Your message dated Sat, 27 Jun 2015 10:21:14 +0000 with message-id <e1z8ney-0002mn...@franck.debian.org> and subject line Bug#778161: fixed in velvet 1.2.10+dfsg1-2 has caused the Debian Bug report #778161, regarding velvet: ftbfs with GCC-5 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.) -- 778161: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778161 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:velvet Version: 1.2.10+dfsg1-1 Severity: normal Tags: sid stretch User: debian-...@lists.debian.org Usertags: ftbfs-gcc-5 Please keep this issue open in the bug tracker for the package it was filed for. If a fix in another package is required, please file a bug for the other package (or clone), and add a block in this package. Please keep the issue open until the package can be built in a follow-up test rebuild. The package fails to build in a test rebuild on at least amd64 with gcc-5/g++-5, but succeeds to build with gcc-4.9/g++-4.9. The severity of this report may be raised before the stretch release. The full build log can be found at: http://people.debian.org/~doko/logs/gcc5-20150205/velvet_1.2.10+dfsg1-1_unstable_gcc5.log The last lines of the build log are at the end of this report. To build with GCC 5, either set CC=gcc-5 CXX=g++-5 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t experimental install g++ Common build failures are C11 as the default C mode, new warnings resulting in build failures with -Werror turned on, or new/dropped symbols in Debian symbols files. For other C/C++ related build failures see the porting guide at http://gcc.gnu.org/gcc-5/porting_to.html [...] In file included from src/scaffold.c:32:0: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:29:0: src/readSet.h:64:16: warning: inline function 'isCreateBinary' declared but never defined inline boolean isCreateBinary(); ^ In file included from src/kmerOccurenceTable.c:27:0: src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^ src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^ src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^ src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm obj/run.o: In function `main': /«BUILDDIR»/velvet-1.2.10+dfsg1/src/run.c:245: undefined reference to `isCreateBinary' /«BUILDDIR»/velvet-1.2.10+dfsg1/src/run.c:291: undefined reference to `isCreateBinary' obj/splayTable.o: In function `inputSequenceArrayIntoSplayTableAndArchive': /«BUILDDIR»/velvet-1.2.10+dfsg1/src/splayTable.c:982: undefined reference to `isCreateBinary' collect2: error: ld returned 1 exit status make[2]: *** [velveth] Error 1 Makefile:70: recipe for target 'velveth' failed make[2]: Leaving directory '/«BUILDDIR»/velvet-1.2.10+dfsg1' dh_auto_build: make -j1 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS=-D_FORTIFY_SOURCE=2 CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security LDFLAGS=-Wl,-z,relro returned exit code 2 make[1]: *** [build_long_versions] Error 2 debian/rules:23: recipe for target 'build_long_versions' failed make[1]: Leaving directory '/«BUILDDIR»/velvet-1.2.10+dfsg1' make: *** [build-arch] Error 2 debian/rules:7: recipe for target 'build-arch' failed dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
