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

[Olivier Sallou]

On 10/18/2018 12:15 PM, Olivier Sallou wrote:
>
> 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....

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


[0] https://bugs.openjdk.java.net/browse/JDK-8204646

Olivier
>>> ... 
>>>>> 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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