Author: tille
Date: 2012-04-18 16:38:30 +0000 (Wed, 18 Apr 2012)
New Revision: 10405
Removed:
trunk/packages/biojava/trunk/debian/libbiojava-java.lintian-overrides
trunk/packages/biojava/trunk/debian/libbiojava1.7-java.lintian-overrides
Modified:
trunk/packages/biojava/trunk/debian/changelog
trunk/packages/biojava/trunk/debian/compat
trunk/packages/biojava/trunk/debian/control
trunk/packages/biojava/trunk/debian/copyright
trunk/packages/biojava/trunk/debian/patches/buildxml.patch
trunk/packages/biojava/trunk/debian/rules
trunk/packages/biojava/trunk/debian/source/format
Log:
Commit patch from Jari Aalto + several other enhancements to get a lintian
compliant package with DEP5 copyright
Modified: trunk/packages/biojava/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava/trunk/debian/changelog 2012-04-18 15:26:20 UTC
(rev 10404)
+++ trunk/packages/biojava/trunk/debian/changelog 2012-04-18 16:38:30 UTC
(rev 10405)
@@ -1,14 +1,34 @@
-biojava-live (1:3.0.2-1) UNRELEASED; urgency=low
+biojava-live (1:1.7.1-2) UNRELEASED; urgency=low
- * New upstream version
- Closes: #65982
+ [ Jari Aalto ]
+ * Remove quilt and upgrade to packaging format "3.0 quilt" which
+ includes patch management built-in.
+ * Update buildxml.patch to DEP-3 and run "quilt refresh" to make it
+ apply cleanly.
+ * Update to Standards-Version to 3.9.3 (no changes needed) and debhelper 9.
+ * Update obsolete depends default-jdk-builddep to default-jdk.
+ Closes: #669122
+ * Fix wrong-section-according-to-package-name (Lintian) by changing
+ section from science to java.
+ * Fix needless-dependency-on-jre (Lintian) by removing jre dependencies.
+ * Fix duplicate-short-description (Lintian).
+ * Fix extended-description-is-probably-too-short (Lintian).
+
+ [ Andreas Tille ]
+ * debian/control: Java 1.7 API is missleading regarding JDK version - rather
+ add the version at the end and declare the version-less metapackage as
+ default version
* debian/watch: enable detecting new versions
- * debian/upstream: Took over citations from tasks file
+ * debian/{control,upstream}: Moved citations from long description to
+ upstream file
+ * libbiojava*.lintian: removed because now useless
+ * debian/compat: 9
+ * debian/copyright: Rewritten to be compliant with DEP5 and verified
+ using `cme fix dpkg-copyright`
+ * debian/rules: s/dh_clean -k/dh_prep/
- TODO: Use maven_helper
+ -- Andreas Tille <[email protected]> Wed, 18 Apr 2012 08:50:31 +0200
- -- Andreas Tille <[email protected]> Thu, 29 Mar 2012 14:57:14 +0200
-
biojava-live (1:1.7.1-1) unstable; urgency=low
* New upstream version.
