Your message dated Tue, 26 Jul 2016 22:22:34 +0000 with message-id <e1bsake-00016q...@franck.debian.org> and subject line Bug#811859: fixed in berkeley-express 1.5.1-2 has caused the Debian Bug report #811859, regarding berkeley-express: FTBFS with GCC 6: no matching function for call to 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.) -- 811859: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: berkeley-express Version: 1.5.1-1 Severity: important User: debian-...@lists.debian.org Usertags: ftbfs-gcc-6 gcc-6-no-match This package fails to build with GCC 6. GCC 6 has not been released yet, but it's expected that GCC 6 will become the default compiler for stretch. Note that only the first error is reported; there might be more. You can find a snapshot of GCC 6 in experimental. To build with GCC 6, you can set CC=gcc-6 CXX=g++-6 explicitly. You may be able to find out more about this issue at https://gcc.gnu.org/gcc-6/changes.html > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux ... > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/sequence.cpp.o -c /<<PKGBUILDDIR>>/src/sequence.cpp > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/bundles.cpp.o -c /<<PKGBUILDDIR>>/src/bundles.cpp > [ 94%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/targets.pb.cc.o -c > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/targets.pb.cc > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/alignments.pb.cc.o -c > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/alignments.pb.cc > In file included from /<<PKGBUILDDIR>>/src/main.cpp:42:0: > /<<PKGBUILDDIR>>/src/update_check.h: In function 'bool > get_current_version(char*)': > /<<PKGBUILDDIR>>/src/update_check.h:89:28: warning: argument to 'sizeof' in > 'void bzero(void*, size_t)' call is the same expression as the destination; > did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] > bzero(curr_version, sizeof(curr_version)); > ^ > > /<<PKGBUILDDIR>>/src/targets.cpp: In member function 'double > Target::sample_likelihood(bool, const std::vector<const Target*>*) const': > /<<PKGBUILDDIR>>/src/targets.cpp:116:62: error: no matching function for call > to 'Target::cached_effective_length(const boost::shared_ptr<BiasBoss>&) const' > double tot_eff_len = cached_effective_length(lib.bias_table); > ^ > > In file included from /<<PKGBUILDDIR>>/src/targets.cpp:10:0: > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: candidate: double > Target::cached_effective_length(bool) const > double cached_effective_length(bool with_bias=true) const; > ^~~~~~~~~~~~~~~~~~~~~~~ > > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: no known conversion for > argument 1 from 'const boost::shared_ptr<BiasBoss>' to 'bool' > /<<PKGBUILDDIR>>/src/targets.cpp:121:77: error: no matching function for call > to 'Target::cached_effective_length(const boost::shared_ptr<BiasBoss>&) const' > > neighbor->cached_effective_length(lib.bias_table)); > ^ > > In file included from /<<PKGBUILDDIR>>/src/targets.cpp:10:0: > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: candidate: double > Target::cached_effective_length(bool) const > double cached_effective_length(bool with_bias=true) const; > ^~~~~~~~~~~~~~~~~~~~~~~ > > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: no known conversion for > argument 1 from 'const boost::shared_ptr<BiasBoss>' to 'bool' > src/CMakeFiles/express.dir/build.make:225: recipe for target > 'src/CMakeFiles/express.dir/targets.cpp.o' failed > make[3]: *** [src/CMakeFiles/express.dir/targets.cpp.o] Error 1 -- Martin Michlmayr Linux for HPE Helion, Hewlett Packard Enterprise
