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Commits on Source
7
test removing modules
· 68ea0c8a
Olivier Sallou
authored
Oct 16, 2018
68ea0c8a
fix path to java lib
· 9d8ed2ad
Olivier Sallou
authored
Oct 16, 2018
9d8ed2ad
add xml module for exec
· 76617f74
Olivier Sallou
authored
Oct 16, 2018
76617f74
add missing libs to runtime and add default log4j properties
· aacdf6a8
Olivier Sallou
authored
Oct 16, 2018
aacdf6a8
add log4j logger
· 4fc57e0b
Olivier Sallou
authored
Oct 16, 2018
4fc57e0b
update status
· 0dea0295
Olivier Sallou
authored
Oct 16, 2018
0dea0295
merge updates
· eaa95f1c
Olivier Sallou
authored
Oct 16, 2018
eaa95f1c
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debian/bin/igv
View file @
eaa95f1c
#!/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
View file @
eaa95f1c
...
...
@@ -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@debian.org> Mon, 01 Oct 2018 21:14:39 +0200
...
...
debian/igv.jlibs
View file @
eaa95f1c
igv.jar
build_java9/libs/
igv.jar
debian/log4j.xml
0 → 100644
View file @
eaa95f1c
<?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
View file @
eaa95f1c
...
...
@@ -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
View file @
eaa95f1c
...
...
@@ -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/