[Debian-med-packaging] Bug#868073: bioperl-run: FTBFS: t/Bowtie.t failure

[Niko Tyni]

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   ntyni at debian.org