Your message dated Mon, 10 Sep 2018 20:36:33 +0000 with message-id <e1fzsvb-000iic...@fasolo.debian.org> and subject line Bug#897867: fixed in spades 3.12.0+dfsg-1 has caused the Debian Bug report #897867, regarding spades: ftbfs with GCC-8 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.) -- 897867: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897867 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:spades Version: 3.11.1+dfsg-1 Severity: normal Tags: sid buster User: debian-...@lists.debian.org Usertags: ftbfs-gcc-8 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-8/g++-8, but succeeds to build with gcc-7/g++-7. The severity of this report will be raised before the buster release. The full build log can be found at: http://aws-logs.debian.net/2018/05/01/gcc8/spades_3.11.1+dfsg-1_unstable_gcc8.log.gz The last lines of the build log are at the end of this report. To build with GCC 8, either set CC=gcc-8 CXX=g++-8 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t=experimental install g++ Common build failures are 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-8/porting_to.html [...] cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/io -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common -isystem /<<BUILDDIR>>/spades-3.11.1+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/spades-3.11.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/io/sam/sam_reader.cpp [ 52%] Linking CXX static library libinput.a cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades' [ 52%] Built target input make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades' cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/spades-3.11.1+dfsg/src /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= Dependee "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake" is newer than depender "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Dependee "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Scanning dependencies of target pipeline make[4]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades' [ 52%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common -isystem /<<BUILDDIR>>/spades-3.11.1+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/spades-3.11.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/stage.cpp.o -c /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.cpp In file included from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/seq.hpp:38, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/sequence.hpp:16, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/io/reads/single_read.hpp:12, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/index/edge_position_index.hpp:11, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/graph_pack.hpp:10, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.hpp:11, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.cpp:8: /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/nucl.hpp: In member function 'bool nucl_complement_functor::operator()(char) const': /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/nucl.hpp:84:19: warning: ?: using integer constants in boolean context [-Wint-in-bool-context] return cc ? cc : 'N'; ~~~^~~~~~~~~~ In file included from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/visualization/graph_labeler.hpp:12, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/graph_pack.hpp:13, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.hpp:11, from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.cpp:8: /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'bool omnigraph::GapDescription<Graph>::has_filling() const': /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/paths/mapping_path.hpp:390:16: error: cannot convert 'const boost::optional<Sequence>' to 'bool' in return return filling_seq_; ^~~~~~~~~~~~ make[4]: *** [common/pipeline/CMakeFiles/pipeline.dir/build.make:63: common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o] Error 1 make[4]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades' make[3]: *** [CMakeFiles/Makefile2:815: common/pipeline/CMakeFiles/pipeline.dir/all] Error 2 make[3]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades' make[2]: *** [Makefile:152: all] Error 2 make[2]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades' make[1]: *** [debian/rules:41: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg' make: *** [debian/rules:23: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
