[med-svn] r3057 - trunk/packages/bioperl/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Mon Jan 26 08:20:47 UTC 2009
Author: plessy
Date: 2009-01-26 08:20:47 +0000 (Mon, 26 Jan 2009)
New Revision: 3057
Removed:
trunk/packages/bioperl/trunk/debian/README.Debian
trunk/packages/bioperl/trunk/debian/README.source
trunk/packages/bioperl/trunk/debian/patches/
Modified:
trunk/packages/bioperl/trunk/debian/changelog
trunk/packages/bioperl/trunk/debian/control
trunk/packages/bioperl/trunk/debian/rules
trunk/packages/bioperl/trunk/debian/watch
Log:
Simplification of build process. Tests disabled and some build-deps removed for experimental upload.
Deleted: trunk/packages/bioperl/trunk/debian/README.Debian
===================================================================
--- trunk/packages/bioperl/trunk/debian/README.Debian 2009-01-25 23:18:54 UTC (rev 3056)
+++ trunk/packages/bioperl/trunk/debian/README.Debian 2009-01-26 08:20:47 UTC (rev 3057)
@@ -1,15 +0,0 @@
-BioPerl for DEBIAN
-----------------------
-
-* The Debian package for bioperl suggests the installation of all the perl
- modules that are 'recommended' in the Build.PL file. As an exception to this,
- libio-string-perl, libwww-perl, liburi-perl and libxml-writer-perl will be
- installed by default, as they are more frequently used (see
- http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html for the
- discussion).
-
- To install bioperl and all the suggested Debian packages, you can use the
- option ~Rsuggests:^package$ of the `aptitude' package manager, or the command
- `apt-get -o APT::Install-Suggests=true install'.
-
- -- Fri, 21 Sep 2007 22:52:22 +0900
Deleted: trunk/packages/bioperl/trunk/debian/README.source
===================================================================
--- trunk/packages/bioperl/trunk/debian/README.source 2009-01-25 23:18:54 UTC (rev 3056)
+++ trunk/packages/bioperl/trunk/debian/README.source 2009-01-26 08:20:47 UTC (rev 3057)
@@ -1,12 +0,0 @@
-BioPerl for Debian
-------------------
-
- This package uses quilt to manage all modifications to the upstream
- source. Changes are stored in the source package as diffs in
- debian/patches and applied during the build.
-
- To read how to use quilt, please read the official documentation at
-
- /usr/share/doc/quilt/README.source
-
- -- David Paleino <d.paleino at gmail.com> Sat, 10 Jan 2009 21:08:54 +0100
Modified: trunk/packages/bioperl/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl/trunk/debian/changelog 2009-01-25 23:18:54 UTC (rev 3056)
+++ trunk/packages/bioperl/trunk/debian/changelog 2009-01-26 08:20:47 UTC (rev 3057)
@@ -1,30 +1,32 @@
-bioperl (1.5.9.3-1) UNRELEASED; urgency=low
+bioperl (1.6.0-1) experimental; urgency=low
- TODO: run installation interactively and figure out new dependancies.
-
[ Charles Plessy ]
* debian/control
- - Added libdata-stag-perl, libmath-random-perl, libace-perl,
- libsvg-graph-perl, libbio-asn1-entrezgene-perl to Build-Depends-Indep.
+ - Updated dependancies according to the new upstream release.
+ - Added the CPAN dependancies of BioPerl to Build-Depends-Indep in order to
+ run the tests at build time.
- Added bioperl-run to the recommended packages.
- Updated my email address.
- * debian/rules build:
- - building Makefile.PL as bioperl does not use it by default anymore.
- - re-enabled the tests.
- * debian/README.Debian: reference transferred to debian/reference.
+ - Uses Debhelper 7 (debian/compat modified accordingly).
+ * debian/patches: removed as not needed (no downloads by default).
+ * debian/rules:
+ - Uses Build.PL instead of Makefile.PL.
+ - Tests disabled for the experimental upload: not all dependancies are available yet.
+ * debian/README.{Debian,source}: removed as not needed anymore
* debian/watch: BioPerl is now mixed case.
[ David Paleino ]
- * New upstream release
- - fixes Bio::AlignIO::next_aln bug (Closes: #266921)
+ * New upstream stable release:
+ - fixes Bio::AlignIO::next_aln bug (Closes: #266921).
+ - New modules, deprecated modules,… please consult Upsteam documents in
+ /usr/share/doc/bioperl.
* debian/control:
- fields values rewrapped to easily spot diffs in commit mails
- dropped B-D-I versioning on perl, since Etch already has a greater
version
- - Standards-Version bumped to 3.8.0:
- + debian/README.source added
+ - Standards-Version bumped to 3.8.0 (no changes needed).
