Your message dated Wed, 05 Sep 2018 15:19:27 +0000 with message-id <[email protected]> and subject line Bug#906341: fixed in bowtie 1.2.2+dfsg-4 has caused the Debian Bug report #906341, regarding bowtie: FTBFS in buster/sid 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 [email protected] immediately.) -- 906341: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=906341 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: src:bowtie Version: 1.2.2+dfsg-3 Severity: serious Tags: ftbfs Dear maintainer: I tried to build this package in buster but it failed: -------------------------------------------------------------------------------- [...] debian/rules build-indep dh build-indep dh_update_autotools_config -i dh_autoreconf -i dh_auto_configure -i debian/rules override_dh_auto_build make[1]: Entering directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg' /usr/bin/make allall make[2]: Entering directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg' g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bowtie-1.2.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem /usr/include/seqan \ -o bowtie-build-s ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bowtie_build_main.cpp \ [... snipped ...] ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_ftab != NULL) delete[] _ftab; _ftab = NULL; ^~~~~ ebwt.h:827:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~ ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_eftab != NULL) delete[] _eftab; _eftab = NULL; ^~~~~~ ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_isa != NULL) delete[] _isa; _isa = NULL; ^~ ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_isa != NULL) delete[] _isa; _isa = NULL; ^~~~ ebwt.h:834:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_plen != NULL) delete[] _plen; _plen = NULL; ^~ ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_plen != NULL) delete[] _plen; _plen = NULL; ^~~~~ ebwt.h:835:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~ ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; ^~~~~~~~ ebwt.h: In member function 'uint32_t* Ebwt<TStr>::isa() const': ebwt.h:865:44: error: cannot convert 'TIndexOffU* const' {aka 'long unsigned int* const'} to 'uint32_t*' {aka 'unsigned int*'} in return uint32_t* isa() const { return _isa; } /* check */ ^~~~ In file included from ebwt.h:27, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; TIndexOffU = long unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<long unsigned int, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Packed<> >; TIndexOffU = long unsigned int]': blockwise_sa.h:287:23: required from here blockwise_sa.h:297:26: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<long unsigned int, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare] make[2]: *** [Makefile:273: bowtie-build-l] Error 1 make[2]: Leaving directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg' make[1]: *** [debian/rules:17: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<<BUILDDIR>>/bowtie-1.2.2+dfsg' make: *** [debian/rules:14: build-indep] Error 2 dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit status 2 -------------------------------------------------------------------------------- The build was made with "dpkg-buildpackage -A" in my autobuilder. Most probably, it also fails here in reproducible builds: https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/bowtie.html where you can get a full build log if you need it. If this is really a bug in one of the build-depends, please use reassign and affects, so that this is still visible in the BTS web page for this package. Thanks.
