleted by
- this release.
- - refreshed the 02at_docs_web.diff patch that redirects the links for the
- suppressed PDF files to the upstream website.
- * debian/rules converted to debhelper (the build system is too odd to be
- handled gently by CDBS without patches).
- * Mangled ‘~dfsg’ from the Debian version number in debian/watch.
- * Converted debian/copyright to a machine-readable format.
- * Documented the PDF deletion and the patching in ‘debian/README.source’.
- * Turned the get-orig-source shell script into a debian/rule target.
- * Added an experimental collection of upstream metadata in YAML format
- (debian/upstream-metadata.yaml).
-
- -- Charles Plessy <plessy at debian.org> Mon, 12 Oct 2009 18:12:18 +0900
-
-mummer (3.20-3) unstable; urgency=low
-
- * Changed the doc-base section according to the new policy.
- * Added myself to the `Uploaders' field in `debian/control'.
- * Removed `debian/mummer.dirs', that was only creating empty directories.
-
- -- Charles Plessy <plessy at debian.org> Mon, 07 Jul 2008 10:33:20 +0900
-
-mummer (3.20-2) unstable; urgency=low
-
- [ Charles Plessy ]
- * XS-DM-Upload-Allowed: Yes
-
- [ Steffen Moeller ]
- * Changed e-mail address in uploaders
- * Stripped long description of mummer-doc
-
- [ Andreas Tille ]
- * Do not install mummer.desktop because it is a command line
- application (Fixed debian/mummer.desktop anyway)
- * Standards-Version: 3.7.3 (no changes needed)
-
- -- Andreas Tille <tille at debian.org> Thu, 10 Jan 2008 12:13:24 +0100
-
-mummer (3.20-1) unstable; urgency=low
-
- * New upstream version
- * Fixed watch file (Thanks to Nelson A. de Oliveira <naoliv at gmail.com>)
- Closes: #450211
- * Do not autogenerate debian/control
- * debian/rules: get-orig-source target that removes non-free docs
- * debian/rules: Fixed building docs
- * Separated patches tigr and kurtz; better Makefile for scripts
- * Added manpage link for dnadiff and mentioned dnadiff in debian/mummer.1
- * Used "Office" as main Freedesktop.Org category (not sure whether this
- is a really good choice)
-
- -- Andreas Tille <tille at debian.org> Wed, 07 Nov 2007 13:25:34 +0100
-
-mummer (3.19-1) unstable; urgency=low
-
- * Initial Release (Closes: Bug#201761).
- Thanks to Steffen Moeller <moeller at inb.uni-luebeck.de> who
- prepared a package for version 3.17 and just some
- cleanups were left.
- * New Standards-Version (no changes needed)
- * Switched to cdbs to simplify handling of patches
- * debian/compat: 5
-
- -- Andreas Tille <tille at debian.org> Mon, 07 May 2007 14:11:09 +0200
Copied: trunk/packages/mummer/tags/3.23~dfsg-1/debian/changelog (from rev 9607, trunk/packages/mummer/trunk/debian/changelog)
===================================================================
--- trunk/packages/mummer/tags/3.23~dfsg-1/debian/changelog (rev 0)
+++ trunk/packages/mummer/tags/3.23~dfsg-1/debian/changelog 2012-02-07 06:25:55 UTC (rev 9608)
@@ -0,0 +1,124 @@
+mummer (3.23~dfsg-1) unstable; urgency=low
+
+ * New upstream release adding -D and --banded option to nucmer.
+ * Updated debian/patches/02at_docs_web.diff.
+ * Corrected VCS URLs (debian/control).
+ * Conforms to Policy 3.9.2 (debian/control, no other changes needed).
+ * Using Debhelper 8 (debian/control, debian/compat).
+ * Support DEB_BUILD_OPTIONS via Debhelper (debian/rules).
+ * Use dpkg source format 3.0 (quilt) as a patch system (debian/rules,
+ debian/control, debian/source/format).
+ * Simplify debian/rules using dh.
+ * Pass Dpkg build flags in CFLAGS (debian/rules).
+
+ -- Charles Plessy <plessy at debian.org> Tue, 07 Feb 2012 15:01:26 +0900
+
+mummer (3.22~dfsg-2) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * Make sure scripts will use the installation path instead of
+ the temporary build path
+ Closes: #575105
+ * Make real use of debian/sh-replacement-scripts and drop csh
+ (build-)dependency
+ * incremented Standards-Version to reflect concordance with Debian Policy
+ 3.8.4 (no changes needed).
