Your message dated Thu, 08 Dec 2016 19:48:28 +0000 with message-id <e1cf4g8-0005tr...@fasolo.debian.org> and subject line Bug#846708: fixed in fastqc 0.11.5+dfsg-6 has caused the Debian Bug report #846708, regarding fastqc: FTBFS: [javac] /<<BUILDDIR>>/fastqc-0.11.5+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java:30: error: cannot find symbol to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 846708: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=846708 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: fastqc Version: 0.11.5+dfsg-5 Severity: serious Tags: stretch sid User: debian...@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 [javac] warning: [options] source value 1.5 is obsolete and will be 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 [javac] warning: [options] target value 1.5 is obsolete and will be 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.
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--- Begin Message ---Source: fastqc Source-Version: 0.11.5+dfsg-6 We believe that the bug you reported is fixed in the latest version of fastqc, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 846...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Sascha Steinbiss <sa...@debian.org> (supplier of updated fastqc package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 08 Dec 2016 15:40:00 +0000 Source: fastqc Binary: fastqc Architecture: source all Version: 0.11.5+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: fastqc - quality control for high throughput sequence data Closes: 846708 Changes: fastqc (0.11.5+dfsg-6) unstable; urgency=medium . * Team upload. * Avoid use of SAMFileReader to fix FTBFS. Closes: #846708 * Add autopkgtest cases and accompanying test data for SAM/BAM input files. * Make sure jar dependencies are found. Before fixing this, htsjdk classes were not found at runtime. This problem only surfaced with BAM/SAM inputs, which were not tested so far. Checksums-Sha1: 7ffed7f477c847de14e25b9c0abc55eb4c8c9fc4 2181 fastqc_0.11.5+dfsg-6.dsc 72ebe244e115ec8a370ec8d20be418fd146e17e5 15740 fastqc_0.11.5+dfsg-6.debian.tar.xz cca5ea0c4c04cadc49a11769ce6396c6372cb882 374572 fastqc_0.11.5+dfsg-6_all.deb b013200d8c42e72c3d4a78fa0144eb020723c09b 9711 fastqc_0.11.5+dfsg-6_amd64.buildinfo Checksums-Sha256: 47fbac4dbd58211bcd344236256b1eae959bf03f9763e06bf61b4f7f9a27c401 2181 fastqc_0.11.5+dfsg-6.dsc d5b65162b03f811233ee8e6343291f248d7907bd8c908e1a9f69fbbb7938d399 15740 fastqc_0.11.5+dfsg-6.debian.tar.xz 3866b68196d412b6716e907e8d67e8913b66e7f6a3426108548c6d1801e05da8 374572 fastqc_0.11.5+dfsg-6_all.deb 4a969a0d25b1af438172d18d8d86909f425946e792388ec1fc5e962311514faa 9711 fastqc_0.11.5+dfsg-6_amd64.buildinfo Files: 924e2dcda6c5f2d1fa2d1bd988002d64 2181 science optional fastqc_0.11.5+dfsg-6.dsc e5d6af54e98dfde548c66112efce5f98 15740 science optional fastqc_0.11.5+dfsg-6.debian.tar.xz 5194eeb087c75354cd97cbb71685c7c3 374572 science optional fastqc_0.11.5+dfsg-6_all.deb 75bfe9b0c6ffc97ef6c73d4f789adfab 9711 science optional fastqc_0.11.5+dfsg-6_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAlhJtl0ACgkQ6NN64vCf SHJP7w/+Oaz5KFUzS+VrwBoTr5Uomcm0wAav8SD4+f3TW3ck91e452Dmh+K+fzvl yPcrIsqxtNDUgeQNcv5PFpTeZL6UMdpV8C2u52RDjV8Blr3nb3TVJ28VrYQ3cYtL ka/vOjQEUXMEi7f5Z3gmJEQOvdKBM4cu5re19Odtb3XcLrNZwPzAPDC+NqnwlfFI usOMaM3wDGUATLBdtqxnH58ptU+a6fidgzB6NUNJRFybVHQmiKApcE776IRCxmYb W2rYGxwQctJNcOxj2wRQUuaAlwox48WpSjKv0Jzmr6GIHT9lpdi1pfKwSXHCD+X7 J2uHoNe2e2Lz1abVeW8CIZkob6ZS/yJMssr/Dv5BYYOnDvjWnNQ4GSJBhcFMD0en SstseeHuLG3J2m3QBxnODiw63Q4RFzcy5h/NrPRBSDreizmQihuiUne1rzCJPctF HNyMTf3gejT7Kp/w2PmUbCXN4WRxv7X8BDbMthXfpEOpXoK7Nxa46irr9swru092 nhoNC7y6lHzVs+US/BeKRhNK0VtxJUQ8SAhOPkLXESW77KproR7lXy088PXMMWVn qCwvyYfiFHehj4AARSsdTCeKt8iinC9h/uUR9qVu+BeA6rqBOz8gIw5/h7dqsIgd zyi7HSIRowD0n4+re2lTS4bSsY+vfpwKWIpPeEhTr9mH2rGYrWM= =h+Zu -----END PGP SIGNATURE-----
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