----- Mail original ----- > De: "Olivier Sallou" <[email protected]> > À: "Andreas Tille" <[email protected]> > Cc: "Debian Med Project List" <[email protected]> > Envoyé: Dimanche 17 Août 2014 14:11:58 > Objet: Re: [Help] Latest version of IGV fails to build > > > > ----- Mail original ----- > > De: "Andreas Tille" <[email protected]> > > À: "Debian Med Project List" <[email protected]> > > 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...
There is indeed an issue. The samtools library (picard-tools) in Debian has a private access to the BAMFileWriter but does not offer public method to create one with a stream. There is possibility to do so for a File, but not a stream. so there is no way to adapt this method for the moment with the library in Debian. We need the method: public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final OutputStream stream) Latest in picard-tools does not provide such method, while available at [0] An other option is to comment this method (as well in tests), this is what I made in current patch I pushed to git repo (though I also put the expected but not available method to use). Method on streams does not seem to be used elsewhere.... and compilation/basic run goes fine. But could there be any side effect ? People using igv.jar as a library? I also udpated 01-build.xml patch that had some errors with batik-codec and goby jars. I did not upload however, according to decision to be made if methods should be commented or not, waiting to get available methods in picard-tools. [0] https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/SAMFileWriterFactory.java Olivier > > > 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 > > > > > > -- > > To UNSUBSCRIBE, email to [email protected] > > with a subject of "unsubscribe". Trouble? Contact > > [email protected] > > Archive: https://lists.debian.org/[email protected] > > > > > > > -- > To UNSUBSCRIBE, email to [email protected] > with a subject of "unsubscribe". Trouble? Contact [email protected] > Archive: > https://lists.debian.org/[email protected] > > -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