+ * install tandem-repeat.awk which was lacking from installation
+ previousely
+
+ [ Charles Plessy ]
+ * Updated upstream-metadata.yaml to use simple key=value form
+ instead of BibTeX entry
+
+ -- Andreas Tille <tille at debian.org> Wed, 24 Mar 2010 17:10:43 +0000
+
+mummer (3.22~dfsg-1) unstable; urgency=low
+
+ * New upstream release:
+ 3.22
+ - Significant 'dnadiff' bug fixes.
+ - Unaligned contig output format switched to match show-diff format.
+ - Dynamic memory allocation for run-mummer1.
+ - Turned off output of the near useless .cluster files from nucmer and
+ promer (let us know if you still want them).
+ 3.21
+ - gcc compatibility fix.
+ * debian/get-orig-source: rename mutilated upstream tarball.
+ * debian/control:
+ - incremented Standards-Version to reflect concordance with Debian Policy
+ 3.8.3 (no changes needed).
+ - mummer-docs depends on ${misc:Depends}.
+ - dropped versionned dependencies when they are even satisfied in oldstable.
+ - dropped dependency on CDBS and patchutils, and added dependency on quilt.
+ - using Debhelper 7 (debian/compat).
+ - build-depend on csh for correct interpreter path detection.
+ * debian/patches:
+ - replaces some Makefile patches by environment variables in debian/rules.
+ - replaced 02at_scripts.diff by separate files in sh-replacement-scripts.
+ - added a series file to use Quilt.
+ - dropped the patch ‘01sm_src_tigr.diff’ that allowed to use MUMmer on
+ computers with less that 512 Mo of memory and is now obsoleted by
+ this release.
+ - refreshed the 02at_docs_web.diff patch that redirects the links for the
+ suppressed PDF files to the upstream website.
+ * debian/rules converted to debhelper (the build system is too odd to be
+ handled gently by CDBS without patches).
+ * Mangled ‘~dfsg’ from the Debian version number in debian/watch.
+ * Converted debian/copyright to a machine-readable format.
+ * Documented the PDF deletion and the patching in ‘debian/README.source’.
+ * Turned the get-orig-source shell script into a debian/rule target.
+ * Added an experimental collection of upstream metadata in YAML format
+ (debian/upstream-metadata.yaml).
+
+ -- Charles Plessy <plessy at debian.org> Mon, 12 Oct 2009 18:12:18 +0900
+
+mummer (3.20-3) unstable; urgency=low
+
+ * Changed the doc-base section according to the new policy.
+ * Added myself to the `Uploaders' field in `debian/control'.
+ * Removed `debian/mummer.dirs', that was only creating empty directories.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 07 Jul 2008 10:33:20 +0900
+
+mummer (3.20-2) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * XS-DM-Upload-Allowed: Yes
+
+ [ Steffen Moeller ]
+ * Changed e-mail address in uploaders
+ * Stripped long description of mummer-doc
+
+ [ Andreas Tille ]
+ * Do not install mummer.desktop because it is a command line
+ application (Fixed debian/mummer.desktop anyway)
+ * Standards-Version: 3.7.3 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Thu, 10 Jan 2008 12:13:24 +0100
+
+mummer (3.20-1) unstable; urgency=low
+
+ * New upstream version
+ * Fixed watch file (Thanks to Nelson A. de Oliveira <naoliv at gmail.com>)
+ Closes: #450211
+ * Do not autogenerate debian/control
+ * debian/rules: get-orig-source target that removes non-free docs
+ * debian/rules: Fixed building docs
+ * Separated patches tigr and kurtz; better Makefile for scripts
+ * Added manpage link for dnadiff and mentioned dnadiff in debian/mummer.1
+ * Used "Office" as main Freedesktop.Org category (not sure whether this
+ is a really good choice)
+
+ -- Andreas Tille <tille at debian.org> Wed, 07 Nov 2007 13:25:34 +0100
+
+mummer (3.19-1) unstable; urgency=low
+
+ * Initial Release (Closes: Bug#201761).
+ Thanks to Steffen Moeller <moeller at inb.uni-luebeck.de> who
+ prepared a package for version 3.17 and just some
+ cleanups were left.
