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
