Your message dated Wed, 20 Sep 2017 15:49:53 +0000
with message-id <e1duhg5-0000if...@fasolo.debian.org>
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
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misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
868073: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=868073
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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 nt...@debian.org
--- End Message ---
--- 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 868...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----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
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
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
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Files:
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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
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