[Bioperl-l] test failures in main trunk

[Scott Cain]

With Chris trying to get a release out, I wanted to report these test  
failures from a fairly virgin system Ubuntu server 8.04.

Scott



t/SeqIO/raw.t ................................ 1/24 Can't locate  
Algorithm/Diff.pm in @INC (@INC contains: t/lib . /home/gmod/bioperl- 
live/blib/lib /home/gmod/bioperl-live/blib/arch /home/gmod/bioperl- 
live /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 / 
usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 / 
usr/local/lib/site_perl) at t/SeqIO/raw.t line 72.
BEGIN failed--compilation aborted at t/SeqIO/raw.t line 72.
# Looks like you planned 24 tests but ran 1.
# Looks like your test exited with 2 just after 1.
t/SeqIO/raw.t ................................ Dubious, test returned  
2 (wstat 512, 0x200)

t/SeqTools/Backtranslate.t ................... Can't locate ok.pm in  
@INC (@INC contains: t/lib /home/gmod/bioperl-live/blib/lib /home/gmod/ 
bioperl-live/blib/arch /home/gmod/bioperl-live /etc/perl /usr/local/ 
lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/ 
perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/ 
site_perl .) at t/SeqTools/Backtranslate.t line 9.
BEGIN failed--compilation aborted at t/SeqTools/Backtranslate.t line 9.
# Looks like your test exited with 2 before it could output anything.
t/SeqTools/Backtranslate.t ................... Dubious, test returned  
2 (wstat 512, 0x200)
Failed 8/8 subtests

t/SeqTools/SeqPattern.t ...................... 1/28
#   Failed test 'use Bio::Tools::SeqPattern;'
#   at t/SeqTools/SeqPattern.t line 12.
#     Tried to use 'Bio::Tools::SeqPattern'.
#     Error:  Can't locate List/MoreUtils.pm in @INC (@INC contains: t/ 
lib . /home/gmod/bioperl-live/blib/lib /home/gmod/bioperl-live/blib/ 
arch /home/gmod/bioperl-live /etc/perl /usr/local/lib/perl/5.8.8 /usr/ 
local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/ 
5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl) at Bio/Tools/ 
SeqPattern/Backtranslate.pm line 22.
# BEGIN failed--compilation aborted at Bio/Tools/SeqPattern/ 
Backtranslate.pm line 22.
# Compilation failed in require at Bio/Tools/SeqPattern.pm line 212.
# Compilation failed in require at (eval 17) line 2.
# BEGIN failed--compilation aborted at (eval 17) line 2.
Use of uninitialized value in concatenation (.) or string at Bio/Tools/ 
SeqPattern.pm line 431.
Use of uninitialized value in concatenation (.) or string at Bio/Tools/ 
SeqPattern.pm line 432.

#   Failed test at t/SeqTools/SeqPattern.t line 25.
#          got: '(CT).{1,80}(C[[]]CT).(AGGGG){1,200}'
#     expected: '(CT).{1,80}(C[GA][GA]CT).(AGGGG){1,200}'
Use of uninitialized value in concatenation (.) or string at Bio/Tools/ 
SeqPattern.pm line 431.
Use of uninitialized value in concatenation (.) or string at Bio/Tools/ 
SeqPattern.pm line 432.

#   Failed test at t/SeqTools/SeqPattern.t line 31.
#          got: '(CT).(C[][]CT){1,80}.(AGGGG){1,200}'
#     expected: '(CT).(C[AG][AG]CT){1,80}.(AGGGG){1,200}'
Use of uninitialized value in concatenation (.) or string at Bio/Tools/ 
SeqPattern.pm line 371.
Use of uninitialized value in concatenation (.) or string at Bio/Tools/ 
SeqPattern.pm line 372.

#   Failed test at t/SeqTools/SeqPattern.t line 38.
#          got: 'A[][]H'
#     expected: 'A[EQ][DN]H'
"_reverse_translate_motif" is not exported by the  
Bio::Tools::SeqPattern::Backtranslate module
Can't continue after import errors at Bio/Tools/SeqPattern.pm line 539
# Looks like you planned 28 tests but ran 9.
# Looks like you failed 4 tests of 9 run.
# Looks like your test exited with 255 just after 9.
t/SeqTools/SeqPattern.t ...................... Dubious, test returned  
255 (wstat 65280, 0xff00)
Failed 23/28 subtests


-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research