Re: [Help] Latest version of IGV fails to build
----- Mail original -----
> De: "Andreas Tille" <andreas@an3as.eu>
> À: "Debian Med Project List" <debian-med@lists.debian.org>
> Envoyé: Vendredi 15 Août 2014 13:29:27
> Objet: [Help] Latest version of IGV fails to build
>
> Hi,
>
> I commited the packaging for last IGV to Git but it fails to build:
>
> compile:
> [javac] /tmp/buildd/igv-2.3.34+dfsg/build.xml:175: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last;
> set to false for repeatable builds
> [javac] Compiling 864 source files to /tmp/buildd/igv-2.3.34+dfsg/tmp
> [javac] warning: [options] bootstrap class path not set in conjunction
> with -source 1.6
> [javac]
> /tmp/buildd/igv-2.3.34+dfsg/src/org/broad/igv/sam/SAMWriter.java:58:
> error: BAMFileWriter is not public in net.sf.samtools; cannot be
> accessed from outside package
> [javac] writer = new BAMFileWriter(stream, null);
> [javac] ^
> [javac] Note: Some input files use or override a deprecated API.
> [javac] Note: Recompile with -Xlint:deprecation for details.
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [javac] 1 error
> [javac] 1 warning
>
> BUILD FAILED
>
>
> I guess for a Java-knowledged person this is easy to fix but I have no
> idea how. I also have the impression we could extend our
> "Files-Excluded" to some more JARs which are distributed with IGV
> source.
>
Hi,
I dont't if you found someone to fix this in the meanwhile, but I think it is a matter of version of samtools library between the one originally used by igv and the one available in Debian.
This issue is related to a matter of method visibility inside/outside the samtools package. The method was certainly public in original library and is now private. Maybe a new method should be used, we should check the samtools API.
https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/BAMFileWriter.java shows that BAMFileWriter is protected, so cannot be used by external libraries.
Maybe something like, from SAMFileWriterFactory.java, could do the job:
write = makeBAMWriter(mySamFileHeader,false,one_output_file);
but we need to map the stream to one_ouput_file, and see what could be mapped to mySamFileHeader...
So, this is a way to fix this, but with an API quite different, ie adapting IVG to the samtools version available in Debian.
I will try to see if I can try to fix this next week, but it may not be so easy... and more complex to maintain.
Olivier
> Feel free to fix and upload the package (or just commit a fix to Git and
> tell me to upload)
>
> Andreas.
>
> --
> http://fam-tille.de
>
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