Package: biojava-live Severity: normal Tags: patch Hi,
The build depends lists package that has been obsoleted. See attached patch to help to fix this and other things related to new features and items reported by Lintian etc. Let me know if there is anything that needs adjusting. Thanks, Jari
>From d02b23e1fcfe726b3e0fa3a34afcb0bc08114699 Mon Sep 17 00:00:00 2001 From: Jari Aalto <jari.aa...@cante.net> Date: Tue, 17 Apr 2012 17:26:35 +0300 Subject: [PATCH] format-3.0 Organization: Private Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Signed-off-by: Jari Aalto <jari.aa...@cante.net> --- debian/changelog | 17 +++++++++++++++++ debian/control | 15 +++++++++------ debian/patches/buildxml.patch | 23 +++++++++++++++-------- debian/rules | 9 +++------ debian/source/format | 1 + 5 files changed, 45 insertions(+), 20 deletions(-) create mode 100644 debian/source/format diff --git a/debian/changelog b/debian/changelog index 6a3f8ed..b2ca471 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,20 @@ +biojava-live (1:1.7.1-1.1) unstable; urgency=low + + * Non-maintainer upload. + * 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. + * 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). + + -- Jari Aalto <jari.aa...@cante.net> Tue, 17 Apr 2012 17:15:32 +0300 + biojava-live (1:1.7.1-1) unstable; urgency=low * New upstream version. diff --git a/debian/control b/debian/control index f7672ce..2d396af 100644 --- a/debian/control +++ b/debian/control @@ -1,5 +1,5 @@ Source: biojava-live -Section: science +Section: java Priority: optional Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> DM-Upload-Allowed: yes @@ -8,21 +8,21 @@ Uploaders: Steffen Moeller <moel...@debian.org>, 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: debhelper (>= 5), quilt, cdbs, ant -Standards-Version: 3.8.3 +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 1.7 API to biological data and applications 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 @@ -75,5 +75,8 @@ Depends: ${misc:Depends} Recommends: konqueror|html-browser Suggests: libbiojava-java-demos, libbiojava-java Description: [Biology] Documentation for BioJava + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. + . This package contains the HTML documentation describing the API of BioJava which was generated automatically by JavaDoc. diff --git a/debian/patches/buildxml.patch b/debian/patches/buildxml.patch index d1b5ea3..9e93e20 100644 --- a/debian/patches/buildxml.patch +++ b/debian/patches/buildxml.patch @@ -1,8 +1,15 @@ ---- biojava-live-1.7.svn.20090419.orig/build.xml -+++ biojava-live-1.7.svn.20090419/build.xml +From: Unknown +Subject: Adjust ANT build proterties, like using more memory. + +--- + build.xml | 14 +++++++------- + 1 file changed, 7 insertions(+), 7 deletions(-) + +--- a/build.xml ++++ b/build.xml @@ -51,7 +51,7 @@ <tstamp /> - <property name="version" value="live" /> + <property name="version" value="1.7.1" /> <property name="build.compiler" value="javac1.5" /> - <property name="classpath" value="bytecode.jar:commons-cli.jar:commons-collections-2.1.jar:commons-dbcp-1.1.jar:commons-pool-1.1.jar:hsqldb.jar:jgrapht-jdk1.5.jar:junit-4.4.jar" /> + <property name="classpath" value="/usr/share/java/bytecode.jar:/usr/share/java/commons-cli.jar:/usr/share/java/commons-collections.jar:/usr/share/java/commons-dbcp.jar:/usr/share/java/commons-pool.jar:/usr/share/java/hsqldb.jar:/usr/share/java/jgrapht-0.7.jar:/usr/share/java/junit4.jar" /> @@ -18,7 +25,7 @@ <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; offline="false"/> <group title="Core biological packages" -@@ -465,7 +465,7 @@ +@@ -464,7 +464,7 @@ source="1.5" windowtitle="${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}" /> diff --git a/debian/rules b/debian/rules index 73ede26..f500e7b 100755 --- a/debian/rules +++ b/debian/rules @@ -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 @@ export JAVA_HOME := $(shell /usr/sbin/update-java-alternatives -l | head -1 | cu # version are the first two decimals SOVERSION=$(shell echo $(DEB_UPSTREAM_VERSION) | cut -f1,2 -d. ) -build: patch build-stamp +build: build-stamp build-stamp: dh_testdir @@ -33,7 +30,7 @@ build-stamp: touch build-stamp -clean: unpatch +clean: dh_testdir dh_testroot rm -f build-stamp @@ -55,7 +52,7 @@ install: build 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 diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) -- 1.7.9.5
