----- 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... 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]
