[med-svn] [Git][med-team/igv][master] 2 commits: add ant dependency

Olivier Sallou gitlab at salsa.debian.org
Tue Dec 18 09:39:52 GMT 2018 

Olivier Sallou pushed to branch master at Debian Med / igv


Commits:
aa58fc0f by Olivier Sallou at 2018-12-18T08:01:31Z
add ant dependency

- - - - -
eaa4f44b by Olivier Sallou at 2018-12-18T09:34:46Z
add ant to java depends and build

- - - - -


4 changed files:

- debian/bin/igv
- debian/changelog
- debian/control
- debian/patches/fix_gradle.patch


Changes:

=====================================
debian/bin/igv
=====================================
@@ -1,5 +1,5 @@
 #!/bin/sh
 set -eu
 
-exec java -cp /usr/share/java/jaxb-api.jar:/usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar org.broad.igv.ui.Main "$@"
+exec java -cp /usr/share/java/ant.jar:/usr/share/java/jaxb-api.jar:/usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar org.broad.igv.ui.Main "$@"
 


=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-igv (2.4.16+dfsg-1) UNRELEASED; urgency=medium
+igv (2.4.16+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Drop Build-Depends: libmysql-java, Recommends: libmariadb-java


=====================================
debian/control
=====================================
@@ -39,7 +39,8 @@ Build-Depends: default-jdk,
                libjide-oss-java,
                libfest-assert-java,
                libfest-util-java,
-               libfest-reflect-java
+               libfest-reflect-java,
+               ant
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/igv
 Vcs-Git: https://salsa.debian.org/med-team/igv.git


=====================================
debian/patches/fix_gradle.patch
=====================================
@@ -5,7 +5,7 @@ Description: gradle build file needs to add debian based libraries
  case, system tries to get it from Jar name, so module names need also to be
  adapted for those libraries to match Debian jar names.
 Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2018-10-15
+Last-Updated: 2018-10-17
 Forwarded: no
 --- a/build_java9.gradle
 +++ b/build_java9.gradle
@@ -21,7 +21,7 @@ Forwarded: no
  import org.apache.tools.ant.filters.ReplaceTokens
  
  ext.moduleName = 'org.igv'
-@@ -30,6 +33,12 @@ ext.mainClassName = 'org.broad.igv.ui.Ma
+@@ -30,6 +33,12 @@
  // Despite this, it is recommended that Java 8 vs. 9 builds be run in different locations.
  buildDir = 'build_java9' 
  
@@ -34,7 +34,7 @@ Forwarded: no
  sourceSets {
      main {
          java {
-@@ -45,6 +54,28 @@ sourceSets {
+@@ -45,6 +54,29 @@
  dependencies {
      // Use the newer JIDE lib for Java 9 builds
      compile fileTree(dir: 'lib', include: '*.jar', exclude: 'jide-oss-3.5.5.jar') + fileTree(dir: 'lib_java9', include: '*.jar')
@@ -60,10 +60,11 @@ Forwarded: no
 +    compile "org.apache.logging.log4j:log4j-core:debian"
 +    compile "org.swinglabs:swing-layout:debian"
 +    compile "com.github.samtools:htsjdk:debian"
++    compile "org.apache.ant:ant:debian"
      testCompile fileTree(dir: 'test/lib', include: '*.jar')
  }
  
-@@ -52,8 +83,8 @@ task wrapper(type: Wrapper) {
+@@ -52,8 +84,8 @@
      gradleVersion = '4.4.1'
  }
  
@@ -74,7 +75,7 @@ Forwarded: no
  
  processResources {
      // Set the current timestamp for release builds; pass in a blank property to enable (i.e. -Ptimestamp="" at CLI)
-@@ -93,12 +124,9 @@ task tooljar(type: Jar, dependsOn: jar)
+@@ -93,12 +125,9 @@
  }
  
  compileJava {
@@ -91,7 +92,7 @@ Forwarded: no
  
 --- a/src/main/java9/module-info.java
 +++ b/src/main/java9/module-info.java
-@@ -5,11 +5,11 @@ module org.igv {
+@@ -5,11 +5,11 @@
      
      requires AbsoluteLayout;
      requires ant;
@@ -107,7 +108,7 @@ Forwarded: no
      requires htsjdk;
      requires java.datatransfer;
      requires java.desktop;
-@@ -22,5 +22,5 @@ module org.igv {
+@@ -22,5 +22,5 @@
      requires log4j;
      requires org.apache.logging.log4j;
      requires org.apache.logging.log4j.core;
@@ -116,7 +117,7 @@ Forwarded: no
  }
 --- a/src/main/java/org/broad/igv/util/stream/IGVSeekableBufferedStream.java
 +++ b/src/main/java/org/broad/igv/util/stream/IGVSeekableBufferedStream.java
-@@ -87,16 +87,6 @@ public class IGVSeekableBufferedStream e
+@@ -87,16 +87,6 @@
          return actualSkip;
      }
  
@@ -133,7 +134,7 @@ Forwarded: no
      public void seek(final long position) throws IOException {
          this.position = position;
      }
-@@ -215,4 +205,4 @@ public class IGVSeekableBufferedStream e
+@@ -215,4 +205,4 @@
              bufferSize = tmpBufferSize;
          }
      }



View it on GitLab: https://salsa.debian.org/med-team/igv/compare/f5e67620bd6119e91dddf7a57917b69eb25e1192...eaa4f44b997ae1463e5c3a59a319578e2789c608

-- 
View it on GitLab: https://salsa.debian.org/med-team/igv/compare/f5e67620bd6119e91dddf7a57917b69eb25e1192...eaa4f44b997ae1463e5c3a59a319578e2789c608
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20181218/0dfc4363/attachment-0001.html>

More information about the debian-med-commit mailing list