- -- Charles Plessy <plessy at debian.org> Mon, 19 Jan 2009 21:44:48 +0900
+ -- Charles Plessy <plessy at debian.org> Mon, 26 Jan 2009 12:58:28 +0900
bioperl (1.5.2.102-3) unstable; urgency=low
Modified: trunk/packages/bioperl/trunk/debian/control
===================================================================
--- trunk/packages/bioperl/trunk/debian/control 2009-01-25 23:18:54 UTC (rev 3056)
+++ trunk/packages/bioperl/trunk/debian/control 2009-01-26 08:20:47 UTC (rev 3057)
@@ -6,23 +6,24 @@
Uploaders: Charles Plessy <plessy at debian.org>,
Steffen Moeller <moeller at debian.org>,
David Paleino <d.paleino at gmail.com>
-Build-Depends: debhelper (>= 5), quilt
+Build-Depends: debhelper (>= 7), quilt
Build-Depends-Indep: perl,
libmodule-build-perl (>= 0.2808-0.2),
libtest-harness-perl (>= 2.62),
libio-string-perl,
libdata-stag-perl,
# Recommended in Build.PL (we want them to run the tests)
- libace-perl,
- libalgorithm-munkres-perl,
+#
+# libace-perl,
+# libalgorithm-munkres-perl,
libarray-compare-perl,
libbio-asn1-entrezgene-perl,
libclone-perl,
- libconvert-binary-c-perl,
+# libconvert-binary-c-perl,
libgraph-perl,
libgraphviz-perl,
libhtml-parser-perl,
- libmath-random-perl,
+# libmath-random-perl,
libpostscript-perl,
libset-scalar-perl,
libsoap-lite-perl,
@@ -46,11 +47,7 @@
Package: bioperl
Architecture: all
Depends: libio-string-perl, ${perl:Depends}
-Recommends: bioperl-run,
- libwww-perl,
- liburi-perl,
- libxml-writer-perl
-Suggests:
+Recommends: bioperl-run ( >= 1.6.0 ),
# Recommended in Build.PL
libace-perl,
libalgorithm-munkres-perl,
Modified: trunk/packages/bioperl/trunk/debian/rules
===================================================================
--- trunk/packages/bioperl/trunk/debian/rules 2009-01-25 23:18:54 UTC (rev 3056)
+++ trunk/packages/bioperl/trunk/debian/rules 2009-01-26 08:20:47 UTC (rev 3057)
@@ -5,19 +5,18 @@
build: patch build-stamp
build-stamp:
dh_testdir
- perl Build.PL
- ./Build manifest
- ./Build distmeta
- echo "n" | perl Makefile.PL INSTALLDIRS=vendor
- $(MAKE) OPTIMIZE="-O2 -g -Wall"
- touch $@
+ perl Build.PL < /dev/null # non-interactive, uses defaults
+ ./Build
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+# Tests are temporarly disabled in the experimental package.
+# ./Build test
+endif
+ touch build-stamp
clean: unpatch
dh_testdir
dh_testroot
-
- [ ! -f Makefile ] || $(MAKE) realclean
-
+ [ ! -f Build ] || ./Build realclean
dh_clean build-stamp install-stamp bioperl.conf biodatabases.pod \
biodesign.pod bioperl.pod bioscripts.pod
@@ -25,23 +24,23 @@
install-stamp: build
dh_testdir
dh_testroot
- dh_clean -k
- dh_installdirs usr/share/perl5
- $(MAKE) install PREFIX=$(CURDIR)/debian/bioperl/usr INSTALLMAN3DIR=$(CURDIR)/debian/bioperl/usr/share/man/man3
- find debian/bioperl -type f -name .packlist | xargs rm -f
+ dh_prep
+ ./Build install \
+ --install_base /usr \
+ --install_path lib=/usr/share/perl5 \
+ --install_path bindoc=/usr/share/man/man1 \
+ --install_path libdoc=/usr/share/man/man3 \
+ --destdir $(CURDIR)/debian/bioperl
+ find debian/bioperl -type f -name .packlist | xargs rm
+ rmdir $(CURDIR)/debian/bioperl/usr/lib/perl5/powerpc-linux-gnu-thread-multi/auto/Bio/
# prename is the rename utility written in perl usually available as /usr/bin/rename in Debian.
prename s/.pl$$// debian/bioperl/usr/bin/*pl
prename s/.pl.1p$$/.1p/ debian/bioperl/usr/share/man/man1/*1p
+ touch install-stamp
- touch $@
-
-test: build
- ./Build test
-
-binary-indep: build install test
+binary-indep: build install
dh_testdir
dh_testroot
-# chmod a-x -R debian/bioperl/usr/share/doc/bioperl/examples
dh_installchangelogs Changes
dh_installdocs
dh_installexamples examples/*
Modified: trunk/packages/bioperl/trunk/debian/watch
===================================================================
--- trunk/packages/bioperl/trunk/debian/watch 2009-01-25 23:18:54 UTC (rev 3056)
+++ trunk/packages/bioperl/trunk/debian/watch 2009-01-26 08:20:47 UTC (rev 3057)
@@ -1,2 +1,2 @@
version=3
-http://www.bioperl.org/DIST/BioPerl-([\d\.]+)_(\d*)\.tar\.gz
+http://www.bioperl.org/DIST/BioPerl-([\d\.]+)\.tar\.gz
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