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--- Begin Message ---Source: velvet Source-Version: 1.2.10+dfsg1-2 We believe that the bug you reported is fixed in the latest version of velvet, 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 778...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated velvet 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: Sat, 27 Jun 2015 11:44:54 +0200 Source: velvet Binary: velvet velvet-long velvet-example velvet-tests Architecture: source all amd64 Version: 1.2.10+dfsg1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: velvet - Nucleic acid sequence assembler for very short reads velvet-example - Example data for the Velvet sequence assembler velvet-long - Nucleic acid sequence assembler for very short reads, long versio velvet-tests - Test data for the Velvet sequence assembler Closes: 778161 Changes: velvet (1.2.10+dfsg1-2) unstable; urgency=medium . * Fix gcc-5 build issue by adapting upstream patch Closes: #778161 * cme fix dpkg-control Checksums-Sha1: bdd9841a4ac9489f0e0afdc95f6c2aba9648bbb8 2279 velvet_1.2.10+dfsg1-2.dsc bf944f18e6fc04453bc1ecfed4bd3ff1a1a73c97 13492 velvet_1.2.10+dfsg1-2.debian.tar.xz 27bd660143085bfb898a1828d5717d2909d5bb3c 3335184 velvet-example_1.2.10+dfsg1-2_all.deb 79e45507c208d40670280a9f0ccd8450cb4c9f06 188214 velvet-long_1.2.10+dfsg1-2_amd64.deb 19f37be559b23c8f391feecdcf2d081759eeeb7c 10752520 velvet-tests_1.2.10+dfsg1-2_all.deb a7bc98762347b6812831e424a3caaed2a3f76db6 684628 velvet_1.2.10+dfsg1-2_amd64.deb Checksums-Sha256: e9f3faf959cafa6b65110af7310dca881c9e71b9f4439b76334a35d3dec414ff 2279 velvet_1.2.10+dfsg1-2.dsc e9495e5628cdce21c4ee37bc17e2a347274a66097fddfe45e0e4b6037ca79deb 13492 velvet_1.2.10+dfsg1-2.debian.tar.xz a9d677d72e96a550ac796b8493302bca3c073c6c63dd536819c4f4f95721ea13 3335184 velvet-example_1.2.10+dfsg1-2_all.deb 730c2a3ab9058ccf847f7a450285a00c57d11ae013af6976729f64043b047ed8 188214 velvet-long_1.2.10+dfsg1-2_amd64.deb e4336d11d503701f9612a896d3ebc2ce3f1d1a98a66de33f754dd0cc38790eb9 10752520 velvet-tests_1.2.10+dfsg1-2_all.deb a8d7f661f32b328db4b3f2f3dab62f89f3f63663ae2044f2a495970bd455c8ec 684628 velvet_1.2.10+dfsg1-2_amd64.deb Files: c749902ffed1da649cee9538081b19f3 2279 science optional velvet_1.2.10+dfsg1-2.dsc 7c5fc398aeddce54b746454a3c55addf 13492 science optional velvet_1.2.10+dfsg1-2.debian.tar.xz af43c2c70e5eee92f84a5f8ada8f6af0 3335184 science optional velvet-example_1.2.10+dfsg1-2_all.deb 0a472a615b926e7a7947dbc83676d20f 188214 science optional velvet-long_1.2.10+dfsg1-2_amd64.deb 145bff06d9ed708e796c0ed447472cc8 10752520 science optional velvet-tests_1.2.10+dfsg1-2_all.deb dccb0cac4db36e0db96f117df0ab4916 684628 science optional velvet_1.2.10+dfsg1-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJVjnMDAAoJEFeKBJTRxkbRrnAP/ijTUGUiH3nSwOfEhAmUqO/D hbUyiFoIFDbNHv1NnExBQY0TN8qTFKCcmy32Ja9IbFzyXHrWYIOp6lauw0l2cY3Z p8NnelsFGFSocKQeScbEdv+d3fJwx1dJA/Lw4U7lNNLChhV2HGLc33bnr8jsLgLt 6b31qATbVabr1uhdkO45IXBk/sLfEchDeqUkv2Yrj/2ihlEYyPqJc0wbMr94lkB3 ohmjBsvFRBr7D/88mANwBN81JmBMpfqMD3auR6YsuvtYcR16ZD21UuKod7QsPljs /maiMnSmm3BVaS91WPalMI7El0MLi3BJdbzkbEqzNXoBQ3SAAcWDSMylh5+fkwao d/xaIpEamvZuSma87IMK9QLjMcd7BA+MQuaasul6a4NANDXvVqTtQaVZajCTnzG+ nHR9sWZWJoZ00aUOzXlmJ3n/GdWuZcUT4FqJ0G+pFWNJfzpC07SQtSoo633qsHtm MeypamMGT7sLCyAV+mGgX7g4d6wzWnZ0FahLSfmPhUCFbaospZgzR0I8OVjt66Qj l3TPlILxTEfAWtO56D3rbfPAXC1O6FDTr9Crv9OOcQck9ymtzw5sxq5ptUUDRKGj /3Rd+aS4mi5a73OZpphW+j35TmJmoWReFkKnAv/kMStDi++rpXolgMvTycR2Lk1e xgBGNxrXW2KmcOzNYMDr =vIKA -----END PGP SIGNATURE-----
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