[med-svn] r18084 - trunk/packages/phylip/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Mon Sep 22 10:08:38 UTC 2014
Author: tille
Date: 2014-09-22 10:08:38 +0000 (Mon, 22 Sep 2014)
New Revision: 18084
Added:
trunk/packages/phylip/trunk/debian/build.xml
trunk/packages/phylip/trunk/debian/jlibs
Modified:
trunk/packages/phylip/trunk/debian/control
trunk/packages/phylip/trunk/debian/copyright
trunk/packages/phylip/trunk/debian/phylip.lintian-overrides
trunk/packages/phylip/trunk/debian/rules
Log:
Upstream now has officially released a free version of PHYLIP, try to build JAR file from source as well
Added: trunk/packages/phylip/trunk/debian/build.xml
===================================================================
--- trunk/packages/phylip/trunk/debian/build.xml (rev 0)
+++ trunk/packages/phylip/trunk/debian/build.xml 2014-09-22 10:08:38 UTC (rev 18084)
@@ -0,0 +1,57 @@
+<?xml version="1.0" ?>
+<project name="drawtree" default="jar" basedir=".">
+ <!-- Directory structure -->
+ <property name="build.dir" location="build"/>
+ <property name="dist.dir" location="dist"/>
+ <property name="src.dir" location="src/javasrc"/>
+ <property name="lib.dir" location="/usr/share/java"/>
+ <property name="class.dir" location="${build.dir}/classes"/>
+
+ <property name="project.name" value="drawphylip"/>
+ <property name="debug" value="true"/>
+ <property name="optimized" value="true"/>
+ <property name="project.version" value="3.696"/>
+ <property environment="env"/>
+ <property name="project.jarfile.name" value="DrawTree.jar"/>
+
+ <property name="class.path" value="jna.jar"/>
+
+ <path id="compile.classpath">
+ <fileset dir="${lib.dir}">
+ </fileset>
+ <fileset dir="${dist.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ </path>
+
+
+ <target name="clean">
+ <echo level="info">Cleaning build directories</echo>
+ <delete verbose="true" includeEmptyDirs="true">
+ <fileset dir="${build.dir}" includes="**"/>
+ <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
+ </delete>
+ </target>
+
+ <target name="compile">
+ <mkdir dir="${class.dir}"/>
+ <mkdir dir="${dist.dir}"/>
+ <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
+ </javac>
+ </target>
+
+ <target name="jar" depends="compile">
+ <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
+ <manifest>
+ <attribute name="Built-By" value="Debian-Med team"/>
+ <attribute name="Main-Class" value="drawtree"/>
+ <attribute name="Class-Path" value="${class.path}"/>
+ <attribute name="Specification-Title" value="drawtree"/>
+ <attribute name="Specification-Version" value="${project.version}"/>
+ </manifest>
+ </jar>
+ </target>
+
+</project>
+
+
Modified: trunk/packages/phylip/trunk/debian/control
===================================================================
--- trunk/packages/phylip/trunk/debian/control 2014-09-22 10:06:22 UTC (rev 18083)
+++ trunk/packages/phylip/trunk/debian/control 2014-09-22 10:08:38 UTC (rev 18084)
@@ -7,7 +7,10 @@
Build-Depends: debhelper (>= 9),
libx11-dev,
libxt-dev,
- libxaw7-dev
+ libxaw7-dev,
+ ant,
+ default-jdk,
+ libjna-java
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylip/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/phylip/trunk/
Modified: trunk/packages/phylip/trunk/debian/copyright
===================================================================
--- trunk/packages/phylip/trunk/debian/copyright 2014-09-22 10:06:22 UTC (rev 18083)
+++ trunk/packages/phylip/trunk/debian/copyright 2014-09-22 10:08:38 UTC (rev 18084)
@@ -1,8 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: PHYLIP
Upstream-Contact: Joe Felsenstein <joe at gs.washington.edu>
-Source: https://www.dropbox.com/sh/7hgizw3xererb49/AABBtaabaW7t7L6Cmchcqa0ma?dl=0
-FIXME: The path is just temporary!!!!
