Your message dated Fri, 14 Sep 2018 18:49:39 +0000 with message-id <[email protected]> and subject line Bug#906337: fixed in bioperl-run 1.7.2-4 has caused the Debian Bug report #906337, regarding bioperl-run: FTBFS in buster/sid (autobuilder hangs) 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.) -- 906337: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=906337 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: src:bioperl-run Version: 1.7.2-3 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 debian/rules override_dh_auto_configure make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_configure -- --install_scripts perl -I. Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --install_scripts Checking prerequisites... recommends: * Bio::FeatureIO is not installed * Config::Any is not installed * File::Sort is not installed [... snipped ...] ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok # Required executable for Bio::Tools::Run::Hmmer is not present t/Hmmer.t ..................... 1..27 ok 1 - use Bio::Tools::Run::Hmmer; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer' ok 5 ok 6 ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- E: Build killed with signal TERM after 60 minutes of inactivity -------------------------------------------------------------------------------- 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/bioperl-run.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: bioperl-run Source-Version: 1.7.2-4 We believe that the bug you reported is fixed in the latest version of bioperl-run, 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. Andreas Tille <[email protected]> (supplier of updated bioperl-run 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: Fri, 14 Sep 2018 20:10:08 +0200 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: source Version: 1.7.2-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: bioperl-run - BioPerl wrappers: scripts libbio-perl-run-perl - BioPerl wrappers: modules Closes: 906337 Changes: bioperl-run (1.7.2-4) unstable; urgency=medium . * (Build-)Depends: ncoils * do not run tests parallel to get sensibly sorted output * Allow MPI oversubscription (as in phyml build since phyml caused problems inside build time tests) This is also not reliable - skip phyml test at all Closes: #906337 * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Fix Homepage * Lintian-override for script-with-language-extension Checksums-Sha1: 7a7c1f47680efca44b0a453ffea507f0a446d65d 2553 bioperl-run_1.7.2-4.dsc 7c7e9dd8ad9e192e72f22f283e1c81552ac07a12 14100 bioperl-run_1.7.2-4.debian.tar.xz 06c25a66a9803e4279427cd8c849728b6b5d1986 11524 bioperl-run_1.7.2-4_amd64.buildinfo Checksums-Sha256: 99058888a1aac77c95e677c737250036b112863989d0d53df41219ed156f2a6e 2553 bioperl-run_1.7.2-4.dsc fedab5520861580bd23eb0c552932f7da3a1fb776cbc42cbe3de843dd1417c5b 14100 bioperl-run_1.7.2-4.debian.tar.xz c94a454b3cd70dfb676ef668df02557e58bf5ef9e5ba99ba302f5054714a023d 11524 bioperl-run_1.7.2-4_amd64.buildinfo Files: 0c4b65174a7f3746f5a8823c0e9d6c9a 2553 science optional bioperl-run_1.7.2-4.dsc 19e2f991a7da340c0e6c7e6fc9bad238 14100 science optional bioperl-run_1.7.2-4.debian.tar.xz e924793a9a102570b3c4d983803ebea2 11524 science optional bioperl-run_1.7.2-4_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlub//4RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHDDw//WBgI43kHSeEKHexQyXo4BoRFcx+1kFcI 8hz4FB7gA06N6qPO9eD2B4lA8joCvUUvPnm5iHqerxMoNEFUDuHB2W43dNlFLT8B fCtZ+7PzUQnrdK8CV4KU9rFMaQjSUxzJ2fI3eETAcBAgYQ22Z2Dp3t5cJeM05LGv BUNz4h8NErkqawb8Gf2MeG++Ad7XraU9MFR0eh+KLxzKz/j44gXbcBinglhLpV9e VXhHcI9x8OTa2i9lY/pppoSC02YGlRMF+5iYKA0ElA8Gr1Xy79mtr89WDBbMWDuZ b9lQl8wkrV/pKB8YLbOmotj7m/l9Tem0qxS0pZ8r2qqFdvWky5jrZMFXOyUhDx8r 86dMFk0yssSIJ7/iAdRmY7oMnibL1pthdBguXT7RKL8dUVzGYswArvZhjAxv/lrF RK8vOTwZHGaJIL6ieIu5Wxs6arT6POdEgflmKTpLjbGLQqYbTz68P+75nYTF8Fe2 y1a6tHA8vYpHs7XSG7MCOCyZxOmUN2Pg8rMzfh+Whb2mwsB89BOcrOHwzbsKtlRT 9YFyWAoVV+DxTXsKceYqxwqaMJUkdaslTrtK0XucHj7dydxRCY9w9SiTLYPzV/Vo cWiNuJnOmuygM0POJaIKWZA1+c7cq0osLnQt/yMIkdjNzk2sLiTycw1MXNnzsUZn t0HtRR5IcxQ= =Jb4z -----END PGP SIGNATURE-----
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