[med-svn] r4411 - trunk/packages/libtfbs-perl/trunk/debian

Charles Plessy plessy at alioth.debian.org
Sat Nov 28 06:07:11 UTC 2009 

Author: plessy
Date: 2009-11-28 06:07:00 +0000 (Sat, 28 Nov 2009)
New Revision: 4411

Added:
   trunk/packages/libtfbs-perl/trunk/debian/README.Debian
   trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml
Modified:
   trunk/packages/libtfbs-perl/trunk/debian/changelog
   trunk/packages/libtfbs-perl/trunk/debian/control
   trunk/packages/libtfbs-perl/trunk/debian/copyright
   trunk/packages/libtfbs-perl/trunk/debian/rules
Log:
Update fixing an RC bug and syncing on Upstream SVN.

  * 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 ?\226?\128?\152nocheck?\226?\128?\153 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.


Added: trunk/packages/libtfbs-perl/trunk/debian/README.Debian
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/README.Debian	2009-11-28 06:07:00 UTC (rev 4411)
@@ -0,0 +1,14 @@
+Notes on how this package is tested.
+──────────────────────────────────── 
+
+The regression tests of this Perl module are executed at build time. You can
+therefore consult the result in the build logs:
+
+https://buildd.debian.org/libtfbs-perl
+
+Network access is not guaranteed in our auto-builder infrastructure. Tests that
+depend on the network are therefore disabled. Nevertheless these tests are
+checked by the package maintainer before upload, by building the package with
+the DEB_MAINTAINER_MODE=1 option.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 28 Nov 2009 13:52:06 +0900

Modified: trunk/packages/libtfbs-perl/trunk/debian/changelog
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/changelog	2009-11-27 12:59:42 UTC (rev 4410)
+++ trunk/packages/libtfbs-perl/trunk/debian/changelog	2009-11-28 06:07:00 UTC (rev 4411)
@@ -1,3 +1,19 @@
+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:

Modified: trunk/packages/libtfbs-perl/trunk/debian/control
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/control	2009-11-27 12:59:42 UTC (rev 4410)
+++ trunk/packages/libtfbs-perl/trunk/debian/control	2009-11-28 06:07:00 UTC (rev 4411)
@@ -1,11 +1,11 @@
 Source: libtfbs-perl
 Section: perl
 Priority: optional
-Build-Depends: debhelper (>= 7), perl (>= 5.6.10-12), pdl, bioperl, libwww-perl, libdbi-perl
+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: 3.8.0
+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/

Modified: trunk/packages/libtfbs-perl/trunk/debian/copyright
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/copyright	2009-11-27 12:59:42 UTC (rev 4410)
+++ trunk/packages/libtfbs-perl/trunk/debian/copyright	2009-11-28 06:07:00 UTC (rev 4411)
@@ -1,32 +1,38 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=226
-Upstream-Name: TFBS
-Upstream-Maintainer: Boris Lenhard <Boris.Lenhard at bccs.uib.no>
-Upstream-Source: http://www.ii.uib.no/svn/lenhard/TFBS/
-Packaged-by: Steffen Moeller <moeller at debian.org>
-Packaged-date: Fri, 18 Jul 2008 15:21:37 +0200
+Name    : TFBS
+Contact : Boris Lenhard <Boris.Lenhard at bccs.uib.no>
+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: Artistic | GPL1+
- This Perl module is distributed under the same license as Perl itself.
-X-Comment: 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.
-X-Comment: On Debian GNU/Linux systems, the complete text 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'.
+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 Charles Plessy   <plessy at debian.org>
+Copyright: ©  2008  Steffen Moeller <moeller at debian.org>
+           © 2008–9 Charles Plessy   <plessy at debian.org>
 License: same as TFBS itself
  (see above)

Modified: trunk/packages/libtfbs-perl/trunk/debian/rules
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/rules	2009-11-27 12:59:42 UTC (rev 4410)
+++ trunk/packages/libtfbs-perl/trunk/debian/rules	2009-11-28 06:07:00 UTC (rev 4411)
@@ -15,6 +15,13 @@
 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
@@ -30,7 +37,9 @@
 	# Add commands to compile the package here
 	echo "n" | $(PERL) Makefile.PL INSTALLDIRS=vendor
 	$(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH=""
-	$(MAKE) test
+ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS)))
+	prove --blib $(TEST_FILES) Ext/t/*.t
+endif
 	touch $@
 
 clean:
@@ -44,7 +53,7 @@
 install-stamp: build-stamp
 	dh_testdir
 	dh_testroot
-	dh_clean -k
+	dh_prep
 	# Add commands to install the package into $(TMP)
 	$(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
 	[ ! -d $(TMP)/usr/share/perl5 ] || \
@@ -59,20 +68,7 @@
 
 # Build architecture-dependent files here.
 binary-arch: build install
-	dh_testdir
-	dh_testroot
-	dh_installexamples examples/*
-	dh_installdocs BUGS README
-	dh_installchangelogs Changes
-	dh_shlibdeps
-	dh_strip
-	dh_perl
-	dh_compress
-	dh_fixperms
-	dh_installdeb
-	dh_gencontrol
-	dh_md5sums
-	dh_builddeb
+	dh binary-arch
 
 get-orig-source:
 	v=0.5.svn.`date +"%Y%m%d"|tr -d '\n'` ; \

Added: trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml	2009-11-28 06:07:00 UTC (rev 4411)
@@ -0,0 +1,15 @@
+Contact: Boris.Lenhard at bccs.uib.no
+DOI: 10.1093/bioinformatics/18.8.1135
+Homepage: http://tfbs.genereg.net/
+Name: TFBS
+PMID: 12176838
+Reference-Journal: Bioinformatics
+Reference-Title: TFBS: Computational framework for transcription factor binding site analysis
+Reference-Authors: Lenhard, Boris and Wasserman, Wyeth W.
+Reference-Volume: 18
+Reference-Number: 8
+Reference-Pages: 1135-1136
+Reference-Year: 2002
+Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135
+Repository: http://www.ii.uib.no/svn/lenhard/TFBS/
+Watch: http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz

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