+Source: http://evolution.gs.washington.edu/phylip/download/
Files-Excluded: *.exe
*.jar
*.so
Added: trunk/packages/phylip/trunk/debian/jlibs
===================================================================
--- trunk/packages/phylip/trunk/debian/jlibs (rev 0)
+++ trunk/packages/phylip/trunk/debian/jlibs 2014-09-22 10:08:38 UTC (rev 18084)
@@ -0,0 +1 @@
+dist/*.jar
Modified: trunk/packages/phylip/trunk/debian/phylip.lintian-overrides
===================================================================
--- trunk/packages/phylip/trunk/debian/phylip.lintian-overrides 2014-09-22 10:06:22 UTC (rev 18083)
+++ trunk/packages/phylip/trunk/debian/phylip.lintian-overrides 2014-09-22 10:08:38 UTC (rev 18084)
@@ -36,19 +36,3 @@
phylip: hardening-no-fortify-functions usr/lib/phylip/bin/retree
phylip: hardening-no-fortify-functions usr/lib/phylip/bin/seqboot
phylip: hardening-no-fortify-functions usr/lib/phylip/bin/treedist
-# No idea why upstream is providing duplicated files - they are small in any case
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dollop/dollopinfile.txt usr/share/doc/phylip/examples/testdata/mix/mixinfile.txt usr/share/doc/phylip/examples/testdata/pars/parsinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/fitch/fitchinfile.txt usr/share/doc/phylip/examples/testdata/kitsch/kitschinfile.txt usr/share/doc/phylip/examples/testdata/neighbor/neighborinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnacomp/dnacompinfile.txt usr/share/doc/phylip/examples/testdata/dnapars/dnaparsinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/mammal.txt usr/share/doc/phylip/examples/testdata/drawtree/mammal.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/14tip.txt usr/share/doc/phylip/examples/testdata/drawtree/14tip.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlcats.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkcats.txt usr/share/doc/phylip/examples/testdata/proml/promlcats.txt usr/share/doc/phylip/examples/testdata/promlk/promlkcats.txt usr/share/doc/phylip/examples/testdata/protdist/protdistcats.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape2.txt usr/share/doc/phylip/examples/testdata/drawtree/ape2.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlweights.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkweights.txt usr/share/doc/phylip/examples/testdata/proml/promlweights.txt usr/share/doc/phylip/examples/testdata/promlk/promlkweights.txt usr/share/doc/phylip/examples/testdata/protdist/protdistweights.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/contml/contmlinfile.txt usr/share/doc/phylip/examples/testdata/gendist/gendistinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/dnaml/dnamlinfile.txt usr/share/doc/phylip/examples/testdata/dnamlk/dnamlkinfile.txt usr/share/doc/phylip/examples/testdata/proml/promlinfile.txt usr/share/doc/phylip/examples/testdata/promlk/promlkinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistoutfile.txt usr/share/doc/phylip/examples/testdata/restml/restmloutfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/clique/cliqueinfile.txt usr/share/doc/phylip/examples/testdata/dolmove/dolmoveinfile.txt usr/share/doc/phylip/examples/testdata/move/moveinfile.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/cats.txt usr/share/doc/phylip/examples/testdata/drawtree/cats.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/drawgram/ape1.txt usr/share/doc/phylip/examples/testdata/drawtree/ape1.txt
-phylip: duplicate-files usr/share/doc/phylip/examples/testdata/restdist/restdistinfile.txt usr/share/doc/phylip/examples/testdata/restml/restmlinfile.txt
Modified: trunk/packages/phylip/trunk/debian/rules
===================================================================
--- trunk/packages/phylip/trunk/debian/rules 2014-09-22 10:06:22 UTC (rev 18083)
+++ trunk/packages/phylip/trunk/debian/rules 2014-09-22 10:08:38 UTC (rev 18084)
@@ -2,11 +2,15 @@
# debian/rules for phylip using dh
# Andreas Tille <tille at debian.org>, GPL
+export JAVA_HOME=/usr/lib/jvm/default-java
+
%:
dh $@
override_dh_auto_build:
dh_auto_build --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx all
+ cp debian/build.xml build.xml
+ ant
override_dh_auto_install:
dh_auto_install --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx install DATADIR=../fonts
@@ -18,3 +22,10 @@
override_dh_auto_clean:
dh_auto_clean --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx clean
rm -fr exe/* fonts/ src/*.so
+ if [ -e build.xml ] ; then \
+ ant clean ; \
+ rm -rf dist build.xml ; \
+ fi
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compress xz
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