Your message dated Thu, 08 Dec 2016 09:18:20 +0000 with message-id <e1ceuqk-000424...@fasolo.debian.org> and subject line Bug#846671: fixed in artemis 16.0.17+dfsg-1 has caused the Debian Bug report #846671, 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.) -- 846671: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=846671 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 [javac] warning: [options] source value 1.5 is obsolete and will be 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 [javac] warning: [options] target value 1.5 is obsolete and will be 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: artemis Source-Version: 16.0.17+dfsg-1 We believe that the bug you reported is fixed in the latest version of artemis, 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 artemis 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 09:39:12 +0100 Source: artemis Binary: artemis Architecture: source all Version: 16.0.17+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sascha Steinbiss <sa...@debian.org> Description: artemis - genome browser and annotation tool Closes: 846671 Changes: artemis (16.0.17+dfsg-1) unstable; urgency=medium . [ Sascha Steinbiss ] * Team upload. * New upstream release. * Refresh patches. * Avoid use of deprecated SAM access method to fix FTBFS. Closes: 846671 . [ Andreas Tille ] * Cleanup patches and add DEP3 headers * debhelper 10 * cme fix dpkg-control * d/watch: version=4 Checksums-Sha1: 59fc35e87baddb8f8b7d53ea95f6e92004220a14 2239 artemis_16.0.17+dfsg-1.dsc 9f9361f816741204a5aaf44e0ee80dc20358a31c 5248100 artemis_16.0.17+dfsg.orig.tar.gz d32fab38c209528309168d6fbab2399dee9ed2d6 29812 artemis_16.0.17+dfsg-1.debian.tar.xz 794190e341678c83172e4cbd9de75fe320d2c101 2622116 artemis_16.0.17+dfsg-1_all.deb 7114e8aac02661bb799ae41653431c51e1faf573 11653 artemis_16.0.17+dfsg-1_amd64.buildinfo Checksums-Sha256: c97cee3250f3622775dd381f95693a8c419f153f4132cc9b80a348429bfacaf7 2239 artemis_16.0.17+dfsg-1.dsc 0d43165d8b7aed53d5fdbb490af5877fb0f1d49b03b35eb5cc625c49ba659534 5248100 artemis_16.0.17+dfsg.orig.tar.gz e0d220a8c87fc56fc4aab0f02d64dd924bb9248a79d99514c24db410657d4158 29812 artemis_16.0.17+dfsg-1.debian.tar.xz baeba52561775e4af072dabfb49940d2d11e5650f40e4ae2df37233a084e1220 2622116 artemis_16.0.17+dfsg-1_all.deb 0a7e50ed997c9fe3d0bca5b66ce95251ac4ef4b030315e55c0b82c9637f6021c 11653 artemis_16.0.17+dfsg-1_amd64.buildinfo Files: f9043cb2e6e6709339f4fd2920d1d6f1 2239 science optional artemis_16.0.17+dfsg-1.dsc 6e6218a1e2ac68c075146a9aa52c0777 5248100 science optional artemis_16.0.17+dfsg.orig.tar.gz 50362ee90bff3d9303ef659513d30e31 29812 science optional artemis_16.0.17+dfsg-1.debian.tar.xz 2afbfc87e8c094d384d9a8f520b2d1b3 2622116 science optional artemis_16.0.17+dfsg-1_all.deb dbe12e3cfd8b00b5749ce19d1e6889d9 11653 science optional artemis_16.0.17+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJYSR+vAAoJEFeKBJTRxkbRvl4P/1eAcIOWovTTGpHfPmxVrXgU q30tnqF7o5Z2c9kz7H/UzdAyGPb+lYkQMCCY2knzyFomfNZQWCoA8lQSO4ffLlpx 6GW0P7JzWcMt5jYBIj+SdzycEIXhL4E1r/1MSjmoUKi78iT3qkgFf3GEuijfz4xF rWIHMupx9NKuIh+0bxeUosSGma+WOEyHuEYI1xiVTXlfj93UQjMQGll/nvqyQBtN T4c2FY/RjRyfPDTKbrZ82hfbVLnOzwxffMI41gi/bGYIIMADO9UFkMDCDEEWbdhW BAAcaVboU8DG+hU5KIxi8dE4SR7yhVBKfg2qsHay6+zXnWbjoFDcLlsbxzoaglLA BbN59nopqV7JjobexyVYIlqp5cKDgB5o4mI5ha7bnscnwxgJdjxP9/zuWOl3y1Rn zD1mp/GkRWRQzZ/n6q3RD5tOnSHFiJlMEa5KXnzm5/Bjy6y2WfGy1c45LCoJSSTg 4aBVboJszJKzjrM9pXWGgsIZ0TFrYmJOsFWpYuENexFiR3GdLhgLutRfb075Os5z QauftI7pPWzP865jNBOd+seB73ru9Mbom+i/ShALmwaw2r7cOkTg50CkPc3JMtTB BsEOQbWSJ+320SSBs9pG4jwGAsHl0apWjiX7zTsOkDvnF7HAuBVuJOzAmntrBWWX XqTOxMjzg0J3OhUhrBAn =YpBR -----END PGP SIGNATURE-----
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