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--- Begin Message ---Source: bowtie Source-Version: 1.2.2+dfsg-4 We believe that the bug you reported is fixed in the latest version of bowtie, 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alexandre Mestiashvili <[email protected]> (supplier of updated bowtie 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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 05 Sep 2018 14:34:56 +0000 Source: bowtie Binary: bowtie bowtie-examples Architecture: source amd64 all Version: 1.2.2+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Alexandre Mestiashvili <[email protected]> Description: bowtie - Ultrafast memory-efficient short read aligner bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al Closes: 906341 Changes: bowtie (1.2.2+dfsg-4) unstable; urgency=medium . [ Andreas Tille ] * spelling * Upload to unstable . [ Dylan Aïssi ] * Update metadata: Add bio.tools ref . [ Alexandre Mestiashvili ] * Add patch fixing FTBFS, thanks to ch4rr0 at github.com Closes: #906341 * Check for DEB_BUILD_OPTIONS and nocheck Checksums-Sha1: 1ddbe08cb2068273b3270056c3bab9781826d9bf 2351 bowtie_1.2.2+dfsg-4.dsc d3d738ab8177b0c12e4bca1d9a9828812b03daa4 20008 bowtie_1.2.2+dfsg-4.debian.tar.xz b4a7fa98eb8e81495ec44d3c39de79d1e2ace660 23284868 bowtie-dbgsym_1.2.2+dfsg-4_amd64.deb a7d5439e7da8540ea715142695b55b6a6014ebd8 6306496 bowtie-examples_1.2.2+dfsg-4_all.deb 2775cab47f0e955e5f4179bb6b005ffba92dfefd 6635 bowtie_1.2.2+dfsg-4_amd64.buildinfo fa02125944cd1e5c3453c0c51afbf482fda15f7b 1670332 bowtie_1.2.2+dfsg-4_amd64.deb Checksums-Sha256: 4c8dc94e8d36f4ebd0a35bcb6a9b22723c1c86a3d15d2de9299932bad2a8b849 2351 bowtie_1.2.2+dfsg-4.dsc 5d5704d11cfdbcf0469f5465b7d0afc698ce31a453e0afefe01b42cba4749860 20008 bowtie_1.2.2+dfsg-4.debian.tar.xz f94bfcd829584687335f3d2b9e5ed93aaafc3e154889ef3780c381629c553bdc 23284868 bowtie-dbgsym_1.2.2+dfsg-4_amd64.deb 7ce9bcde1f6ec2096b43099a502f90cf295beab994128f6fb65a923af5e6ccd3 6306496 bowtie-examples_1.2.2+dfsg-4_all.deb 038dc237335bd1d810ad73dbe88e5313d40e6a46355087f0bb621544dccb177b 6635 bowtie_1.2.2+dfsg-4_amd64.buildinfo 19a6c0c50a4955970b762146e910db2540c399a9bb39f04fdba205f2f331bc7c 1670332 bowtie_1.2.2+dfsg-4_amd64.deb Files: bb52e99741141a677ba45b59e9576d90 2351 science optional bowtie_1.2.2+dfsg-4.dsc 4b513f153f89e2fd1d4c453f82e0646a 20008 science optional bowtie_1.2.2+dfsg-4.debian.tar.xz 5510e071d2a338c3bc3427a256289ce3 23284868 debug optional bowtie-dbgsym_1.2.2+dfsg-4_amd64.deb f39146c2f99958edd52e9b480e6a3707 6306496 science optional bowtie-examples_1.2.2+dfsg-4_all.deb 2eaff60dc288dbabc68bb47151a58b49 6635 science optional bowtie_1.2.2+dfsg-4_amd64.buildinfo f1aead1d283038e3b45c2eb887e38c96 1670332 science optional bowtie_1.2.2+dfsg-4_amd64.deb -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEsaUesned0BdDzBm6HPeSERtSKLAFAluP7d4ACgkQHPeSERtS KLCyiQ/+PhtrDsjZJ3ixdDJujm8sM6bl62SWTPPZfSLsBoZ4H5jAlVVEJ2QrCd4N zl6mgIlKbkZ5WQqvaQ4SPrkdov9hzN+j6ONw3qFoGUST8VOolQD5Ge4FMB763kdz b5MWh3tADwzvlxn3NtO3NeKHJTluWwU+w4r5oJPuN6gCleRee/TuEIKlGYm57TUi QwZbeodnouvJVrQIBgezcG43mizOb8Gtm6gkXL1k/4MgtJ+Ki/1yOB3OpktunKL7 I84oR5uF8/fUyXCc3pTX0Tlaf2RFLdvkMaj5KcAWOWayNx4rmdIqqy8jBelKFPcq kYpVLSIIWSnF3Cin/aXxt+hE80Pl5Nps7rCViDHiBf6EWy/0uZbUlw7Sg3YTn8tX LpttqPX8yYu5ffOqdr5Jk0GbCuFM4nohloj61J2xpYXUcL7jKOBxRH0mJSoaf617 eDyWnir3+dgIMHR4Lepi01amjMFIx6I5EsLrTqAKDW29/OI3LJurzzNw4UpmZdgf +EQeGLNQ5FsEV5Tg1z0NhOHvwgu0aGKe6xBl/voRneyE/n6HAIaxESxgYsiiYGFD gkjuvSwJPEdH9NARvng7CoeCC4QFpkrIzyGFQ7iW2d910lcgxzUvdY7QA/Nzdxav 0vxMcDa1/maMxUp7J9IYxFjnxm23VhZWZPQUhmaC6jkNfLSeTag= =GN8d -----END PGP SIGNATURE-----
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