Modified: trunk/packages/biojava/trunk/debian/compat
===================================================================
--- trunk/packages/biojava/trunk/debian/compat 2012-04-18 15:26:20 UTC (rev
10404)
+++ trunk/packages/biojava/trunk/debian/compat 2012-04-18 16:38:30 UTC (rev
10405)
@@ -1 +1 @@
-5
+9
Modified: trunk/packages/biojava/trunk/debian/control
===================================================================
--- trunk/packages/biojava/trunk/debian/control 2012-04-18 15:26:20 UTC (rev
10404)
+++ trunk/packages/biojava/trunk/debian/control 2012-04-18 16:38:30 UTC (rev
10405)
@@ -1,29 +1,28 @@
Source: biojava-live
-Section: science
+Section: java
Priority: optional
Maintainer: Debian Med Packaging Team
<[email protected]>
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <[email protected]>,
- Andreas Tille <[email protected]>,
- Michael Heuer <[email protected]>
+ Andreas Tille <[email protected]>
Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
libbytecode-java (>= 0.92.cvs.20070925),
-
default-jdk-builddep|openjdk-6-jdk|sun-java6-jdk|sun-java5-jdk|sun-j2sdk1.4|java2-compiler,
junit4,
+ default-jdk, junit4,
ant-optional
-Build-Depends: quilt, debhelper (>= 5), cdbs, ant
-Standards-Version: 3.9.0
+Build-Depends: debhelper (>= 9), cdbs, ant
+Standards-Version: 3.9.3
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biojava/trunk/
Homepage: http://www.biojava.org
Package: libbiojava1.7-java
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, libcommons-pool-java (>= 1.1),
libcommons-collections-java (>= 2.1), libcommons-dbcp-java (>= 1.1),
libhsqldb-java, libbytecode-java,
default-jre-headless|openjdk-6-jre|sun-java6-jre|sun-java5-jre|java2-runtime
+Depends: ${shlibs:Depends}, ${misc:Depends}, libcommons-pool-java (>= 1.1),
libcommons-collections-java (>= 2.1), libcommons-dbcp-java (>= 1.1),
libhsqldb-java, libbytecode-java, default-jre-headless
Suggests: java-virtual-machine, libjgrapht-java, libbiojava-java,
libbiojava-java-doc
Conflicts: libbiojava1.6-java
Replaces: libbiojava1.6-java
-Description: Java API to biological data and applications
+Description: Java API to biological data and applications (version 1.7)
This package presents the Open Source Java API to biological databases
and a series of mostly sequence-based algorithms. The APIs are not
compatible between versions. In analogy to the dealing with shared
@@ -37,7 +36,7 @@
Depends: libbiojava1.7-java, ${misc:Depends}
Conflicts: libbiojava1.6-java
Replaces: libbiojava1.6-java
-Description: Java API to biological data and applications
+Description: Java API to biological data and applications (default version)
BioJava is an open-source project dedicated to providing a Java framework
for processing biological data. It includes objects for manipulating
sequences, file parsers, DAS client and server support, access to BioSQL
@@ -51,11 +50,6 @@
for everybody active in the field because of the many tricks of the
trade one learns just by communicating on the mailing list.
.
- If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock,
- A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates,
- M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework
- for Bioinformatics" Bioinformatics 24(18):2096-2097.
- .
This is a wrapper package which should enable smooth upgrades to new
versions.
@@ -76,5 +70,8 @@
Recommends: konqueror|html-browser
Suggests: libbiojava-java-demos, libbiojava-java
Description: [Biology] Documentation for BioJava
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data.
+ .
This package contains the HTML documentation describing the API of BioJava
which was generated automatically by JavaDoc.
Modified: trunk/packages/biojava/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava/trunk/debian/copyright 2012-04-18 15:26:20 UTC
(rev 10404)
+++ trunk/packages/biojava/trunk/debian/copyright 2012-04-18 16:38:30 UTC
(rev 10405)
@@ -1,12 +1,11 @@
-This package was debianized by Steffen Moeller <[email protected]> on
-Wed, 31 Dec 2008 01:26:45 +0100
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BioJava
+Source: http://www.biojava.org/download/source
-It was downloaded from http://www.biojava.org/download/source
-
+Files: *
Copyright: 1999-2008 the Individual authors who contributed the code,
as identified by the @authors tag of the respective source file.
-
-Upstream Authors: BioJava Developers <[email protected]>
+ BioJava Developers <[email protected]>
Namely: Alan Li, Andreas Dräger <[email protected]>,
Andreas Prlic,
Andy Hammer, Andy Yates, Andy Yates, Aroul Ramadass, Bradford Powell,
Brian Gilman, Brian King, Bubba Puryear, Colin Hardman , David Allen,
@@ -26,19 +25,16 @@
Shuvankar Mukherjee, Simon Brocklehurst, Simon Foote, Stuart Johnston ,
Susanne Merz, Tamas Horvath, Tanya Vavouri, Thad Welch, Thomas Down,
Tim Dilks , Tobias Thierer, Todd Riley
-
-
License: LGPL-2.1+
-
BioJava is an open source project. The project is distributed under the GNU
Lesser General Public Licence. We do not consider Java class loading to
constitute the production of a derivative work. We do not consider consider
sub-classing of Java classes or implementations of Java interfaces to
constitute
the production of a derivative work.
