Your message dated Wed, 20 Sep 2017 15:49:53 +0000 with message-id <[email protected]> and subject line Bug#868073: fixed in bioperl-run 1.7.2-1 has caused the Debian Bug report #868073, regarding bioperl-run: FTBFS: t/Bowtie.t failure 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.) -- 868073: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=868073 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: bioperl-run Version: 1.7.1-3 Severity: serious This package falis to build on current sid/amd64. >From the build log: ------------- EXCEPTION ------------- MSG: /usr/bin/bowtie call crashed: There was a problem running /usr/bin/bowtie : Encountered a space parsing the quality string for read r1 If this is a FASTQ file with integer (non-ASCII-encoded) qualities, please re-run Bowtie with the --integer-quals option. TBB Warning: Exact exception propagation is requested by application but the linked library is built without support for it Command: bowtie-align --wrapper basic-0 -l 28 -n 2 -e 70 -S --12 t/data/bowtie/reads/e_coli.cb t/data/bowtie/indexes/e_coli /tmp/Wi1GtfHq3S/B2MCI6vGnb.sam STACK Bio::Tools::Run::WrapperBase::_run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1032 STACK Bio::Tools::Run::Bowtie::run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/Bowtie.pm:358 STACK toplevel t/Bowtie.t:234 ------------------------------------- # Looks like your test exited with 29 just after 57. t/Bowtie.t .................... 1..70 ok 1 - make a factory using command 'assemble' ok 2 - parameters changed on construction ok 3 - access parameter ok 4 - parameters_changed cleared on read ok 5 - set a param not set in constructor ok 6 - parameters_changed set ok 7 - parameter really set ok 8 - original parameter unchanged ok 9 - parameters_changed cleared on read ok 10 - change an original parameter ok 11 - parameter really changed ok 12 - reset parameters with arg ok 13 - original parameters undefined ok 14 - parameter really reset via arg ok 15 - set an exclusive group parameter ok 16 - parameter really set ok 17 - set an incompatible parameter ok 18 - parameter really set ok 19 - original exclusive parameter really unset ok 20 - parameters changed ok 21 - all available options ok 22 - available parameters ok 23 - available switches ok 24 - parameters changed ok 25 - all available options ok 26 - available parameters ok 27 - available switches ok 28 - get_parameters correct ok 29 - command attribute set ok 30 - internal command array set ok 31 - internal prefix hash set ok 32 - commands filtered by prefix ok 33 - translate_params: options correct ok 34 - make unpaired reads bowtie factory ok 35 - read raw sequence ok 36 - bowtie success ok 37 - read fasta sequence ok 38 - bowtie success ok 39 - read fastq sequence ok 40 - bowtie success ok 41 - make paired reads bowtie factory ok 42 - read paired fasta sequence ok 43 - bowtie success ok 44 - read paired fastq sequence ok 45 - bowtie success ok 46 - make a single alignment factory ok 47 - command attribute set ok 48 - seed mismatch param set ok 49 - seed length param set ok 50 - quality mismatch param set ok 51 - return type set ok 52 - make file based alignment ok 53 - make readable output ok 54 - number of alignments ok 55 - change mode ok 56 - make a crossbow alignment factory ok 57 - command attribute set Dubious, test returned 29 (wstat 7424, 0x1d00) Failed 13/70 subtests [...] Test Summary Report ------------------- t/Bowtie.t (Wstat: 7424 Tests: 57 Failed: 0) Non-zero exit status: 29 Parse errors: Bad plan. You planned 70 tests but ran 57. Files=76, Tests=1783, 90 wallclock secs ( 0.20 usr 0.06 sys + 86.61 cusr 2.41 csys = 89.28 CPU) Result: FAIL -- Niko Tyni [email protected]
