Hi Olivier,
On Thu, Oct 18, 2018 at 01:05:12PM +0200, Olivier Sallou wrote:
> > I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
> > fails with other X11 errors
> >
> > 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
> > java.lang.IllegalArgumentException: Window must not be zero
> > at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
> > at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
> > ......
> >
> > this is above my knowledge of gui system in java....
>
> in fact it seems to work. X11 error occurs when having multiple screens
> and seems to relate to an openjdk bug [0].
> With a single screen I could open and manipulate the GUI
>
> I have pushed the patch update to manage current hstjdk debian version
Sounds good. Unfortunately I made an unfortunate observation: If I
apply the following patch:
diff --git a/debian/copyright b/debian/copyright
index defa779..5305639 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,31 +1,21 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://www.broadinstitute.org/igv/projects/downloads
Files-Excluded:
- igv.jar
- batik-codec.jar
- igv.bat
- igv.command
- lib/Jama-*
lib/batik*
lib/commons*
- lib/concurrent*
lib/guava*
- lib/jargs*
+ */htsjdk*.jar
lib/jcommon*
lib/jfreechart*
- lib/junit-*
+ */junit-*.jar
lib/log4j-*
- lib/sam-*
+ */picard-*.jar
+ */snappy-java-*.jar
lib/swing-layout-*
- lib/xml-apis-*
- lib/bcprov*
- lib/jgrapht*
lib/jide-oss-*
- lib/cofoja*
- lib/mysql-connector*
lib/gson*
- test/lib/ant.jar
- test/lib/fest-assert*.jar
+ */ant.jar
+ */fest-Assert*.jar
test/lib/fest-util*.jar
test/lib/fest-reflect*.jar
Disclaimer: This package is not part of the Debian operating system.
which does not mention not existing jars but more importantly removes
those jars we **think** we don't need - specifically */htsjdk*.jar -
recreate the tarball and try to build ... the build fails again. :-( Its
also some htsjdk related error and I think there are more issues in this
approach. It seems for whatever reason the build is done against the
internal copy but the result tries somehow to take the Debian installed
version. I'm hesitating to push my changes since than we have a broken
IGV again.
What do you suggest as next step? I might create a branch to let others
have a look.
Kind regards
Andreas.
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http://fam-tille.de