[med-svn] [Git][med-team/igv][master] 7 commits: test removing modules
Olivier Sallou
gitlab at salsa.debian.org
Tue Oct 16 11:04:39 BST 2018
Olivier Sallou pushed to branch master at Debian Med / igv
Commits:
68ea0c8a by Olivier Sallou at 2018-10-16T08:43:08Z
test removing modules
- - - - -
9d8ed2ad by Olivier Sallou at 2018-10-16T08:43:08Z
fix path to java lib
- - - - -
76617f74 by Olivier Sallou at 2018-10-16T08:43:08Z
add xml module for exec
- - - - -
aacdf6a8 by Olivier Sallou at 2018-10-16T08:43:08Z
add missing libs to runtime and add default log4j properties
- - - - -
4fc57e0b by Olivier Sallou at 2018-10-16T08:43:08Z
add log4j logger
- - - - -
0dea0295 by Olivier Sallou at 2018-10-16T08:43:08Z
update status
- - - - -
eaa95f1c by Olivier Sallou at 2018-10-16T10:04:30Z
merge updates
- - - - -
6 changed files:
- debian/bin/igv
- debian/changelog
- debian/igv.jlibs
- + debian/log4j.xml
- debian/patches/fix_gradle.patch
- debian/rules
Changes:
=====================================
debian/bin/igv
=====================================
@@ -1,5 +1,5 @@
#!/bin/sh
set -eu
-exec java -cp /usr/share/java/igv.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 "$@"
+exec java --add-modules java.xml.bind -cp /usr/share/java/igv.jar:/usr/share/java/log4j-api.jar:/usr/share/java/log4j-core.jar:/usr/share/java/htsjdk.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-css.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-gui-util.jar:/usr/share/java/batik-gvt.jar:/usr/share/java/batik-parser.jar:/usr/share/java/batik-svg-dom.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-transcoder.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:/usr/share/java/commons-io.jar:/usr/share/java/commons-logging.jar:/usr/share/java/commons-math.jar:/usr/share/java/commons-net.jar:/usr/share/java/concurrent.jar:/usr/share/java/gson.jar:/usr/share/java/guava.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/jama.jar:/usr/share/java/jargs.jar:/usr/share/java/jcommon.jar:/usr/share/java/jfreechart.jar:/usr/share/java/jhdf5.jar:/usr/share/java/net.sourceforge.jlibdeps.jar:/usr/share/java/junit4.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/sam.jar:/usr/share/java/swing-layout.jar:/usr/share/java/xml-apis.jar:/usr/share/java/xml-apis-ext.jar:/usr/share/java/AbsoluteLayout.jar:/usr/share/java/bcprov.jar:/usr/share/java/jgrapht0.8.jar:/usr/share/java/jide-oss.jar:/usr/share/java/commons-io.jar:/usr/share/java/cofoja.jar:/usr/share/java/gson.jar org.broad.igv.ui.Main "$@"
=====================================
debian/changelog
=====================================
@@ -16,17 +16,7 @@ igv (2.4.14+dfsg-1) UNRELEASED; urgency=medium
[ Olivier Sallou]
* d/patches/fix_gradle.patch: adapt build to Debian
-
-
- * TODO there is still an issue with batik:
- - if defined, there are some conflicts
- (see https://stackoverflow.com/questions/42358084/package-conflicts-with-automatic-modules-in-java-9)
- where some batik share some package names.
- - for javafx libs, they are found but marked as not visible.... though
- should be seen as unnamed modules.
- javafx libs should be declared as modules with exported packages but
- needs lib refactoring or we should find a way to put them as "standard"
- libs and not modules (but how?)
+ Remove java module support as some Debian libs are not modularized yet
-- Andreas Tille <tille at debian.org> Mon, 01 Oct 2018 21:14:39 +0200
=====================================
debian/igv.jlibs
=====================================
@@ -1 +1 @@
-igv.jar
+build_java9/libs/igv.jar
=====================================
debian/log4j.xml
=====================================
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+<log4j:configuration debug="true"
+ xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+ <appender name="console" class="org.apache.log4j.ConsoleAppender">
+ <layout class="org.apache.log4j.PatternLayout">
+ <param name="ConversionPattern"
+ value="%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n" />
+ </layout>
+ </appender>
+
+ <logger name="org.broad.igv">
+ <level value="INFO" />
+ <appender-ref ref="console" />
+ </logger>
+
+</log4j:configuration>
=====================================
debian/patches/fix_gradle.patch
=====================================
@@ -43,8 +43,8 @@ Forwarded: no
+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-base/debian/javafx-base-debian-linux.jar")
+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-swing/debian/javafx-swing-debian-linux.jar")
+ compile files ("/usr/share/maven-repo/org/openjfx/javafx-fxml/debian/javafx-fxml-debian-linux.jar")
-+ //compile "org.apache.xmlgraphics:batik-dom:debian"
-+ //compile "org.apache.xmlgraphics:batik-svggen:debian"
++ compile "org.apache.xmlgraphics:batik-dom:debian"
++ compile "org.apache.xmlgraphics:batik-svggen:debian"
+ compile "com.google.guava:guava:debian"
+ compile "commons-io:commons-io:debian"
+ compile "org.apache.commons:commons-math:debian"
@@ -62,6 +62,23 @@ Forwarded: no
testCompile fileTree(dir: 'test/lib', include: '*.jar')
}
+@@ -93,12 +123,13 @@
+ }
+
+ compileJava {
+- inputs.property("moduleName", moduleName)
++ //inputs.property("moduleName", moduleName)
+ doFirst {
+ options.compilerArgs = [
+- '--module-path', classpath.asPath,
++ // '--module-path', classpath.asPath,
++ '--add-modules', 'java.xml.bind'
+ ]
+- classpath = files()
++ // classpath = files()
+ }
+ }
+
--- a/src/main/java9/module-info.java
+++ b/src/main/java9/module-info.java
@@ -93,11 +93,11 @@
=====================================
debian/rules
=====================================
@@ -9,6 +9,8 @@ JAVA_HOME=/usr/lib/jvm/default-java
dh $@ --buildsystem=gradle --with javahelper
override_dh_clean:
+ if [ -e src/main/resources/log4j.xml ] ; then rm src/main/resources/log4j.xml ; fi
+ if [ -e src/main/java9/module-info.java.skip ] ; then mv src/main/java9/module-info.java.skip src/main/java9/module-info.java ; fi
if [ -e build_java8.gradle ] ; then mv build_java8.gradle build.gradle ; fi
rm -f goby-io-igv.jar
rm -f batik-codec.jar
@@ -17,3 +19,5 @@ override_dh_clean:
override_dh_auto_configure:
mv build.gradle build_java8.gradle
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/
View it on GitLab: https://salsa.debian.org/med-team/igv/compare/39037318fb7938efdddf8632f5b91023c0e2046f...eaa95f1c5d56003c91984f1e2036bbf8bae7fec0
--
View it on GitLab: https://salsa.debian.org/med-team/igv/compare/39037318fb7938efdddf8632f5b91023c0e2046f...eaa95f1c5d56003c91984f1e2036bbf8bae7fec0
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