[med-svn] [Git][med-team/igv][master] fix for FTBS openjdk 11, closes 895765
Olivier Sallou
gitlab at salsa.debian.org
Mon Nov 12 10:45:09 GMT 2018
Olivier Sallou pushed to branch master at Debian Med / igv
Commits:
f028c8d9 by Olivier Sallou at 2018-11-12T10:44:54Z
fix for FTBS openjdk 11, closes 895765
- - - - -
6 changed files:
- debian/bin/igv
- debian/changelog
- debian/control
- debian/igv.manifest
- debian/patches/fix_gradle.patch
- debian/rules
Changes:
=====================================
debian/bin/igv
=====================================
@@ -1,5 +1,5 @@
#!/bin/sh
set -eu
-exec java --add-modules java.xml.bind -cp /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 "$@"
+exec java -cp /usr/share/java/jaxb-api.jar:/usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar org.broad.igv.ui.Main "$@"
=====================================
debian/changelog
=====================================
@@ -1,6 +1,7 @@
igv (2.4.14+dfsg-2) UNRELEASED; urgency=medium
- TODO: check debian/igv.manifest that all dependencies are OK
+ [ Olivier Sallou ]
+ fix for FTBS openjdk 11, Closes: #895765
-- Andreas Tille <tille at debian.org> Tue, 23 Oct 2018 14:55:18 +0200
@@ -282,13 +283,13 @@ igv (1.5.05-1) UNRELEASED; urgency=low
igv (1.5.03-1) unstable; urgency=low
- * New upstream release.
+ * New upstream release.
-- Shaun Jackman <sjackman at debian.org> Tue, 06 Jul 2010 13:42:43 -0700
igv (1.5.01-1) UNRELEASED; urgency=low
- * New upstream release.
+ * New upstream release.
-- Shaun Jackman <sjackman at debian.org> Fri, 02 Jul 2010 10:26:19 -0700
=====================================
debian/control
=====================================
@@ -17,6 +17,7 @@ Build-Depends: default-jdk,
libcommons-net-java,
libhttpclient-java,
libhttpcore-java,
+ libjaxb-api-java,
libjcommon-java,
libjfreechart-java,
libjhdf5-java,
=====================================
debian/igv.manifest
=====================================
@@ -1,2 +1,2 @@
usr/share/java/igv.jar:
- Class-Path: /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
+ Class-Path: /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/jaxb-api.jar
=====================================
debian/patches/fix_gradle.patch
=====================================
@@ -63,18 +63,27 @@ Forwarded: no
testCompile fileTree(dir: 'test/lib', include: '*.jar')
}
-@@ -93,12 +124,13 @@
+@@ -52,8 +83,8 @@
+ gradleVersion = '4.4.1'
+ }
+
+-sourceCompatibility = 1.9
+-targetCompatibility = 1.9
++//sourceCompatibility = 1.11
++//targetCompatibility = 1.11
+
+ processResources {
+ // Set the current timestamp for release builds; pass in a blank property to enable (i.e. -Ptimestamp="" at CLI)
+@@ -93,12 +124,9 @@
}
compileJava {
- inputs.property("moduleName", moduleName)
+ //inputs.property("moduleName", moduleName)
doFirst {
- options.compilerArgs = [
+- options.compilerArgs = [
- '--module-path', classpath.asPath,
-+ // '--module-path', classpath.asPath,
-+ '--add-modules', 'java.xml.bind'
- ]
+- ]
- classpath = files()
+ // classpath = files()
}
=====================================
debian/rules
=====================================
@@ -14,6 +14,7 @@ override_dh_clean:
if [ -e build_java8.gradle ] ; then mv build_java8.gradle build.gradle ; fi
rm -f goby-io-igv.jar
rm -f batik-codec.jar
+ rm -f lib/jaxb-api.jar
dh_clean
override_dh_auto_configure:
@@ -21,3 +22,4 @@ override_dh_auto_configure:
cp -a build_java9.gradle build.gradle
mv src/main/java9/module-info.java src/main/java9/module-info.java.skip
cp debian/log4j.xml src/main/resources/
+ cp /usr/share/java/jaxb-api.jar $(CURDIR)/lib/
View it on GitLab: https://salsa.debian.org/med-team/igv/commit/f028c8d97b3210551d92ee407e18b523ce43c457
--
View it on GitLab: https://salsa.debian.org/med-team/igv/commit/f028c8d97b3210551d92ee407e18b523ce43c457
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