Author: plessy Date: 2011-08-25 04:21:19 +0000 (Thu, 25 Aug 2011) New Revision: 7544
Added: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/changelog trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/compat trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/control trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/copyright trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/rules Removed: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/changelog trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/compat trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/control trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/copyright trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/rules Log: [svn-buildpackage] Tagging libtfbs-perl 0.5.svn.20100421-1 Deleted: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/changelog =================================================================== --- trunk/packages/libtfbs-perl/trunk/debian/changelog 2011-08-24 16:47:14 UTC (rev 7538) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/changelog 2011-08-25 04:21:19 UTC (rev 7544) @@ -1,42 +0,0 @@ -libtfbs-perl (0.5.svn.20091128-1) unstable; urgency=low - - * New upstream SVN snapshot, adding JASPAR5 support. - * Skip test that needs a network connection unless in maintainer mode. - (debian/rules). Thanks to Gregor Herrmann (Closes: #533995). - * Updated to Policy 3.8.3: - - Incremented Standards-Version (debian/control) - - Dropped version in build dependency on Perl (debian/control). - - Honor the ‘nocheck’ build option (debian/rules). - * Documented how this package is tested in debian/README.Debian. - * Added meta-information in debian/upstream-metadata.yaml. - * Refreshed debian/copyright to latest experimentations on the format. - * Debhelper 7: use dh_prep and dh binary-arch in debian/rules. - - -- Charles Plessy <[email protected]> Sat, 28 Nov 2009 14:14:36 +0900 - -libtfbs-perl (0.5.svn.20080722-2) unstable; urgency=low - - * debian/control: - - Added bioperl to the build dependencies (Closes: #493341). - - Dropped quilt build dependency (see below). - - Added myself to the Uploaders field. - - Added `libgd-gd2-perl | libgd-gd2-noxpm-perl' as recommended package. - * debian/compat, debian/control: - - Using debhelper 7. - * debian/rules: - - Refreshed with `dh-make-perl --refresh'. - - Removes /usr/lib/perl5/pwm_searchPFF.c and /usr/lib/perl5/pwm_search.h, - that should not be installed there. - * debian/patches, debian/rules: - - Disabling the MySQL tests with `echo "n" |' instead of patches. - * debian/copyright: - - Converted to machine-readable format. - - Added myself to the Hall of Fame. - - -- Charles Plessy <[email protected]> Mon, 11 Aug 2008 13:27:45 +0900 - -libtfbs-perl (0.5.svn.20080722-1) unstable; urgency=low - - * Initial release (closes: #491714). - - -- Steffen Moeller <[email protected]> Tue, 22 Jul 2008 00:07:17 +0200 Copied: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/changelog (from rev 7543, trunk/packages/libtfbs-perl/trunk/debian/changelog) =================================================================== --- trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/changelog (rev 0) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/changelog 2011-08-25 04:21:19 UTC (rev 7544) @@ -0,0 +1,56 @@ +libtfbs-perl (0.5.svn.20100421-1) unstable; urgency=low + + * New upstream SVN snapshot fixing issue related to new naming conventions. + * Arranged the get-orig-source target of debian/rules to pick the date + of the last upstream commit. + * Corrected Vcs fields in debian/control. + * Conforms with Policy 3.9.2: + - Incremented Standards-Version in debian/control. + - Mention GPL version 1 in debian/copyright. + * Switch to Debhelper 8 and dh rules. + * Converted debian/copyright to DEP-5 format. + + -- Charles Plessy <[email protected]> Thu, 25 Aug 2011 13:10:21 +0900 + +libtfbs-perl (0.5.svn.20091128-1) unstable; urgency=low + + * New upstream SVN snapshot, adding JASPAR5 support. + * Skip test that needs a network connection unless in maintainer mode. + (debian/rules). Thanks to Gregor Herrmann (Closes: #533995). + * Updated to Policy 3.8.3: + - Incremented Standards-Version (debian/control) + - Dropped version in build dependency on Perl (debian/control). + - Honor the ‘nocheck’ build