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This queue is for tickets about the Bio-Grep CPAN distribution.

Report information
The Basics
Id: 28656
Status: resolved
Priority: 0/
Queue: Bio-Grep

People
Owner: Nobody in particular
Requestors: MEC [...] Stowers-Institute.org
Cc:
AdminCc:

Bug Information
Severity: Important
Broken in:
  • v0.8.3
  • v0.8.4
Fixed in: v0.8.5



Subject: Failed test 'Agrep SYNOPSIS compiles'
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looking forward to a clean install editted cpan install log follows: CPAN.pm: Going to build L/LI/LIMAONE/Bio-Grep-v0.8.3.tar.gz Checking if your kit is complete... Looks good Writing Makefile for Bio::Grep ... PERL_DL_NONLAZY=1 /l/site/inst/Linux-i686/sys/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/00.checkprereq......ok 1/1# # ***************************************************************************** # * Bioperl : FOUND * # * Bioperl-run: FOUND * # * EMBOSS : FOUND * # ... t/30.Utils............ok t/40.synopsis.........ok 1/8 # Failed test 'Agrep SYNOPSIS compiles' # at t/40.synopsis.t line 238. t/40.synopsis.........NOK 5/8# # ------------- EXCEPTION: Bio::Root::IOException ------------- # MSG: Can't copy t/TestRevCom.fasta to t/data/TestRevCom.fasta # VALUE: No such file or directory # STACK: Error::throw # STACK: Bio::Root::Root::throw /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 # STACK: Bio::Grep::Backend::BackendI::_copy_fasta_file_and_create_nfo /root/.cpan/build/Bio-Grep-v0.8.3-n5wwzy/blib/lib/Bio/Grep/Backend/BackendI.pm:367 # STACK: main::code_eval /root/.cpan/build/Bio-Grep-v0.8.3-n5wwzy/blib/lib/Bio/Grep/Backend/Agrep.pm:104 # STACK: t/40.synopsis.t:238 # ------------------------------------------------------------- t/40.synopsis.........ok 6/8 # Failed test 'RE SYNOPSIS compiles' t/40.synopsis.........NOK 7/8# at t/40.synopsis.t line 346. # # ------------- EXCEPTION: Bio::Root::IOException ------------- # MSG: Can't copy t/TestRevCom.fasta to t/data/TestRevCom.fasta # VALUE: No such file or directory # STACK: Error::throw # STACK: Bio::Root::Root::throw /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 # STACK: Bio::Grep::Backend::BackendI::_copy_fasta_file_and_create_nfo /root/.cpan/build/Bio-Grep-v0.8.3-n5wwzy/blib/lib/Bio/Grep/Backend/BackendI.pm:367 # STACK: main::code_eval /root/.cpan/build/Bio-Grep-v0.8.3-n5wwzy/blib/lib/Bio/Grep/Backend/Agrep.pm:104 # STACK: t/40.synopsis.t:346 # ------------------------------------------------------------- # Failed test 'Cookbook recipe motifs solution b compiles' t/40.synopsis.........NOK 8/8# at t/40.synopsis.t line 363. # Can't opendir(GLOB(0xaa37760), t/data): No such file or directory at (eval 67) line 7 One or more DATA sections were not processed by Inline. # Looks like you planned 8 tests but ran 1 extra. # Looks like you failed 3 tests of 9 run. t/40.synopsis.........dubious Test returned status 3 (wstat 768, 0x300) DIED. FAILED tests 5, 7-9 Failed 4/8 tests, 50.00% okay (less 5 skipped tests: -1 okay, -12.50%) t/perlcritic..........skipped all skipped: Test::Perl::Critic required for PBP tests t/pod-coverage........ok 12/12One or more DATA sections were not processed by Inline. t/pod-coverage........ok t/pod.................ok Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/40.synopsis.t 3 768 8 4 5 7-9 2 tests and 315 subtests skipped. Failed 1/11 test scripts. 2/540 subtests failed. Files=11, Tests=540, 128 wallclock secs (47.06 cusr + 55.07 csys = 102.13 CPU) Failed 1/11 test programs. 2/540 subtests failed. make: *** [test_dynamic] Error 255 LIMAONE/Bio-Grep-v0.8.3.tar.gz /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force Failed during this command: LIMAONE/Bio-Grep-v0.8.3.tar.gz : make_test NO
Thanks Malcolm. This bug should be fixed in v0.8.5.


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