[med-svn] r7544 - in trunk/packages/libtfbs-perl/tags: . 0.5.svn.20100421-1/debian
Charles Plessy
plessy at alioth.debian.org
Thu Aug 25 04:21:19 UTC 2011
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 <plessy at debian.org> 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 <plessy at debian.org> Mon, 11 Aug 2008 13:27:45 +0900
-
-libtfbs-perl (0.5.svn.20080722-1) unstable; urgency=low
-
- * Initial release (closes: #491714).
-
- -- Steffen Moeller <moeller at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> Mon, 11 Aug 2008 13:27:45 +0900
+
+libtfbs-perl (0.5.svn.20080722-1) unstable; urgency=low
+
+ * Initial release (closes: #491714).
+
+ -- Steffen Moeller <moeller at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
-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 <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
+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 <Boris.Lenhard at bccs.uib.no>
-Source : http://www.ii.uib.no/svn/lenhard/TFBS/
-
-
-Copyright: © 2005-2007 Boris Lenhard <Boris.Lenhard at bccs.uib.no>,
- Stephen Montgomery <smontgom at bcgsc.bc.ca>,
- 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 <moeller at debian.org>
- © 2008–9 Charles Plessy <plessy at debian.org>
-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 <Boris.Lenhard at bccs.uib.no>,
+ Stephen Montgomery <smontgom at bcgsc.bc.ca>,
+ 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 <moeller at debian.org>
+ © 2008–11 Charles Plessy <plessy at debian.org>
+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 <marc at dch-faq.de> 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)
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