option (debian/rules). + * Documented how this package is tested in debian/README.Debian. + * Added meta-information in debian/upstream-metadata.yaml. + * Refreshed debian/copyright to latest experimentations on the format. + * Debhelper 7: use dh_prep and dh binary-arch in debian/rules. + + -- Charles Plessy <[email protected]> Sat, 28 Nov 2009 14:14:36 +0900 + +libtfbs-perl (0.5.svn.20080722-2) unstable; urgency=low + + * debian/control: + - Added bioperl to the build dependencies (Closes: #493341). + - Dropped quilt build dependency (see below). + - Added myself to the Uploaders field. + - Added `libgd-gd2-perl | libgd-gd2-noxpm-perl' as recommended package. + * debian/compat, debian/control: + - Using debhelper 7. + * debian/rules: + - Refreshed with `dh-make-perl --refresh'. + - Removes /usr/lib/perl5/pwm_searchPFF.c and /usr/lib/perl5/pwm_search.h, + that should not be installed there. + * debian/patches, debian/rules: + - Disabling the MySQL tests with `echo "n" |' instead of patches. + * debian/copyright: + - Converted to machine-readable format. + - Added myself to the Hall of Fame. + + -- Charles Plessy <[email protected]> Mon, 11 Aug 2008 13:27:45 +0900 + +libtfbs-perl (0.5.svn.20080722-1) unstable; urgency=low + + * Initial release (closes: #491714). + + -- Steffen Moeller <[email protected]> Tue, 22 Jul 2008 00:07:17 +0200 Deleted: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/compat =================================================================== --- trunk/packages/libtfbs-perl/trunk/debian/compat 2011-08-24 16:47:14 UTC (rev 7538) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/compat 2011-08-25 04:21:19 UTC (rev 7544) @@ -1 +0,0 @@ -7 Copied: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/compat (from rev 7542, trunk/packages/libtfbs-perl/trunk/debian/compat) =================================================================== --- trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/compat (rev 0) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/compat 2011-08-25 04:21:19 UTC (rev 7544) @@ -0,0 +1 @@ +8 Deleted: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/control =================================================================== --- trunk/packages/libtfbs-perl/trunk/debian/control 2011-08-24 16:47:14 UTC (rev 7538) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/control 2011-08-25 04:21:19 UTC (rev 7544) @@ -1,28 +0,0 @@ -Source: libtfbs-perl -Section: perl -Priority: optional -Build-Depends: debhelper (>= 7), perl, pdl, bioperl, libwww-perl, libdbi-perl -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Steffen Moeller <[email protected]>, Charles Plessy <[email protected]> -Standards-Version: 3.8.3 -Homepage: http://tfbs.genereg.net -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libtfbs-perl/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libtfbs-perl/trunk/ - -Package: libtfbs-perl -Architecture: any -Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, pdl, bioperl, libwww-perl, libdbi-perl -Recommends: libgd-gd2-perl | libgd-gd2-noxpm-perl -Description: scanning DNA sequence with a position weight matrix - The TFBS perl modules comprise a set of routines to interact with the - Transfac and Jaspar databases that describe a special family of proteins, - the transcription factors. These bind to genomic DNA to initiate (or - prevent) the readout of a gene. Once multiple binding sites are known - for a transcription factor, these are gathered in a single file and are - aligned in order to find position-specific characteristica that might - be used to predict such binding events in novel DNA sequences. - . - If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002) - TFBS: Computational framework for transcription factor binding site analysis. - Bioinformatics 18:1135-1136". Copied: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/control (from rev 7542, trunk/packages/libtfbs-perl/trunk/debian/control) =================================================================== --- trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/control (rev 0) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/control 2011-08-25 04:21:19 UTC (rev 7544) @@ -0,0 +1,28 @@ +Source: libtfbs-perl +Section: perl +Priority: optional +Build-Depends: debhelper (>= 8), perl, pdl, bioperl, libwww-perl, libdbi-perl +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller <[email protected]>, Charles Plessy <[email protected]> +Standards-Version: 3.9.2 +Homepage: http://tfbs.genereg.net +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libtfbs-perl/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/libtfbs-perl/trunk/ + +Package: libtfbs-perl +Architecture: any +Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, pdl, bioperl, libwww-perl, libdbi-perl +Recommends: libgd-gd2-perl | libgd-gd2-noxpm-perl +Description: scanning DNA sequence with a position weight matrix + The TFBS perl modules comprise a set of routines to interact with the + Transfac and Jaspar databases that describe a special family of proteins, + the transcription factors. These bind to genomic DNA to initiate (or + prevent) the readout of a gene. Once multiple binding sites are known + for a transcription factor, these are gathered in a single file and are + aligned in order to find position-specific characteristica that might + be used to predict such binding events in novel DNA sequences. + . + If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002) + TFBS: Computational framework for transcription factor binding site analysis. + Bioinformatics 18:1135-1136". Deleted: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/copyright =================================================================== --- trunk/packages/libtfbs-perl/trunk/debian/copyright 2011-08-24 16:47:14 UTC (rev 7538) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/copyright 2011-08-25 04:21:19 UTC (rev 7544) @@ -1,38 +0,0 @@ -Name : TFBS -Contact : Boris Lenhard <[email protected]> -Source : http://www.ii.uib.no/svn/lenhard/TFBS/ - - -Copyright: © 2005-2007 Boris Lenhard <[email protected]>, - Stephen Montgomery <[email protected]>, - Leonardo Marino-Ramirez, - Wynand Alkema, -License: Perl - - This Perl module is distributed under the same license as Perl itself. - - - -Perl license: -───────────── - - This program is free software; you can redistribute it and/or modify - it under the terms of either: - - a) the GNU General Public License as published by the Free Software - Foundation; either version 1, or (at your option) any later - version, or - - b) the "Artistic License" which comes with Perl. - - -On Debian GNU/Linux systems, the complete text of the latest version of the GNU -General Public License can be found in ‘/usr/share/common-licenses/GPL’ and the -Artistic Licence in ‘/usr/share/common-licenses/Artistic’. - - -Files: debian/* -Copyright: © 2008 Steffen Moeller <[email protected]> - © 2008–9 Charles Plessy <[email protected]> -License: same as TFBS itself - (see above) Copied: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/copyright (from rev 7543, trunk/packages/libtfbs-perl/trunk/debian/copyright) =================================================================== --- trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/copyright (rev 0) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/copyright 2011-08-25 04:21:19 UTC (rev 7544) @@ -0,0 +1,27 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: http://www.ii.uib.no/svn/lenhard/TFBS/ + +Files: * +Copyright: © 2005-2007 Boris Lenhard <[email protected]>, + Stephen Montgomery <[email protected]>, + Leonardo Marino-Ramirez, + Wynand Alkema, +License: Perl + +License: Perl + This program is free software; you can redistribute it and/or modify + it under the terms of either: + . + a) the GNU General Public License as published by the Free Software + Foundation; either version 1, or (at your option) any later + version, or + . + b) the "Artistic License" which comes with Perl. +Comment: On Debian GNU/Linux systems, the complete text of the GNU General + Public License version 1 can be found in ‘/usr/share/common-licenses/GPL-1’ and + the Artistic Licence in ‘/usr/share/common-licenses/Artistic’. + +Files: debian/* +Copyright: © 2008 Steffen Moeller <[email protected]> + © 2008–11 Charles Plessy <[email protected]> +License: Perl Deleted: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/rules =================================================================== --- trunk/packages/libtfbs-perl/trunk/debian/rules 2011-08-24 16:47:14 UTC (rev 7538) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/rules 2011-08-25 04:21:19 UTC (rev 7544) @@ -1,80 +0,0 @@ -#!