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Core BioPerl 1.x code
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Taxonomy.t Tests Fails for Bio::Perl:: #364

Open joshuakirsch opened 2 years ago

joshuakirsch commented 2 years ago

I am trying to install Bio::Perl on Ubuntu using this command: sudo cpan install Bio::Perl

The installation seems to fail in both Bio::DB::GenBank and Bio::DB::GenPept due to Taxonomy.t

Here are the results of this command:

Loading internal logger. Log::Log4perl recommended for better logging
Reading '/home/josh/.cpan/Metadata'
  Database was generated on Tue, 14 Dec 2021 16:17:03 GMT
Running install for module 'Bio::Perl'
Checksum for /home/josh/.cpan/sources/authors/id/C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz ok
Configuring C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::DB::GenBank 0 not found.
Warning: prerequisite Bio::DB::GenPept 0 not found.
Generating a Unix-style Makefile
Writing Makefile for Bio::Procedural
Writing MYMETA.yml and MYMETA.json
  CJFIELDS/Bio-Procedural-1.7.4.tar.gz
  /usr/local/bin/perl Makefile.PL -- OK
Running make for C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz
---- Unsatisfied dependencies detected during ----
----   CJFIELDS/Bio-Procedural-1.7.4.tar.gz   ----
    Bio::DB::GenBank [requires]
    Bio::DB::GenPept [requires]
Running install for module 'Bio::DB::GenBank'
Checksum for /home/josh/.cpan/sources/authors/id/C/CJ/CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz ok
Configuring C/CJ/CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz with Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::DB::NCBIHelper
Writing MYMETA.yml and MYMETA.json
  CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
  /usr/local/bin/perl Makefile.PL -- OK
Running make for C/CJ/CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
cp lib/Bio/DB/NCBIHelper.pm blib/lib/Bio/DB/NCBIHelper.pm
cp lib/Bio/DB/GenBank.pm blib/lib/Bio/DB/GenBank.pm
cp lib/Bio/DB/Taxonomy/entrez.pm blib/lib/Bio/DB/Taxonomy/entrez.pm
cp lib/Bio/DB/Query/GenBank.pm blib/lib/Bio/DB/Query/GenBank.pm
cp lib/Bio/DB/EntrezGene.pm blib/lib/Bio/DB/EntrezGene.pm
cp lib/Bio/DB/GenPept.pm blib/lib/Bio/DB/GenPept.pm
cp bin/bp_biofetch_genbank_proxy blib/script/bp_biofetch_genbank_proxy
"/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_biofetch_genbank_proxy
cp bin/bp_download_query_genbank blib/script/bp_download_query_genbank
"/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_download_query_genbank
cp bin/bp_query_entrez_taxa blib/script/bp_query_entrez_taxa
"/usr/local/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_query_entrez_taxa
Manifying 3 pod documents
Manifying 6 pod documents
  CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
  /usr/bin/make -- OK
The current configuration of allow_installing_outdated_dists is 'ask/yes', but for this option we would need 'CPAN::DistnameInfo' installed. Please install 'CPAN::DistnameInfo' as soon as possible. As long as we are not equipped with 'CPAN::DistnameInfo' this option does not take effect
Running make test for CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
PERL_DL_NONLAZY=1 "/usr/local/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ......... ok   
t/author-mojibake.t .... skipped: these tests are for testing by the author
t/author-pod-syntax.t .. skipped: these tests are for testing by the author
t/EntrezGene.t ......... ok   
t/GenBank.t ............ ok     
t/GenPept.t ............ ok     
t/Query-Genbank.t ...... ok     
t/RefSeq.t ............. ok   
t/Taxonomy.t ........... 7/? 
#   Failed test at t/Taxonomy.t line 48.
t/Taxonomy.t ........... 68/? 
#   Failed test 'Correct: No hit'
#   at t/Taxonomy.t line 181.
#          got: '2890685'
#     expected: 'No hit'
t/Taxonomy.t ........... 69/? # Looks like you failed 2 tests of 69.
t/Taxonomy.t ........... Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/69 subtests 

