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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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