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

[Olivier Sallou]

On 10/18/2018 12:03 PM, Olivier Sallou wrote:
>
> On 10/18/2018 11:42 AM, Andreas Tille wrote:
>> 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.


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....
>>
>> ... 
>>>> libhtsjdk-java - 2.16.1+dfsg-1
>> while igv includes
>>
>>     htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar
> the problem is org.broad.igv.util.stream.IGVSeekableBufferedStream
> extends a class from htsjdk but redefines a method declared as final,
> this is forbidden.
> Don't understand however why it compiles.....
> Recent htsjdk (as we have), includes those methods and cannot be
> overriden. Version 2.12 did not have those methods.
>
> Using internal has the issue we don't have the source code for it
> (though should match a commit). To get it work, we should simply remove
> htsjdk related "compile" directive in build gradle file (added via our
> patch)
>
>> 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.
>>

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

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