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--- Begin Message ---Source: bioperl-run Source-Version: 1.7.2-1 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: SHA256 Format: 1.8 Date: Wed, 20 Sep 2017 14:29:45 +0200 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: source all Version: 1.7.2-1 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: 868073 Changes: bioperl-run (1.7.2-1) unstable; urgency=medium . * New upstream version * Convert packaging from SVN to Git * For some reason Ensembl.t test is executed in autopkgtest run even if it should be skipped due to missing preconditions (http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm) The test will now be fully removed to make sure it is skipped. * Standards-Version: 4.1.0 (no changes needed) * Do not try to run bowtie tests with wrong bowtie call Closes: #868073 Checksums-Sha1: 8066e074209fefe9ab2bc938ef2981c1e501b634 2525 bioperl-run_1.7.2-1.dsc d7507c64c736135ddf73da47e4e3811c7daa383a 13857201 bioperl-run_1.7.2.orig.tar.gz 02093af5851a7e4e0b708bfcab1ffd62ba8fac4a 14596 bioperl-run_1.7.2-1.debian.tar.xz 0abcd7268eecfa44aa7255f26729c3fa27b15b25 44618 bioperl-run_1.7.2-1_all.deb 3e3ae12e044d4ec3ab70a09f45524920f66a9fce 10676 bioperl-run_1.7.2-1_amd64.buildinfo f89cb18a2d2ed6549b2ce6086fdcc0690598dcb3 748660 libbio-perl-run-perl_1.7.2-1_all.deb Checksums-Sha256: a33b911f668606be9e9de0296e33e9b861859e6ecd064a511b0ffe4b70a073d5 2525 bioperl-run_1.7.2-1.dsc 74ffa2c55edeec65ef9de4838a054da1869125e9f69548bd6923c1086f03cc8d 13857201 bioperl-run_1.7.2.orig.tar.gz b64f8c0b1b3b9c0f9142ce6e82b1ecce3d9e6e296cc4ba5e3f6b53e8eaa09e9f 14596 bioperl-run_1.7.2-1.debian.tar.xz 9ff45b30f14ef90757c234c5c6a28a7a9f3682aa9dbc949c68e645f70fde8053 44618 bioperl-run_1.7.2-1_all.deb 8df560e121b14546206597f6efbd57b535a2c979665c4c5d506bfb369d0ad1b1 10676 bioperl-run_1.7.2-1_amd64.buildinfo 170f25220b4e9502737eae3def828dbd68efa34ae8dd9b747394c3d49430a9e3 748660 libbio-perl-run-perl_1.7.2-1_all.deb Files: eeca8a1e4c3b1ba3ada3379964f20464 2525 science optional bioperl-run_1.7.2-1.dsc f002f7735d390073ad201f53fc16754d 13857201 science optional bioperl-run_1.7.2.orig.tar.gz 429ab93f06b8f8c884029ae0f5ce2344 14596 science optional bioperl-run_1.7.2-1.debian.tar.xz 1ff783d26fffbd7fc80b47acc1ebb2ae 44618 science optional bioperl-run_1.7.2-1_all.deb 1f3363a92e7ba6b385073c3ba33c2d1b 10676 science optional bioperl-run_1.7.2-1_amd64.buildinfo 74b72c682afba6dbb46f62c26c182615 748660 perl optional libbio-perl-run-perl_1.7.2-1_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJZwmFFAAoJEFeKBJTRxkbRh88P/j6fT4k4XGb0eQelazCsFqb8 t6dPT7cJ+3iLDbowx177SFyyFvESAAk4sOr5a25Y/iqUTIf41eWJBYOjwnTFXNkm 76u1PysBYaOy2UUlpodVe+0qFLH4Qd1sHSdl6Y1FztG4G8AYfrJHxdG8OzwnGxTP JVYoVnIN9cWsmqRstq4qsH7rEwVObGJlch4VO1NKRNLfHwcKlSKUiO8C64fyHye6 LZUmoK3/AFrDHiyZyjpW+kABRmSw4iiIqpSH42AOVEwjnxS2zOAuqM032kbg84px tA5BLM0ymAhB9kscClNnSyj5o7T+I0Rg2vtNYK3E8Q2nJMo/V7IRvWVlK/WXATiZ 1sYWBn/xoU6d0hb0C0SfHMt01Sf+qHFRW7uiszz61oHP+RJjmro6Ne3RUtoOsV3F nc6bp0yHAi/fTw1rhcs8bOpInQBT9/PZnVadyoFrojEja9l4k6YNI9VYDytPeIYf RlXAyDtOKdjctTpTJJL7XNxokfpcAFWUGZU4tn2qXaC8lX8WoegbeTobpFH6sXut aypNwVvnArPtw4tVjswpdLNwgm50wrcP/JKTjfLLyNjg8+tN1SC7UPKXH1r0gQ33 BV3auF7/X0QqDTfKnXrNYk0nx3aV9vtnkmVLtS3T8K1lflvuC/uyFmInmAn7UT3o C8RmXY9XiTmlxGco6xNf =HQ2z -----END PGP SIGNATURE-----
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