-
+ .
All .java source files should include the following comment which implies
the
author's agreement to the tearms of the license.
-
+ .
/*
* BioJava development code
*
@@ -59,17 +55,17 @@
* http://www.biojava.org/
*
*/
-
+ .
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
-
+ .
You should have received a copy of the GNU Lesser General Public
License along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-File: /tests/org/biojava/utils/process/AllTests.java
+Files: tests/org/biojava/utils/process/AllTests.java
Copyright: © 2005, BioWeka.org
License: GPL-2+
This program is free software; you can redistribute it and/or modify
@@ -86,15 +82,10 @@
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-The Debian packaging is Copyright 2007-2008, Steffen Moeller
<[email protected]>
-and is licensed under the GNU Lesser General Public License version 2.1 or
higher,
-see `/usr/share/common-licenses/LGPL-2.1'.
-
+Files: debian/*
+Copyright: 2007-2010, Steffen Moeller <[email protected]>
+ 2011-2012, Andreas Tille <[email protected]>
License: LGPL-2.1+
On Debian systems, the complete text of the GNU Lesser General Public License
version 2.1 can be found in `/usr/share/common-licenses/LGPL-2.1'.
-License: GPL-2+
- On Debian systems, the complete text of the GNU General Public License
- version 2 can be found in `/usr/share/common-licenses/GPL-2'.
Deleted: trunk/packages/biojava/trunk/debian/libbiojava-java.lintian-overrides
===================================================================
--- trunk/packages/biojava/trunk/debian/libbiojava-java.lintian-overrides
2012-04-18 15:26:20 UTC (rev 10404)
+++ trunk/packages/biojava/trunk/debian/libbiojava-java.lintian-overrides
2012-04-18 16:38:30 UTC (rev 10405)
@@ -1 +0,0 @@
-W: libbiojava-java: wrong-section-according-to-package-name
Deleted:
trunk/packages/biojava/trunk/debian/libbiojava1.7-java.lintian-overrides
===================================================================
--- trunk/packages/biojava/trunk/debian/libbiojava1.7-java.lintian-overrides
2012-04-18 15:26:20 UTC (rev 10404)
+++ trunk/packages/biojava/trunk/debian/libbiojava1.7-java.lintian-overrides
2012-04-18 16:38:30 UTC (rev 10405)
@@ -1 +0,0 @@
-W: libbiojava1.7-java: wrong-section-according-to-package-name
Modified: trunk/packages/biojava/trunk/debian/patches/buildxml.patch
===================================================================
--- trunk/packages/biojava/trunk/debian/patches/buildxml.patch 2012-04-18
15:26:20 UTC (rev 10404)
+++ trunk/packages/biojava/trunk/debian/patches/buildxml.patch 2012-04-18
16:38:30 UTC (rev 10405)
@@ -1,8 +1,15 @@
---- biojava-live-1.7.svn.20090419.orig/build.xml
-+++ biojava-live-1.7.svn.20090419/build.xml
+From: Unknown
+Subject: Adjust ANT build proterties, like using more memory.
