Your message dated Tue, 13 Dec 2016 15:49:05 +0000 with message-id <e1cgpkd-0002os...@fasolo.debian.org> and subject line Bug#845737: fixed in snakemake 3.9.0+dfsg-1 has caused the Debian Bug report #845737, regarding snakemake: FTBFS randomly (sbuild 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 ow...@bugs.debian.org immediately.) -- 845737: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=845737 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:snakemake Version: 3.7.1+dfsg-1 Severity: serious Dear maintainer: I tried to build this package in stretch with "dpkg-buildpackage -A" (which is what the "Arch: all" autobuilder would do to build it) but it failed: -------------------------------------------------------------------------------- [...] debian/rules build-indep dh build-indep --with python3,sphinxdoc --buildsystem=pybuild --parallel dh_testdir -i -O--buildsystem=pybuild -O--parallel dh_update_autotools_config -i -O--buildsystem=pybuild -O--parallel dh_auto_configure -i -O--buildsystem=pybuild -O--parallel I: pybuild base:184: python3.5 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<<BUILDDIR>>/snakemake-3.7.1+dfsg' dh_auto_build I: pybuild base:184: /usr/bin/python3 setup.py build running build running build_py [... snipped ...] wildcards: sample=a Subsequent jobs will be added dynamically depending on the output of this rule rule random_clusters: input: c.init output: c_clusters/cluster_{*} (dynamic) wildcards: sample=c Subsequent jobs will be added dynamically depending on the output of this rule /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory Dynamically updating jobs 4 of 11 steps (36%) done rule concatenate_clusters: input: b_clusters/cluster_0, b_clusters/cluster_2, b_clusters/cluster_1 output: b_final wildcards: sample=b /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory 5 of 11 steps (45%) done Dynamically updating jobs 6 of 10 steps (60%) done rule concatenate_clusters: input: c_clusters/cluster_1, c_clusters/cluster_2, c_clusters/cluster_0 output: c_final wildcards: sample=c /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory 7 of 10 steps (70%) done Dynamically updating jobs 8 of 9 steps (89%) done rule concatenate_clusters: input: a_clusters/cluster_0, a_clusters/cluster_1, a_clusters/cluster_2 output: a_final wildcards: sample=a /bin/bash: /<<BUILDDIR>>/snakemake-3.7.1+dfsg/.pybuild/pythonX.Y_3.5/.bashrc: No such file or directory 9 of 9 steps (100%) done localrule all: input: a_final, b_final, c_final 10 of 9 steps (111%) done E: Build killed with signal TERM after 60 minutes of inactivity -------------------------------------------------------------------------------- This happens randomly. Sometimes it fails, sometimes it does not. When it fails, it does in this way, and sbuild has to terminate the process. I attach four different build logs. Thanks.