+ * New Standards-Version (no changes needed)
+ * Switched to cdbs to simplify handling of patches
+ * debian/compat: 5
+
+ -- Andreas Tille <tille at debian.org> Mon, 07 May 2007 14:11:09 +0200
Deleted: trunk/packages/mummer/tags/3.23~dfsg-1/debian/control
===================================================================
--- trunk/packages/mummer/trunk/debian/control 2012-02-06 21:30:55 UTC (rev 9603)
+++ trunk/packages/mummer/tags/3.23~dfsg-1/debian/control 2012-02-07 06:25:55 UTC (rev 9608)
@@ -1,35 +0,0 @@
-Source: mummer
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>, Charles Plessy <plessy at debian.org>
-Build-Depends: quilt, debhelper (>= 8), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
-Standards-Version: 3.9.2
-Homepage: http://mummer.sourceforge.net/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mummer/trunk/
-
-Package: mummer
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, perl, gawk
-Description: Efficient sequence alignment of full genomes
- MUMmer is a system for rapidly aligning entire genomes, whether
- in complete or draft form. For example, MUMmer 3.0 can find all
- 20-basepair or longer exact matches between a pair of 5-megabase genomes
- in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop
- computer. MUMmer can also align incomplete genomes; it handles the 100s
- or 1000s of contigs from a shotgun sequencing project with ease, and
- will align them to another set of contigs or a genome using the NUCmer
- program included with the system. If the species are too divergent for
- DNA sequence alignment to detect similarity, then the PROmer program
- can generate alignments based upon the six-frame translations of both
- input sequences.
-
-Package: mummer-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Description: Documentation for MUMmer
- This package contains the documentation for MUMmer, a system for rapidly
- aligning entire genomes.
Copied: trunk/packages/mummer/tags/3.23~dfsg-1/debian/control (from rev 9604, trunk/packages/mummer/trunk/debian/control)
===================================================================
--- trunk/packages/mummer/tags/3.23~dfsg-1/debian/control (rev 0)
+++ trunk/packages/mummer/tags/3.23~dfsg-1/debian/control 2012-02-07 06:25:55 UTC (rev 9608)
@@ -0,0 +1,35 @@
+Source: mummer
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>, Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 8), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
+Standards-Version: 3.9.2
+Homepage: http://mummer.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mummer/trunk/
+
+Package: mummer
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl, gawk
+Description: Efficient sequence alignment of full genomes
+ MUMmer is a system for rapidly aligning entire genomes, whether
+ in complete or draft form. For example, MUMmer 3.0 can find all
+ 20-basepair or longer exact matches between a pair of 5-megabase genomes
+ in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop
+ computer. MUMmer can also align incomplete genomes; it handles the 100s
+ or 1000s of contigs from a shotgun sequencing project with ease, and
+ will align them to another set of contigs or a genome using the NUCmer
+ program included with the system. If the species are too divergent for
+ DNA sequence alignment to detect similarity, then the PROmer program
+ can generate alignments based upon the six-frame translations of both
+ input sequences.
+
+Package: mummer-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Description: Documentation for MUMmer
+ This package contains the documentation for MUMmer, a system for rapidly
+ aligning entire genomes.
Deleted: trunk/packages/mummer/tags/3.23~dfsg-1/debian/rules
===================================================================
--- trunk/packages/mummer/trunk/debian/rules 2012-02-06 21:30:55 UTC (rev 9603)
+++ trunk/packages/mummer/tags/3.23~dfsg-1/debian/rules 2012-02-07 06:25:55 UTC (rev 9608)
@@ -1,76 +0,0 @@
-#!/usr/bin/make -f
-
-include /usr/share/quilt/quilt.make
-
-build:
- # ...
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- # Code to run the package test suite.
-endif
-
-# src/kurtz/mm3src/Makefile and src/kurtz/streesrc/Makefile make a use of CFLAGS that does not allow to override it, hence the following is added:
-CFLAGS += -DSTREEHUGE -I$(CURDIR)/src/kurtz/libbasedir -I$(CURDIR)/src/kurtz/streesrc
-
-TMPDIR = $(CURDIR)/debian/tmp
-BIN_DIR = $(TMPDIR)/usr/bin
-AUX_BIN_DIR = $(TMPDIR)/usr/lib/mummer
-FINAL_BIN_DIR = /usr/bin
-FINAL_AUX_BIN_DIR = /usr/lib/mummer
-FINAL_SCRIPT_DIR = /usr/share/perl5/
-
-build: $(QUILT_STAMPFN) build-stamp
-build-stamp:
-# Unfortunately the upstream makefile does not separate the build and install steps.
-
-install:
-install: build
-# Unfortunately the upstream makefile does not separate the build and install steps.
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs
- [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
- [ -d $(AUX_BIN_DIR) ] || mkdir -p $(AUX_BIN_DIR)
- $(MAKE) BIN_DIR=$(BIN_DIR) AUX_BIN_DIR=$(AUX_BIN_DIR) \
- FINAL_BIN_DIR=$(FINAL_BIN_DIR) FINAL_AUX_BIN_DIR=$(FINAL_AUX_BIN_DIR) \
- FINAL_SCRIPT_DIR=$(FINAL_SCRIPT_DIR) \
- CFLAGS="$(CFLAGS)"
- $(MAKE) -C docs
- $(MAKE) check
-# /usr/bin/annotate renamed /usr/bin/mummer-annotate for namespace and license (Artistic) reasons.
