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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>) - 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 <[email protected]> Wed, 07 Nov 2007 13:25:34 +0100 - -mummer (3.19-1) unstable; urgency=low - - * Initial Release (Closes: Bug#201761). - Thanks to Steffen Moeller <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>) + 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 <[email protected]> Wed, 07 Nov 2007 13:25:34 +0100 + +mummer (3.19-1) unstable; urgency=low + + * Initial Release (Closes: Bug#201761). + Thanks to Steffen Moeller <[email protected]> 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 <[email protected]> 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 <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]>, Charles Plessy <[email protected]> -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 <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]>, Charles Plessy <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
