Your message dated Tue, 24 Oct 2017 07:33:45 +0000 with message-id <e1e6tib-000dmo...@fasolo.debian.org> and subject line Bug#864448: fixed in bowtie 1.2.1.1+dfsg-1 has caused the Debian Bug report #864448, regarding bowtie: FTBFS on mips64el - /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI 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.) -- 864448: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=864448 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: bowtie Version: 1.2.0+dfsg-1 Severity: serious Hi, bowtie FTBFS on mips64el with this error: > g++ -w -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB > -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -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 -Wl,-z,relro > -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -DNO_SPINLOCK > -DWITH_QUEUELOCK=1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 > -fdebug-prefix-map=/«BUILDDIR»/bowtie-1.2.0+dfsg=. -fstack-protector-strong > -Wformat -Werror=format-security -g -O2 > -fdebug-prefix-map=/«BUILDDIR»/bowtie-1.2.0+dfsg=. -fstack-protector-strong > -Wformat -Werror=format-security -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++ -w -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 \ > -I /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 \ > -lpthread -ltbb -ltbbmalloc_proxy > /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI > collect2: error: ld returned 1 exit status > Makefile:258: recipe for target 'bowtie-build-s' failed > make[2]: *** [bowtie-build-s] Error 1 > make[2]: Leaving directory '/«BUILDDIR»/bowtie-1.2.0+dfsg' > debian/rules:17: recipe for target 'override_dh_auto_build' failed > make[1]: *** [override_dh_auto_build] Error 2 > make[1]: Leaving directory '/«BUILDDIR»/bowtie-1.2.0+dfsg' > debian/rules:14: recipe for target 'build-arch' failed > make: *** [build-arch] Error 2 > dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 This is because mips* does not currently support -Wl,--hash-style=both. Unfortunately the MIPS linker (ab)uses the dynamic symbol table making it much harded to add support for this to BFD so it has not been done yet. I think the gnu hash style is just an optimization, so it should be OK to remove this option completely. --hash-style=gnu is already the default on all all other architectures and has been for a few years now so removing it on Debian should not affect other architectures. Thanks, James
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--- Begin Message ---Source: bowtie Source-Version: 1.2.1.1+dfsg-1 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 864...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alexandre Mestiashvili <a...@biotec.tu-dresden.de> (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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 19 Oct 2017 20:35:11 +0200 Source: bowtie Binary: bowtie bowtie-examples Architecture: source Version: 1.2.1.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Alexandre Mestiashvili <a...@biotec.tu-dresden.de> Description: bowtie - Ultrafast memory-efficient short read aligner bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al Closes: 864448 Changes: bowtie (1.2.1.1+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * New upstream version * Moved packaging from SVN to Git * debhelper 10 * Simplified d/watch * Build-Depends: zlib1g-dev . [ Steffen Moeller ] * debian/upstream/metadata: - Completed references to registries - yamllint cleanliness . [ Alexandre Mestiashvili ] * Update d/copyright: - use https for Format field - link to versioned license - add .cvsignore to Files-Excluded list - add myself to debian/* section * Add myself to uploaders, bump Standards-Version * Rearrange patch headers (cme fix dpkg), update spelling.patch * Re-introduce no_hash_style_both_for_mips.patch fixing build on mips64el Closes: #864448 * Update d/rules: - drop get-orig-source target - hardcode binary package name instead of using dpkg-parsechangelog * Disable unit tests for example6 and example9 as the output is different compared to older bowtie versions * Override lintian's warnings for binaries used with wrapper scripts Checksums-Sha1: a09ea1af59756ab86035804746a874afd3d1511c 2419 bowtie_1.2.1.1+dfsg-1.dsc d1388d31442f4b04a10c1d0555249f4555b29e07 6758852 bowtie_1.2.1.1+dfsg.orig.tar.xz 7efb9159ef7a1c9e18319238f9161c1a62757cb0 17128 bowtie_1.2.1.1+dfsg-1.debian.tar.xz 9f1660f9918bed90838434eb66b1c6e27060d0f1 6443 bowtie_1.2.1.1+dfsg-1_amd64.buildinfo Checksums-Sha256: a3801b0bea5e41c747ded6d287e4035f7f137d390bec2b8bb2ca0ae98f51a783 2419 bowtie_1.2.1.1+dfsg-1.dsc b01126d502c57da10bee0fa4b82a99142d6180d903454a2db61bf7fdc9a3566c 6758852 bowtie_1.2.1.1+dfsg.orig.tar.xz 2fb4feaa51e86e76609015b355b4a0047a680d4730fa84b7f22bdea419b7b29d 17128 bowtie_1.2.1.1+dfsg-1.debian.tar.xz 55952c1a6ea484f022482811a1034daaeceef1f48c9361f4cc1de3631f359a85 6443 bowtie_1.2.1.1+dfsg-1_amd64.buildinfo Files: e80135e2e3a038ce2de102ac406a9883 2419 science optional bowtie_1.2.1.1+dfsg-1.dsc 9702897e089b98d109e093746f52729f 6758852 science optional bowtie_1.2.1.1+dfsg.orig.tar.xz ca86b348d84efd51a1bb96e8d1548561 17128 science optional bowtie_1.2.1.1+dfsg-1.debian.tar.xz 6caabe6cae3bbfc853bd4cdb30f41182 6443 science optional bowtie_1.2.1.1+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlnu6WwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG8Kg/+I+J7SrEMMxNsyjzFDzTgC7bcjZxPINyk Mhse3Ju0POq5fUQvyE6WjvaPqKc85kUGCIls/a8Yvd53IiBNoPMr9Xq2zggmVJvs GRf2fe8sCEisXNyIauvxEDbNhf7oZw+Djq6jcOHVHfLWmuOsEowCFD2fm5baE+0c BzvvA55p2h2LcwcvkA8NoJYEt8CLHIMYkm0TzCfz4itdNxM/8rpmVri1MuROSsQl Q7j7L2sYENC5HxXcbfXomrq9KKF6o5cxorbG/3K7zPezF4FCJseXchOwbyRcp0Vm pb5ZTnkC4DID8V0Q38aXgnhgVhOAIiTn4R9uZItdsAe9hdeGytiJTxCDvoqjwsqc eNHpuI9eq3zW2KO3KKBi0YhlYrh52kkouSyP1DER9QBoV6QctmrH3a0cAd69b10a rK+zdaDQcm4d012SutKIDS2a78qotUYMWA/Zl6SyOvsGnrxX8kyt4ZwTIhw5lVRU yiPfILC0BVC5Q18kJnF+hAf/tPj53DshMmOWPxlX10KaIkmsidktA8CnJSSo5Brr DOuw2PrDW0oXC0dZEB9hp99rWBfGmexomYKn0hk+ryHd2NA4z3hDfid4NJYpZul9 FhQxRczTq5imtP3EUrTapYCYZdqwyapMLibAGhNcfU5syWXMUWYxF1ukV0VLvZ9D nJ8xSKfpyHE= =A2ZT -----END PGP SIGNATURE-----
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