- mv $(CURDIR)/debian/tmp/usr/bin/annotate $(CURDIR)/debian/tmp/usr/bin/mummer-annotate
- dh_install
- touch build-stamp
-
-clean: unpatch
- dh clean
-
-binary-indep: build install
- dh binary-indep
-
-binary-arch: build install
- dh binary-arch
-
-override_dh_install:
- dh_install
- [ -f $(BIN_DIR)/annotate ] && mv $(BIN_DIR)/annotate $(BIN_DIR)/mummer-annotate
-
-override_dh_compress:
- dh_compress -Xpdf
-
-NAME = $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-VERSION = $(shell dpkg-parsechangelog | sed -n 's/^Version: //p' | sed 's/~dfsg.*//')
-TARBALL = MUMmer$(VERSION).tar.gz
-
-get-orig-source:
- wget http://downloads.sourceforge.net/sourceforge/$(NAME)/$(TARBALL)
- rm -rf tmp
- mkdir tmp
- cd tmp ;\
- tar -xzf ../$(TARBALL) ;\
- rm -vf `find . -maxdepth 4 -name [MX]*.pdf` ;\
- GZIP="--best --no-name" tar -czf ../$(NAME)_$(VERSION)~dfsg.orig.tar.gz *
- rm -rf tmp
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
Copied: trunk/packages/mummer/tags/3.23~dfsg-1/debian/rules (from rev 9606, trunk/packages/mummer/trunk/debian/rules)
===================================================================
--- trunk/packages/mummer/tags/3.23~dfsg-1/debian/rules (rev 0)
+++ trunk/packages/mummer/tags/3.23~dfsg-1/debian/rules 2012-02-07 06:25:55 UTC (rev 9608)
@@ -0,0 +1,51 @@
+#!/usr/bin/make -f
+%:
+ dh $@
+
+CFLAGS += $(shell dpkg-buildflags --get CFLAGS)
+# src/kurtz/mm3src/Makefile and src/kurtz/streesrc/Makefile make a use of CFLAGS that does not allow to override it, hence the following is added:
+CFLAGS += -DSTREEHUGE -I$(CURDIR)/src/kurtz/libbasedir -I$(CURDIR)/src/kurtz/streesrc
+
+TMPDIR = $(CURDIR)/debian/tmp
+BIN_DIR = $(TMPDIR)/usr/bin
+AUX_BIN_DIR = $(TMPDIR)/usr/lib/mummer
+FINAL_BIN_DIR = /usr/bin
+FINAL_AUX_BIN_DIR = /usr/lib/mummer
+FINAL_SCRIPT_DIR = /usr/share/perl5/
+
+override_dh_auto_build:
+ [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
+ [ -d $(AUX_BIN_DIR) ] || mkdir -p $(AUX_BIN_DIR)
+ $(MAKE) BIN_DIR=$(BIN_DIR) AUX_BIN_DIR=$(AUX_BIN_DIR) \
+ FINAL_BIN_DIR=$(FINAL_BIN_DIR) FINAL_AUX_BIN_DIR=$(FINAL_AUX_BIN_DIR) \
+ FINAL_SCRIPT_DIR=$(FINAL_SCRIPT_DIR) \
+ CFLAGS="$(CFLAGS)"
+ $(MAKE) -C docs
+
+override_dh_auto_test:
+ $(MAKE) check
+
+override_dh_prep:
+# Unfortunately the upstream makefile does not separate the build and install steps.
+ dh_prep -X debian/tmp
+
+override_dh_auto_install:
+# /usr/bin/annotate renamed /usr/bin/mummer-annotate for namespace and license (Artistic) reasons.
+ mv $(BIN_DIR)/annotate $(BIN_DIR)/mummer-annotate
+
+override_dh_compress:
+ dh_compress -Xpdf
+
+NAME = $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+VERSION = $(shell dpkg-parsechangelog | sed -n 's/^Version: //p' | sed 's/~dfsg.*//')
+TARBALL = MUMmer$(VERSION).tar.gz
+
+get-orig-source:
+ wget http://downloads.sourceforge.net/sourceforge/$(NAME)/$(TARBALL)
+ rm -rf tmp
+ mkdir tmp
+ cd tmp ;\
+ tar -xzf ../$(TARBALL) ;\
+ rm -vf `find . -maxdepth 4 -name [MX]*.pdf` ;\
+ GZIP="--best --no-name" tar -czf ../$(NAME)_$(VERSION)~dfsg.orig.tar.gz *
+ rm -rf tmp
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