[Debian-med-packaging] Bug#846708: fastqc: FTBFS: [javac] /<<BUILDDIR>>/fastqc-0.11.5+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java:30: error: cannot find symbol

[Lucas Nussbaum]

Source: fastqc
Version: 0.11.5+dfsg-5
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20161202 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<BUILDDIR>>/fastqc-0.11.5+dfsg'
> dh_auto_build
> 	ant -Duser.name debian
> Buildfile: /<<BUILDDIR>>/fastqc-0.11.5+dfsg/build.xml
> 
> build-subprojects:
> 
> init:
>     [mkdir] Created dir: /<<BUILDDIR>>/fastqc-0.11.5+dfsg/bin
>      [copy] Copying 86 files to /<<BUILDDIR>>/fastqc-0.11.5+dfsg/bin
> 
> build-project:
>      [echo] FastQC: /<<BUILDDIR>>/fastqc-0.11.5+dfsg/build.xml
>     [javac] Compiling 67 source files to /<<BUILDDIR>>/fastqc-0.11.5+dfsg/bin
>     [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
>     [javac] warning: [options] source value 1.5 is obsolete and will be removed in a future release
>     [javac] warning: [options] target value 1.5 is obsolete and will be removed in a future release
>     [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
>     [javac] /<<BUILDDIR>>/fastqc-0.11.5+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java:30: error: cannot find symbol
>     [javac] import htsjdk.samtools.SAMFileReader;
>     [javac]                       ^
>     [javac]   symbol:   class SAMFileReader
>     [javac]   location: package htsjdk.samtools
>     [javac] /<<BUILDDIR>>/fastqc-0.11.5+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java:47: error: cannot find symbol
>     [javac] 	private SAMFileReader br;
>     [javac] 	        ^
>     [javac]   symbol:   class SAMFileReader
>     [javac]   location: class BAMFile
>     [javac] /<<BUILDDIR>>/fastqc-0.11.5+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java:59: error: cannot find symbol
>     [javac] 		SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
>     [javac] 		^
>     [javac]   symbol:   variable SAMFileReader
>     [javac]   location: class BAMFile
>     [javac] /<<BUILDDIR>>/fastqc-0.11.5+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java:63: error: cannot find symbol
>     [javac] 		br = new SAMFileReader(fis);
>     [javac] 		         ^
>     [javac]   symbol:   class SAMFileReader
>     [javac]   location: class BAMFile
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 4 errors
>     [javac] 4 warnings
> 
> BUILD FAILED
> /<<BUILDDIR>>/fastqc-0.11.5+dfsg/build.xml:36: Compile failed; see the compiler error output for details.
> 
> Total time: 1 second
> dh_auto_build: ant -Duser.name debian returned exit code 1
> debian/rules:10: recipe for target 'override_dh_auto_build' failed
> make[1]: *** [override_dh_auto_build] Error 2

The full build log is available from:
   http://aws-logs.debian.net/2016/12/02/fastqc_0.11.5+dfsg-5_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.