Your message dated Sat, 06 Aug 2016 01:21:56 +0000 with message-id <[email protected]> and subject line Bug#833538: fixed in ncbi-blast+ 2.4.0-3 has caused the Debian Bug report #833538, regarding ncbi-blast+: FTBFS on s390x and sparc64: run_with_lock crashes 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.) -- 833538: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=833538 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: ncbi-blast+ Version: 2.4.0-2 Severity: serious Justification: fails to build from source The s390x and sparc64 builds of BLAST+ 2.4.0 have been failing: make[2]: Entering directory '/.../ncbi-blast+-2.4.0/c++/BUILD/build/corelib' /.../ncbi-blast+-2.4.0/c++/src/build-system/Makefile.meta_l:260: recipe for target 'sources.usr.locked' failed make[2]: *** [sources.usr.locked] Segmentation fault make[2]: Leaving directory '/.../ncbi-blast+-2.4.0/c++/BUILD/build/corelib' The problem turned out to be that the build system, as patched by Debian, winds up linking an optional helper tool named run_with_lock with -pie but not compiling it with -fPIE. On most platforms, this inconsistency results in a linker error, and the build system proceeds to fall back on a shell script. However, on these two architectures, the linker nominally succeeds but produces an executable that immediately segfaults. It should be possible to address the problem by supplying hardened CFLAGS and LDFLAGS to configure as {C,LD}FLAGS_FOR_BUILD respectively; we will then also want to add run_with_lock to the blacklist in override_dh_install-arch. I'll take care of these changes when I get a chance, but am looking at a busy weekend.
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--- Begin Message ---Source: ncbi-blast+ Source-Version: 2.4.0-3 We believe that the bug you reported is fixed in the latest version of ncbi-blast+, 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. Aaron M. Ucko <[email protected]> (supplier of updated ncbi-blast+ 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: SHA256 Format: 1.8 Date: Fri, 05 Aug 2016 19:47:24 -0400 Source: ncbi-blast+ Binary: ncbi-blast+ ncbi-blast+-legacy Architecture: source amd64 all Version: 2.4.0-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Aaron M. Ucko <[email protected]> Description: ncbi-blast+ - next generation suite of BLAST sequence search tools ncbi-blast+-legacy - NCBI Blast legacy call script Closes: 833538 833539 833541 Changes: ncbi-blast+ (2.4.0-3) unstable; urgency=medium . * debian/rules: - Properly build (but don't install) run_with_lock. (Closes: #833538.) - Comment out nostrip check, which yielded a useless dbgsym package. * Reinstate and refresh the hurd_fixes patch, which mostly still applies. (Closes: #833539.) * Add a new support_x32 patch to avoid picking up wrong inline assembly. (Closes: #833541.) Checksums-Sha1: 98f9cf6113280fccfba6938d14f54c309f60ad6f 2226 ncbi-blast+_2.4.0-3.dsc 3b9ee3fd18c8811f0d1223fd0c3ae48d28cc8639 28444 ncbi-blast+_2.4.0-3.debian.tar.xz b5e3de08761a3658820221a9cd53455eb873cd5c 149066700 ncbi-blast+-dbgsym_2.4.0-3_amd64.deb 59cfa5b8bc5ffee2813b3b919e849f03daf87784 8812 ncbi-blast+-legacy_2.4.0-3_all.deb 9ef73e94184dba3d974fd94a3608c5120ad4a1e2 9114490 ncbi-blast+_2.4.0-3_amd64.deb Checksums-Sha256: 70c529548b513828734ddee5f5279b297638e97f3b8b3e25df9fe36a1e8cc3ba 2226 ncbi-blast+_2.4.0-3.dsc 944f52bcae0ca3184fd47697f5777b1bd7214791be12f695264dfe70948c6083 28444 ncbi-blast+_2.4.0-3.debian.tar.xz 26e7fee7590802f7587664fe0ec7da2d908dc5ce72357f3fff4856ed2499df1f 149066700 ncbi-blast+-dbgsym_2.4.0-3_amd64.deb 1205164bd82304a1f748f2b04518baa3bab9f070e95b70656938a1ad73fd7415 8812 ncbi-blast+-legacy_2.4.0-3_all.deb 3c2f9f583cde39fff995d1a1956b9a094ed20a5982a0b4e8d0798c4fd2996f5e 9114490 ncbi-blast+_2.4.0-3_amd64.deb Files: 253071fef2f63f2533b36376f0a94fbb 2226 science optional ncbi-blast+_2.4.0-3.dsc a9eb2595e56eae0a7ed03fdfaca103d7 28444 science optional ncbi-blast+_2.4.0-3.debian.tar.xz ed45f11cefa4cf94b6f46d25bbeb7f38 149066700 debug extra ncbi-blast+-dbgsym_2.4.0-3_amd64.deb 38ffd9530fb147ce660780e7b7ac076e 8812 science optional ncbi-blast+-legacy_2.4.0-3_all.deb deee67754756c21742953c3a63d7f595 9114490 science optional ncbi-blast+_2.4.0-3_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJXpTkvAAoJEB5wkbHxSmSiiy0QAJhX0dzGBBngz6SvVw+uTrSO tL+8RUGTK26jINskWadC45LbcAqDr6RUSP2JQ02M0MeLvhXa5gq85uxN3TZx0kKu pcE9rhj9gsU98/EPKyU7E88Z9+830oTSYagSyOooA20GG9tAIgNxSk9KJWsBj9/T M7aPe9nV4bKsTA+rZqopkThjeKa2c7ah1juMAtKxXUwzJXDlFYBxxq8v7cT/Acm4 +HJM2UbXFR6vExpsdSA1eZHepCK5nscblNQAbIghmQQY/c2QlxcSuz073f2cI00N zo2K83vFRE9PNVIwm9rvevDwbcw0B6f7yaDmTMb7TtC3q2ahuxGHaNqtJkAvlqt7 VGL+DpQkRGuiElNslZTkjy1sSfyO4MjrkwK7JTd06u3VizIe93cUApj5hwFgFgzD jPHSJfcskNGI8XMdaaMhN83ZTCu7DBZNmHITNsPKW9MHyv9PYj+j8In9n8+vOvlV b8nb4tm3MP6/TQ/mroTSU5xOXAhHzMI5Qgyisw4DopiyR9XiZLrywiqt6J3dHQ++ Tq75xmFK/WSq2Jd/5cnz9TVv7y/x35jTQN1UoMdaiEX87HZPqVxoJPiHmOw8La3N eJK1XPRVyGo7JjDk6mNdqEmameX1ZHXmZ8czZuMA3jxvcRhYhh4htp8taAmx8Yn5 F6mdeaGaNuY5JQxVNQ2J =XRAM -----END PGP SIGNATURE-----
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