[Debian-med-packaging] Bug#895765: IGV

[Olivier Sallou]

On 10/18/2018 04:06 PM, Andreas Tille wrote:
> 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.

testing with your removals, you only need to add to build gradle file
the ref to htsjdk


diff --git a/debian/patches/fix_gradle.patch
b/debian/patches/fix_gradle.patch
index 421a147..b2a0ac4 100644
--- a/debian/patches/fix_gradle.patch
+++ b/debian/patches/fix_gradle.patch
@@ -34,7 +34,7 @@ Forwarded: no
  sourceSets {
      main {
          java {
-@@ -45,6 +54,27 @@
+@@ -45,6 +54,28 @@
  dependencies {
      // Use the newer JIDE lib for Java 9 builds
      compile fileTree(dir: 'lib', include: '*.jar', exclude:
'jide-oss-3.5.5.jar') + fileTree(dir: 'lib_java9', include: '*.jar')
@@ -59,10 +59,11 @@ Forwarded: no
 +    compile "org.apache.logging.log4j:log4j-1.2-api:debian"
 +    compile "org.apache.logging.log4j:log4j-core:debian"
 +    compile "org.swinglabs:swing-layout:debian"
++    compile "com.github.samtools:htsjdk:debian"
      testCompile fileTree(dir: 'test/lib', include: '*.jar')
  }
 
-@@ -93,12 +123,13 @@
+@@ -93,12 +124,13 @@
  } 
  compileJava {



I pushed the update on patch (but your copyright patch is not yet there)

With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar
removed from upstream source, it compiles fine for me.

Olivier
>
>
> 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.
>
>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
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