+
+---
+ build.xml | 14 +++++++-------
+ 1 file changed, 7 insertions(+), 7 deletions(-)
+
+--- a/build.xml
++++ b/build.xml
@@ -51,7 +51,7 @@
<tstamp />
- <property name="version" value="live" />
+ <property name="version" value="1.7.1" />
<property name="build.compiler" value="javac1.5" />
- <property name="classpath"
value="bytecode.jar:commons-cli.jar:commons-collections-2.1.jar:commons-dbcp-1.1.jar:commons-pool-1.1.jar:hsqldb.jar:jgrapht-jdk1.5.jar:junit-4.4.jar"
/>
+ <property name="classpath"
value="/usr/share/java/bytecode.jar:/usr/share/java/commons-cli.jar:/usr/share/java/commons-collections.jar:/usr/share/java/commons-dbcp.jar:/usr/share/java/commons-pool.jar:/usr/share/java/hsqldb.jar:/usr/share/java/jgrapht-0.7.jar:/usr/share/java/junit4.jar"
/>
@@ -18,7 +25,7 @@
<link href="http://java.sun.com/j2se/1.5.0/docs/api/";
offline="false"/>
<group title="Core biological packages"
-@@ -465,7 +465,7 @@
+@@ -464,7 +464,7 @@
source="1.5"
windowtitle="${Name.demos} API"
doctitle="${Name.demos}"
@@ -27,7 +34,7 @@
<link href="http://java.sun.com/j2se/1.5.0/docs/api/";
offline="false"/>
<link href="../biojava" offline="true"
packagelistLoc="${build.docs.biojava}/package-list}"/>
</javadoc>
-@@ -486,7 +486,7 @@
+@@ -485,7 +485,7 @@
source="1.5"
windowtitle="${Name.apps} API"
doctitle="${Name.apps}"
@@ -36,7 +43,7 @@
<link href="http://java.sun.com/j2se/1.5.0/docs/api/";
offline="false"/>
<link href="../biojava" offline="true"
packagelistLoc="${build.docs.biojava}/package-list}"/>
-@@ -508,7 +508,7 @@
+@@ -507,7 +507,7 @@
description="Run all tests, can be quite slow">
<property name="test.subtree" value="**" />
<echo message="Running tests: ${test.subtree}" />
@@ -45,7 +52,7 @@
<formatter type="plain" usefile="true" />
<classpath>
<!-- main classes from build -->
-@@ -548,7 +548,7 @@
+@@ -547,7 +547,7 @@
classpath="${classpath}"
destdir="${build.doccheck.biojava}"
source="1.5"
@@ -54,7 +61,7 @@
</javadoc>
</target>
-@@ -559,7 +559,7 @@
+@@ -558,7 +558,7 @@
description="Run clean, build and tests for CruiseControl">
<property name="test.subtree" value="**" />
<echo message="Running tests: ${test.subtree}" />
Modified: trunk/packages/biojava/trunk/debian/rules
===================================================================
--- trunk/packages/biojava/trunk/debian/rules 2012-04-18 15:26:20 UTC (rev
10404)
+++ trunk/packages/biojava/trunk/debian/rules 2012-04-18 16:38:30 UTC (rev
10405)
@@ -4,9 +4,6 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-# include macros on how to deal with quilt
-include /usr/share/quilt/quilt.make
-
# include series of variables to become more version-independent
# in this debian/rules file.
include /usr/share/cdbs/1/rules/buildvars.mk
@@ -16,7 +13,7 @@
# version are the first two decimals
SOVERSION=$(shell echo $(DEB_UPSTREAM_VERSION) | cut -f1,2 -d. )
-build: patch build-stamp
+build: build-stamp
build-stamp:
dh_testdir
@@ -27,13 +24,13 @@
src/org/biojavax/bio/phylo/ParsimonyTreeMethod.java
# Add here commands to compile the package.
- ANT_OPTS="-Xms512m -Xmx1024m" ant package-biojava
+ ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava
#ant compile-demos
ant javadocs-biojava
touch build-stamp
-clean: unpatch
+clean:
dh_testdir
dh_testroot
rm -f build-stamp
@@ -46,7 +43,7 @@
install: build
dh_testdir
dh_testroot
- dh_clean -k
+ dh_prep
dh_installdirs
cp ant-build/biojava.jar
$(CURDIR)/debian/libbiojava$(SOVERSION)-java/usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar
@@ -55,7 +52,7 @@
cp -r ant-build/docs/biojava/* $$d
for i in $(CURDIR)/debian/libbiojava-java*; do \
if [ -d "$i" ]; then \
- find $i -name ".svn" | xargs -r rm -r ; \
+ find $i -name ".svn" | xargs -r rm -r ; \
fi ; \
done
Modified: trunk/packages/biojava/trunk/debian/source/format
===================================================================
--- trunk/packages/biojava/trunk/debian/source/format 2012-04-18 15:26:20 UTC
(rev 10404)
+++ trunk/packages/biojava/trunk/debian/source/format 2012-04-18 16:38:30 UTC
(rev 10405)
@@ -1 +1 @@
-3.0 (native)
+3.0 (quilt)
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