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--- Begin Message ---Source: spades Source-Version: 3.12.0+dfsg-1 We believe that the bug you reported is fixed in the latest version of spades, 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 897...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alexandre Mestiashvili <mes...@debian.org> (supplier of updated spades 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: SHA512 Format: 1.8 Date: Mon, 10 Sep 2018 19:37:49 +0000 Source: spades Binary: spades Architecture: source amd64 Version: 3.12.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Alexandre Mestiashvili <mes...@debian.org> Description: spades - genome assembler for single-cell and isolates data sets Closes: 897867 Changes: spades (3.12.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * New upstream version Closes: #897867 * Fix watch file * Add dh-python . [ Alexandre Mestiashvili ] * Add tmp link for tests for spades-bwa * Update override_dh_auto_test: implement a workaround so dh_auto_test can access data files * Add bwa to d/tests/control * Remove *.pyc files * Add patch 0118_adjust_spades_home_again.patch replacing 0113_adjust_paths.patch * Update d/patches/spelling * Remove duplicated docs from /usr/share/spades * Bump Policy to 4.2.1, add myself to uploaders * Use https for copyright Format field, s/MIT/Expat/ * Rename overridden tag to debian-watch-does-not-check-gpg-signature Checksums-Sha1: 1de96f1aab1b242dae32b30e1b700aa120011583 2432 spades_3.12.0+dfsg-1.dsc 453183b65333cd073e7001c085fc72cfb1bfb2b3 2280768 spades_3.12.0+dfsg.orig.tar.xz 8e91a9d7bf39aa617cc35b6861bcc8a2c29778df 20108 spades_3.12.0+dfsg-1.debian.tar.xz ed5607bf9cbf9cb8bbceaf76412aa72a5ecdf255 130885540 spades-dbgsym_3.12.0+dfsg-1_amd64.deb 4372bd7198cc44ef25cdeb8991d724696fcf3657 8952 spades_3.12.0+dfsg-1_amd64.buildinfo 6c20ba4d092a2942dda131dcdb55a184a718023f 4922416 spades_3.12.0+dfsg-1_amd64.deb Checksums-Sha256: 465871d80b6473c070de0b6675d107d0a80517db7900777811a2c6af1ee31315 2432 spades_3.12.0+dfsg-1.dsc 1576593ab3622d96882850724d27f2ba855bf6b60e0e406b80ddedd703f7ef36 2280768 spades_3.12.0+dfsg.orig.tar.xz 3c5101bd25b4018fefe89f18ad0940d51c6dd1194826d29a1cbafe7385150613 20108 spades_3.12.0+dfsg-1.debian.tar.xz babe990a565e886bbd78c94978cb7dc0b2df8de4cb0e47fe29c91b6e70cc4f01 130885540 spades-dbgsym_3.12.0+dfsg-1_amd64.deb 0bdb3c3bc07cc1509cc80b04d985454f6e932649cbd4c75fcd62ef86c443bbaf 8952 spades_3.12.0+dfsg-1_amd64.buildinfo fc11e60e969eac9ff02958976aba792d8a7d15bccd40064f1bda225a36c5bcd0 4922416 spades_3.12.0+dfsg-1_amd64.deb Files: 0df43e6abb7ed3062dad74d109c3b08b 2432 science optional spades_3.12.0+dfsg-1.dsc e19d22ac8179f3a1d0e66a24f5fdc9cb 2280768 science optional spades_3.12.0+dfsg.orig.tar.xz 2d750f46b6446d32138dadf0b0de2988 20108 science optional spades_3.12.0+dfsg-1.debian.tar.xz 751cb2bf2158db8e3bf84e6b73b15fc7 130885540 debug optional spades-dbgsym_3.12.0+dfsg-1_amd64.deb fffdfabfb221af84ac6502a72ebb77ce 8952 science optional spades_3.12.0+dfsg-1_amd64.buildinfo e5a5c9f7a9c6fdebeb332ed2c2ae0fd2 4922416 science optional spades_3.12.0+dfsg-1_amd64.deb -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEsaUesned0BdDzBm6HPeSERtSKLAFAluWzkUSHG1lc3RpYUBk ZWJpYW4ub3JnAAoJEBz3khEbUiiwtjQQAJ+5WhCq9/5y0748/JqvcTt6J8Z7VltY hsS3CBf3CMR/c329OybpWLa3ZfO8QI8UV3K65H49hTywtqq2CzLE5qGWsB1CXJ9A tbiG4h/MorkVD4Jdye1/u/bBZMl622jD6/ST6nUVzOrzB2T5vriWDfXBRym7+Ipn sYFN2wK6cZG/+RgEuKz7k0kkKb/Q8mxUVAlahtmUqz1daOa2h7fUwK6iPIcZQmPN jp54WGgAL/EbzMle+s5Y5WsDiBamLVSR3TBQIqClRXjmTuqGmAnMSrHO4M8d0szw yuONANBt+0DaDVIwVdAW71quO42+M/rzN53QM6fBBWkplPNtK8+sE6G7K9+wVY9q HAwgqrY/Zp7OoFuJcvHjMPcFYxfP1IjQo1Y8mUOHCrNXWqZ/6ZLg5hlgstBgF+PZ 1tbG1ke9M6gtfhP/K/35E01Q2zqyk1r+lYFYjrwqFA4twJHl4FD5+zY0iDiAlsnc lCHdTFps2lYfDP5IaapSX8PnHajDuNOfm6nD7C+kouUSKFdpswL7zrF7XCzshOKB mMWTTtrgPTOBd/egbn73k3VCg/z57z8U+rr3HW0HaWu2nANiN/vYwnvJdS3cD16t CkRNPeikOyBjOvv4YZsw0R7te5bFDTG4YIlf4myOxqBYTwcxrWpUQyS/Qw+24dSV VPz2VD9+9jgq =SxBf -----END PGP SIGNATURE-----
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