Test Summary Report
-------------------
t/Taxonomy.t         (Wstat: 512 Tests: 69 Failed: 2)
  Failed tests:  18, 68
  Non-zero exit status: 2
Files=9, Tests=175, 154 wallclock secs ( 0.10 usr  0.01 sys +  4.53 cusr  0.49 csys =  5.13 CPU)
Result: FAIL
Failed 1/9 test programs. 2/175 subtests failed.
Makefile:967: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 2
  CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
  /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
Running install for module 'Bio::DB::GenPept'
  CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
  Has already been unwrapped into directory /home/josh/.cpan/build/Bio-DB-NCBIHelper-1.7.7-4
  CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
  Has already been prepared
  CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
  Has already been made
  CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz
  Won't repeat unsuccessful test during this command
  CJFIELDS/Bio-Procedural-1.7.4.tar.gz
  Has already been unwrapped into directory /home/josh/.cpan/build/Bio-Procedural-1.7.4-2
  CJFIELDS/Bio-Procedural-1.7.4.tar.gz
  Has already been prepared
Running make for C/CJ/CJFIELDS/Bio-Procedural-1.7.4.tar.gz
Warning: Prerequisite 'Bio::DB::GenBank => 0' for 'CJFIELDS/Bio-Procedural-1.7.4.tar.gz' failed when processing 'CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz' with 'make_test => NO'. Continuing, but chances to succeed are limited.
Warning: Prerequisite 'Bio::DB::GenPept => 0' for 'CJFIELDS/Bio-Procedural-1.7.4.tar.gz' failed when processing 'CJFIELDS/Bio-DB-NCBIHelper-1.7.7.tar.gz' with 'make_test => NO'. Continuing, but chances to succeed are limited.
cp lib/Bio/Perl.pm blib/lib/Bio/Perl.pm
cp lib/Bio/Procedural.pm blib/lib/Bio/Procedural.pm
Manifying 2 pod documents
  CJFIELDS/Bio-Procedural-1.7.4.tar.gz
  /usr/bin/make -- OK
The current configuration of allow_installing_outdated_dists is 'ask/yes', but for this option we would need 'CPAN::DistnameInfo' installed. Please install 'CPAN::DistnameInfo' as soon as possible. As long as we are not equipped with 'CPAN::DistnameInfo' this option does not take effect
Running make test for CJFIELDS/Bio-Procedural-1.7.4.tar.gz
PERL_DL_NONLAZY=1 "/usr/local/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ........... ok   
t/author-eol.t ........... skipped: these tests are for testing by the author
t/author-mojibake.t ...... skipped: these tests are for testing by the author
t/author-no-tabs.t ....... skipped: these tests are for testing by the author
t/author-pod-coverage.t .. skipped: these tests are for testing by the author
t/author-pod-syntax.t .... skipped: these tests are for testing by the author
t/Perl.t ................. ok     
All tests successful.
Files=7, Tests=33, 18 wallclock secs ( 0.05 usr  0.01 sys +  0.68 cusr  0.11 csys =  0.85 CPU)
Result: PASS
  CJFIELDS/Bio-Procedural-1.7.4.tar.gz
Tests succeeded but 2 dependencies missing (Bio::DB::GenBank,Bio::DB::GenPept)
  CJFIELDS/Bio-Procedural-1.7.4.tar.gz
  [dependencies] -- NA
inDane commented 2 years ago

i can confirm, im seeing the same error:

t/Taxonomy.t ........... 7/? 
#   Failed test at t/Taxonomy.t line 48.
t/Taxonomy.t ........... 68/? 
#   Failed test 'Correct: No hit'
#   at t/Taxonomy.t line 181.
#          got: '2890685'
#     expected: 'No hit'
t/Taxonomy.t ........... 69/? # Looks like you failed 2 tests of 69.
t/Taxonomy.t ........... Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/69 subtests 

Test Summary Report
-------------------
t/Taxonomy.t         (Wstat: 512 Tests: 69 Failed: 2)
  Failed tests:  18, 68
  Non-zero exit status: 2
Files=9, Tests=175, 158 wallclock secs ( 0.07 usr  0.03 sys +  3.44 cusr  0.53 csys =  4.07 CPU)
Result: FAIL
Failed 1/9 test programs. 2/175 subtests failed.

This is on Ubuntu 20.04.