[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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