--- End Message ---
--- Begin Message ---Source: berkeley-express Source-Version: 1.5.1-2 We believe that the bug you reported is fixed in the latest version of berkeley-express, 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 811...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Gert Wollny <gw.foss...@gmail.com> (supplier of updated berkeley-express 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: Tue, 26 Jul 2016 18:38:52 +0000 Source: berkeley-express Binary: berkeley-express berkeley-express-doc Architecture: source amd64 all Version: 1.5.1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Gert Wollny <gw.foss...@gmail.com> Description: berkeley-express - Streaming quantification for high-throughput sequencing berkeley-express-doc - Documentation for RNA-Seq tool eXpress Closes: 811859 Changes: berkeley-express (1.5.1-2) unstable; urgency=medium . * Team upload. * d/p/gcc-6: Fix compilation with gcc-6, Closes: #811859 * cme fix dpkg-control: - update standards version to 3.9.8 - update to secure packaging urls * d/p/correct-debug-flags: don't force debug flags and dynamically link to BOOST, protobuf and tcmalloc_minimal * d/rules: enable hardening Checksums-Sha1: ecf78acc467ac7e55b5b06bbd093b0353d47d638 2347 berkeley-express_1.5.1-2.dsc 7b96676d9e422836f81bcb047ed429661aac95d9 7512 berkeley-express_1.5.1-2.debian.tar.xz 93a555e13ebf438bae1b9f056140b38d9eea61c4 3594794 berkeley-express-dbgsym_1.5.1-2_amd64.deb 510b9c65455d6369202701710c8028e9d0589dc0 790594 berkeley-express-doc_1.5.1-2_all.deb 31842f4a52ef09100453492fdfebab6dfb30172a 253264 berkeley-express_1.5.1-2_amd64.deb Checksums-Sha256: 7be205e453b82da8488d3982d3c3a2c20be858cafb814acc499d8eec36013e88 2347 berkeley-express_1.5.1-2.dsc bddad831ce1c6c71104e0c51eb399da93235bf3122bd591efc4790f50199e32e 7512 berkeley-express_1.5.1-2.debian.tar.xz bf86eb500e2d52e0b3720205733a6e976b7c39d818be0964cb8286fb322374e8 3594794 berkeley-express-dbgsym_1.5.1-2_amd64.deb 4b871954337c4b705d87562640d510e9c4caf53bba01963908ae0ac3e17069f2 790594 berkeley-express-doc_1.5.1-2_all.deb b1795056fd179f418411bb1b4f6762c9b1dd7efcea8327363547bcbd1b3408b1 253264 berkeley-express_1.5.1-2_amd64.deb Files: 38be6acbcb4ec31e5a505eaab18524d1 2347 science optional berkeley-express_1.5.1-2.dsc 20c4dd4da6b419d0baa494712edca86f 7512 science optional berkeley-express_1.5.1-2.debian.tar.xz a7a8d3cbd5a82809fdd99fcfd09a5ddd 3594794 debug extra berkeley-express-dbgsym_1.5.1-2_amd64.deb 9e91566f128de52e889bf4e7abbffdc4 790594 doc optional berkeley-express-doc_1.5.1-2_all.deb 8e945f0cf19e9cb4377ba9ef9cd18137 253264 science optional berkeley-express_1.5.1-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXl8YMAAoJEFeKBJTRxkbRFNcP/0xRa3/H0H/UeBt2b8z3Zudv 8XG8pDtKIcUoEp0hm45sLLud9wfU1JjccfOib6rTdyQF4pI6hA10qAwSGZaDD15y VKYoIsdFiCy1Lg90u62ebDB3Q9i2Os8vNMIRsbC2IiS2g5ptR3UUl41CGQvWaK0H fMoPYwQicgLENMMVgq5OhaPX07DKF0asg7CcAmOCIUENSObVr+UF4FAV39D8Txse WTYhpfeVc5qGurbYK1HDUSKoPK1ifym6W7tV6hJ1/QQ2G3HVNjHbgfkXnP/sx88k /91YoQXaFpecSrp/39+91kItIB33N1e6QQfRbeflszQlKAdWx+2uKH3tW0wp1oQ0 HvsnAqxxmOB4wzqSxdLbve7/QpPURs+b7ZZ18iRrCtUCOMzbSkqh3psKXURKAklJ ZKoFQO2p5s/qeH4flgIbc55JXQS9U9ZhpKoGPI4yTIg4Y9m+GZUpjBUnwSIdhq1f 7SUkV46NS807wn5n/OQRNoWB3d0i1aHJ/YrYRwaXB2+5/Zp6g/qM5x54tZVHlvvZ d/Anmw+Z7odNXpcxenpqHbTOks05OydUqiDJKVvY5hMgfR6S/RoJaxTxEcnTSVcM ty3O34Balass/EOdBp2a89JA9QDKQeMqiwOABwa8LCSG6a9QkYIItgjjsVIc45Ua RW+sKkAZmFvYtKRi0aNe =WjoD -----END PGP SIGNATURE-----
--- End Message ---
