#11 Errors and warnings in linux Ubuntu

[Anonymous]

Hello again,
System is Ubuntu and Perl 5.18... Besides previously reported error in 06-seed.t, I got a fail in 05-forbidden.t.

Another strange warning that appear is "Skip: Statistics::R, R or fitdistrplus not found", considering that Statistics::R was correctly installed through "sudo cpan", so I don't understand why is complaining.

Output copied below.

Cheers,

Francisco J. Ossandon

fossandon@ubuntu:~/Documentos/bioperl-repos/BioGrinder$ make test
Skip blib/lib/Grinder/KmerCollection.pm (unchanged)
Skip blib/lib/Grinder/Database.pm (unchanged)
Skip blib/lib/Grinder.pm (unchanged)
cp script/grinder blib/script/grinder
/usr/bin/perl "-Iinc" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/grinder
cp utils/average_genome_size blib/script/average_genome_size
/usr/bin/perl "-Iinc" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/average_genome_size
cp utils/change_paired_read_orientation blib/script/change_paired_read_orientation
/usr/bin/perl "-Iinc" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/change_paired_read_orientation
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'inc', 'blib/lib', 'blib/arch')" t/00-load.t t/01-shotgun.t t/02-mates.t t/03-amplicon.t t/04-abundances.t t/05-forbidden.t t/06-seed.t t/07-diversity.t t/08-shared.t t/09-permuted.t t/10-quality.t t/11-tracking.t t/12-read-length.t t/13-insert-length.t t/14-genome-length-bias.t t/15-multiplex.t t/16-profile.t t/17-libraries.t t/18-amplicon-multiple.t t/19-gene-copy-bias.t t/20-community-structure.t t/21-errors.t t/22-homopolymers.t t/23-chimeras.t t/24-mate-orientation.t t/25-molecule-type.t t/26-combined-errors.t t/27-stdin.t t/28-revcom-amplicon.t t/29-kmer-collection.t t/30-kmer-chimeras.t t/31-shotgun-chimeras.t t/32-database.t t/pod.t
t/00-load.t ................. 1/? # Testing Grinder 0.5.3, Perl 5.018002, /usr/bin/perl
t/00-load.t ................. ok
t/01-shotgun.t .............. ok
t/02-mates.t ................ ok
t/03-amplicon.t ............. ok
t/04-abundances.t ........... ok
t/05-forbidden.t ............ 1/? Error: Could not take a random shotgun read without forbidden characters from reference sequence seq2 (10 attempts made).
Tests were run but no plan was declared and done_testing() was not seen.
Looks like your test exited with 255 just after 13.
t/05-forbidden.t ............ Dubious, test returned 255 (wstat 65280, 0xff00)
All 13 subtests passed
t/06-seed.t ................. 1/?
Failed test at t/06-seed.t line 51.
Structures begin differing at:
$got->[0]{seq} = 'cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc'
$expected->[0]{seq} = 'ccccccccccaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaatttttttttt'
Looks like you failed 1 test of 10.
t/06-seed.t ................. Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/10 subtests
t/07-diversity.t ............ ok
t/08-shared.t ............... ok
t/09-permuted.t ............. ok
t/10-quality.t .............. ok
t/11-tracking.t ............. ok
t/12-read-length.t .......... 1/? Skip: Statistics::R, R or fitdistrplus not found
Use of uninitialized value in string eq at /usr/local/share/perl/5.18.2/Test/More.pm line 1298.
t/12-read-length.t .......... 13/? skip() needs to know $how_many tests are in the block at t/12-read-length.t line 54
Use of uninitialized value in string eq at /usr/local/share/perl/5.18.2/Test/More.pm line 1298.
skip() needs to know $how_many tests are in the block at t/12-read-length.t line 80
t/12-read-length.t .......... ok
t/13-insert-length.t ........ 7/? Skip: Statistics::R, R or fitdistrplus not found
Use of uninitialized value in string eq at /usr/local/share/perl/5.18.2/Test/More.pm line 1298.
skip() needs to know $how_many tests are in the block at t/13-insert-length.t line 63
Use of uninitialized value in string eq at /usr/local/share/perl/5.18.2/Test/More.pm line 1298.
skip() needs to know $how_many tests are in the block at t/13-insert-length.t line 94
t/13-insert-length.t ........ ok
t/14-genome-length-bias.t ... ok
t/15-multiplex.t ............ Warning: 1 communities were requested but the MID file contained 2 sequences. Ignoring extraneous MIDs...
t/15-multiplex.t ............ 1/? Warning: 1 communities were requested but the MID file contained 2 sequences. Ignoring extraneous MIDs...
Warning: 1 communities were requested but the MID file contained 2 sequences. Ignoring extraneous MIDs...
t/15-multiplex.t ............ ok
t/16-profile.t .............. ok
t/17-libraries.t ............ ok
t/18-amplicon-multiple.t .... ok
t/19-gene-copy-bias.t ....... ok
t/20-community-structure.t .. ok
t/21-errors.t ............... 7016/? Skip: Statistics::R, R or fitdistrplus not found
Use of uninitialized value in string eq at /usr/local/share/perl/5.18.2/Test/More.pm line 1298.
skip() needs to know $how_many tests are in the block at t/21-errors.t line 124
t/21-errors.t ............... 7018/? Use of uninitialized value in string eq at /usr/local/share/perl/5.18.2/Test/More.pm line 1298.
skip() needs to know $how_many tests are in the block at t/21-errors.t line 156
t/21-errors.t ............... ok
t/22-homopolymers.t ......... ok
t/23-chimeras.t ............. ok
t/24-mate-orientation.t ..... ok
t/25-molecule-type.t ........ ok
t/26-combined-errors.t ...... ok
t/27-stdin.t ................ ok
t/28-revcom-amplicon.t ...... ok
t/29-kmer-collection.t ...... ok
t/30-kmer-chimeras.t ........ ok
t/31-shotgun-chimeras.t ..... ok
t/32-database.t ............. ok
t/pod.t ..................... skipped: Test::Pod 1.22 required for testing POD

Test Summary Report

t/05-forbidden.t (Wstat: 65280 Tests: 13 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
t/06-seed.t (Wstat: 256 Tests: 10 Failed: 1)
Failed test: 10
Non-zero exit status: 1
Files=34, Tests=37397, 37 wallclock secs ( 2.78 usr 0.31 sys + 30.19 cusr 6.90 csys = 40.18 CPU)
Result: FAIL
Failed 2/34 test programs. 1/37397 subtests failed.
make: *** [test_dynamic] Error 255
fossandon@ubuntu:~/Documentos/bioperl-repos/BioGrinder$

[floflooo]

Hi Francisco,

Regarding the Statistics::R, R, distrplus warning, I suspect that you forgot to install the fitdistrplus R library. I have added some documentation to Grinder to clarify.

The 'skip need to know' warning is harmless. It is an issue of Test::More. Future versions of Test::More will have a fix for this.

Cheers,

Florent

[Anonymous]

Hi Florent, you are right, the fitdistrplus R library was not installed. I had some troubles installing it because the default R package for Ubuntu 14 is 3.0.2, and fitdistrplus requires >= 3.2.0, but in the end I could install it and then it worked.

I don't remember well now, but probably I got confused and thought that the message "Skip: Statistics::R, R or fitdistrplus not found" implied that "fitdistrplus" was included when I installed "Statistics::R", instead of having to install it separately. So now that works, and thanks for updating the documentation. =)