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

[Andreas Tille]

Hi Olivier,

On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
> 
> > Unfortunately if I start the package I get the following output:
> >
> > $ igv                                                                                                                                                                     
> > log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [org.broad.igv] additivity to [true].
> > log4j: Level value for org.broad.igv is  [INFO].
> > log4j: org.broad.igv level set to INFO
> > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > log4j: Setting property [conversionPattern] to [%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n].
> > log4j: Adding appender named [console] to category [org.broad.igv].
> > 2018-10-17 14:37:58 INFO  DirectoryManager:179 - IGV Directory: /home/andreas/igv
> > 2018-10-17 14:37:59 INFO  Main:155 - Startup  IGV Version user not_set
> > 2018-10-17 14:37:59 INFO  Main:156 - Java 10.0.2
> > 2018-10-17 14:37:59 INFO  DirectoryManager:84 - Fetching user directory...
> > 2018-10-17 14:37:59 INFO  Main:157 - Default User Directory: /home/andreas
> > 2018-10-17 14:38:00 INFO  Main:158 - OS: Linux
> >
> >
> > 2018-10-17 14:38:00 INFO  Main:208 - Unknown version: user
> > 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
> > java.lang.VerifyError: class org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
> 
> could be an htsjdk version issue versus what expects igv.....
> or getting 2 different definitions of
> htsjdk.samtools.seekablestream.SeekableStream in classpath

I admit I had the same idea.

... 
> > libhtsjdk-java - 2.16.1+dfsg-1

while igv includes

    htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar

I just realised that the Files-Excluded rules do not even remove this.
I assumed this would be excluded - so what about using the internal
code copy?  (Unfortunately I have no idea what to change to let this
happen.)

Kind regards

      Andreas.

-- 
http://fam-tille.de