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. -- http://fam-tille.de