snakemake_3.7.1+dfsg-1_amd64-20161116T014246Z.gz
Description: application/gzip
Description: application/gzip
Description: application/gzip
Description: application/gzip
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--- Begin Message ---Source: snakemake Source-Version: 3.9.0+dfsg-1 We believe that the bug you reported is fixed in the latest version of snakemake, 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 845...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Kevin Murray <s...@kdmurray.id.au> (supplier of updated snakemake 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: Wed, 07 Dec 2016 09:02:12 +1100 Source: snakemake Binary: snakemake Architecture: source all Version: 3.9.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org> Changed-By: Kevin Murray <s...@kdmurray.id.au> Description: snakemake - pythonic workflow management system Closes: 845737 Changes: snakemake (3.9.0+dfsg-1) unstable; urgency=medium . [ Kevin Murray ] * New upstream version 3.9.0 (Closes: #845737) . [ Andreas Tille ] * debhelper 10 * d/watch: version=4 * Ignore failures of test that might happpen in pbuilder Checksums-Sha1: 2a30d46375b237480be2cd5c61a90dc31c41ad72 2193 snakemake_3.9.0+dfsg-1.dsc 0c3759ff56e878b5f2d20a94c9bcef1a8be2d351 2516229 snakemake_3.9.0+dfsg.orig.tar.gz 2cfd0b2e5d957a64851a99782cf39871f0de66fd 8640 snakemake_3.9.0+dfsg-1.debian.tar.xz 775906a6691c7417e6f00fe7ebb3890838185b69 495908 snakemake_3.9.0+dfsg-1_all.deb 4c998093b6073456bf192eff5dafd58a17416b12 8085 snakemake_3.9.0+dfsg-1_amd64.buildinfo Checksums-Sha256: d36c371bbd4f77a069be2a5c23c9df94b1d3e73d09d1c036a0b2f1beaf01d1cb 2193 snakemake_3.9.0+dfsg-1.dsc 401f6bb8f0baa68884fc664d2eb0e389c3eceb0c657214eff506deb7cd6a1fed 2516229 snakemake_3.9.0+dfsg.orig.tar.gz 549b68c7a7267b5e71eb043acb1b06f25943a7bcbaaa48c3f8ca0f6005fe6488 8640 snakemake_3.9.0+dfsg-1.debian.tar.xz e6d301ee9821a92ed99cc7b26c81de3fdbb05f40249a747ab58e8a97b6ec963a 495908 snakemake_3.9.0+dfsg-1_all.deb 13b9c18c10506c232f1f01adbf7f9bfd7dd11a388b9095c412cfea56f85a4932 8085 snakemake_3.9.0+dfsg-1_amd64.buildinfo Files: 77d808821c39edd0e62aff6eba238f0f 2193 science optional snakemake_3.9.0+dfsg-1.dsc e77825d13e22f43407919e5266d11cb0 2516229 science optional snakemake_3.9.0+dfsg.orig.tar.gz f146c590a1a511142b5935a8002551d7 8640 science optional snakemake_3.9.0+dfsg-1.debian.tar.xz 20521e870f41b9383da8e359df1945f9 495908 science optional snakemake_3.9.0+dfsg-1_all.deb 246318a2c8b1cf2b2daf260c7718163e 8085 science optional snakemake_3.9.0+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlhQEuMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFiaw//bNGtoR41/6qDvvAZk3t4sk5gUHwM1LO+ 7J4zoObWTubtpRx+SQWuElKHWsUVlD3mAkl4m07dfTkTOZFbdMmdHeiAi+PNo+OW HZQWu0hsqs4ADEKA2SjT/c6Wro9wl0ks9RRa1StTO2jrgX7AhDtH1gBLvyx6ykWE slp811Z3rRpiyE39RPHUJF8atSzvcH4MdAK5Z+SlJYrz+zeAYgBNzHaHoQ8rOD6D EWy3cfe5+ANQMokkULgCt8d0uvHqyzZuwDJqjQ+LaFAsV9fbvJuq7EiAW/vL0EPt QekE/D/dyTr0VwcvHZK5O5PkUPhTUrjKjwGRfgzH+/3oFgocvP4EOV+l1eBRViot bGPrDSzvwp2pHizuTlU6RG5f7kflB6EI1GN4MNsDGzBalw0M/sHuQIOKF+78VgUW 24CSQtOz9CSLig+ksjVnGCvEtqqSQGFhPtP4Gx9fb3fArEe6lWnq56YAZGpAlsHA 43kNOsbZBb8KZYXlHKpB3PZffuh07mfStxSFU37nkoun6ZvgeUTnYCeG2ZOVHw8B RoC+0aXkoJU/FncfuuESPgXCS3MosmLWYiPvkMSV5kEDO+nD52ZNVvlDxauD8oD4 TmmY3UUmOZxP0S68hIgn9j3twFEXPEjowoM8bvJhR7xGyrJIFvZ8XiKpAfIgUSLy q2/Tpyfkh2U= =Gi2f -----END PGP SIGNATURE-----
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