This is an automated email from the git hooks/post-receive script. osallou pushed a commit to branch master in repository varscan.
commit 9e4fe2b659e0a964665f4159d90f938dd8fb9798 Author: Olivier Sallou <[email protected]> Date: Thu Apr 17 09:24:14 2014 +0200 add base build.xml fiel to build jar file, add patch to fix an upstream error in conversion --- debian/build.xml | 57 ++++++++++++++++++++++++++++++++++++++++++++++ debian/patches/fix_convert | 20 ++++++++++++++++ debian/patches/series | 1 + 3 files changed, 78 insertions(+) diff --git a/debian/build.xml b/debian/build.xml new file mode 100644 index 0000000..e62cd15 --- /dev/null +++ b/debian/build.xml @@ -0,0 +1,57 @@ +<?xml version="1.0" ?> +<project name="varscan" default="jar" basedir="."> + <!-- Directory structure --> + <property name="build.dir" location="build"/> + <property name="dist.dir" location="dist"/> + <property name="src.dir" location="net"/> + <property name="lib.dir" location="/usr/share/java"/> + <property name="class.dir" location="${build.dir}/classes"/> + + <property name="project.name" value="varscan"/> + <property name="debug" value="true"/> + <property name="optimized" value="true"/> + <property name="project.version" value="2.3.6"/> + <property environment="env"/> + <property name="project.jarfile.name" value="varscan.jar"/> + + <property name="class.path" value=""/> + + <path id="compile.classpath"> + <fileset dir="${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="${class.dir}" > + <manifest> + <attribute name="Built-By" value="Debian-Med team"/> + <attribute name="Main-Class" value="net.sf.varscan.VarScan"/> + <attribute name="Class-Path" value="${class.path}"/> + <attribute name="Specification-Title" value="varscan"/> + <attribute name="Specification-Version" value="${project.version}"/> + </manifest> + </jar> + </target> + +</project> + + diff --git a/debian/patches/fix_convert b/debian/patches/fix_convert new file mode 100644 index 0000000..1e7cb82 --- /dev/null +++ b/debian/patches/fix_convert @@ -0,0 +1,20 @@ +Index: varscan/net/sf/varscan/CopyCaller.java +=================================================================== +--- varscan.orig/net/sf/varscan/CopyCaller.java 2014-04-17 09:07:25.542896601 +0200 ++++ varscan/net/sf/varscan/CopyCaller.java 2014-04-17 09:19:07.938907140 +0200 +@@ -253,7 +253,7 @@ + int gcBin = (int) gcContent; + if(gcBin >= 0 && gcBin <= 100) + { +- gcLogSum[gcBin] += logratio; ++ gcLogSum[gcBin] += (float) logratio; + gcLogNum[gcBin]++; + } + } +@@ -576,4 +576,4 @@ + return(regionRef + "\t" + regionStart + "\t" + regionStop + "\t" + regionCalls + "\t" + regionDepthNormal + "\t" + regionDepthTumor + "\t" + log2ratio); + + } +-} +\ No newline at end of file ++} diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..7dd2fe9 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +fix_convert -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/varscan.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