/usr/bin/make -f -# This debian/rules file is provided as a template for normal perl -# packages. It was created by Marc Brockschmidt <[email protected]> for -# the Debian Perl Group (http://pkg-perl.alioth.debian.org/) but may -# be used freely wherever it is useful. - -# Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 - -# If set to a true value then MakeMaker's prompt function will -# always return the default without waiting for user input. -export PERL_MM_USE_DEFAULT=1 - -PERL ?= /usr/bin/perl -PACKAGE = $(shell dh_listpackages) -TMP = $(CURDIR)/debian/$(PACKAGE) - -# Do not run network test unless in maintainer mode. -ifneq (1,$(DEB_MAINTAINER_MODE)) - TEST_FILES = $(filter-out t/04_DB_TRANSFAC.t,$(shell echo t/*.t)) -else - TEST_FILES = $(shell echo t/*.t) -endif - -# Allow disabling build optimisation by setting noopt in -# $DEB_BUILD_OPTIONS -CFLAGS = -Wall -g -ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) - CFLAGS += -O0 -else - CFLAGS += -O2 -endif - -build: build-stamp -build-stamp: - dh_testdir - # Add commands to compile the package here - echo "n" | $(PERL) Makefile.PL INSTALLDIRS=vendor - $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH="" -ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS))) - prove --blib $(TEST_FILES) Ext/t/*.t -endif - touch $@ - -clean: - dh_testdir - dh_testroot - dh_clean build-stamp install-stamp - # Add commands to clean up after the build process here - [ ! -f Makefile ] || $(MAKE) realclean - -install: install-stamp -install-stamp: build-stamp - dh_testdir - dh_testroot - dh_prep - # Add commands to install the package into $(TMP) - $(MAKE) install DESTDIR=$(TMP) PREFIX=/usr - [ ! -d $(TMP)/usr/share/perl5 ] || \ - rmdir --ignore-fail-on-non-empty --parents --verbose \ - $(TMP)/usr/share/perl5 - rm $(TMP)/usr/lib/perl5/pwm_searchPFF.c $(TMP)/usr/lib/perl5/pwm_search.h # This must fail if the files are not there, so that we do not forget to remove the line when the issue is solved. --Charles - touch $@ - -# Build architecture-independent files here. -binary-indep: build install -# We have nothing to do here for an architecture-dependent package - -# Build architecture-dependent files here. -binary-arch: build install - dh binary-arch - -get-orig-source: - v=0.5.svn.`date +"%Y%m%d"|tr -d '\n'` ; \ - n=libtfbs-perl ; \ - svn co http://www.ii.uib.no/svn/lenhard/TFBS/ ../$$n-$$v ; \ - cd ..; tar --exclude=.svn -czvf $${n}_$${v}.orig.tar.gz $$n-$$v - -binary: binary-indep binary-arch -.PHONY: build clean binary-indep binary-arch binary install Copied: trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/rules (from rev 7542, trunk/packages/libtfbs-perl/trunk/debian/rules) =================================================================== --- trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/rules (rev 0) +++ trunk/packages/libtfbs-perl/tags/0.5.svn.20100421-1/debian/rules 2011-08-25 04:21:19 UTC (rev 7544) @@ -0,0 +1,41 @@ +#!/usr/bin/make -f + +%: + dh $@ + +# Allow disabling build optimisation by setting noopt in +# $DEB_BUILD_OPTIONS +CFLAGS = -Wall -g +ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) +CFLAGS += -O0 +else +CFLAGS += -O2 +endif + +override_dh_auto_configure: + echo "n" | perl Makefile.PL INSTALLDIRS=vendor + $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH="" + +# Do not run network test unless in maintainer mode. +ifneq (1,$(DEB_MAINTAINER_MODE)) +TEST_FILES := $(filter-out t/04_DB_TRANSFAC.t,$(shell echo t/*.t)) +else +TEST_FILES := $(shell echo t/*.t) +endif + +ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS))) +override_dh_auto_test: + prove --blib $(TEST_FILES) Ext/t/*.t +endif + +TMP_DIR := $(shell mktemp --tmpdir --directory libtfbs-perl-build.XXXXXXXXXX) +LAST_REV := $(shell LC_ALL=C svn info http://www.ii.uib.no/svn/lenhard/TFBS/ | grep Date | perl -pe 's/.*(\d\d\d\d)-(\d\d)-(\d\d).*/\1\2\3/') +UPSTREAM_VERSION := 0.5.svn.$(LAST_REV) +REPACK_DIR := $(PACKAGE)-$(UPSTREAM_VERSION).orig +TAR := $(PACKAGE)_$(UPSTREAM_VERSION).orig.tar.gz + +get-orig-source: + svn export -r'{$(LAST_REV)}' http://www.ii.uib.no/svn/lenhard/TFBS/ $(TMP_DIR)/$(REPACK_DIR) + cd $(TMP_DIR); tar -czvf $(TAR) $(REPACK_DIR) + mv $(TMP_DIR)/$(TAR) $(CURDIR)/.. + rm --recursive $(TMP_DIR) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
