Bioperl and Perl 5.10
From BioPerl
So far only a few problems have been detected with perl 5.10 and BioPerl. The following is a quick run using a fresh build of perl 5.10 on Mac OS X 10.5.1 (Intel); all prereqs were preinstalled as well as DBI and DBD:mysql with MySQL 5.0.45, so this process may gloss over some installation issues with Build.PL.
Contents |
Installation issues
bioperl-live
perl 5.10 specific
- BioGraphics.t (filed as Bug #2457) Lincoln has fixed in Subversion
...
ok 32
ok 33
ok 34
ok 35
# Failed test at t/BioGraphics.t line 49.
# got: '7'
# expected: '5'
# Looks like you failed 1 test of 35.
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/35 subtests
- Exception due to uninstalled prerequisite Graph::Directed is not being caught properly. These tests gets skipped like they should under Perl 5.8. Actually, other tests where Graph::Directed is required are properly skipped (e.g. GOterm.t), so those might illuminate the problem. Now fixed in Subversion
t/SeqFeatAnnotated..............ok 1/26Bio::OntologyIO: obo cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::OntologyIO::obo. Can't locate Graph/Directed.pm in @INC (@INC contains: t/lib /Users/dave/src/bioperl- live/blib/lib /Users/dave/src/bioperl-live/blib/arch /Users/dave/src/bioperl-live /usr/local/lib/perl5/5.10.0/darwin-2level /usr/local/lib/perl5/5.10.0 /usr/local/lib/perl5/site_perl/5.10.0/darwin-2level /usr/local/lib/perl5/site_perl/5.10.0 .) at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm line 118. BEGIN failed--compilation aborted at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm line 118. Compilation failed in require at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OBOEngine.pm line 74. BEGIN failed--compilation aborted at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OBOEngine.pm line 74. Compilation failed in require at /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO/obo.pm line 88. BEGIN failed--compilation aborted at /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO/obo.pm line 88. Compilation failed in require at /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm line 420. STACK: Error::throw STACK: Bio::Root::Root::throw /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 STACK: Bio::Root::Root::_load_module /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:422 STACK: Bio::OntologyIO::_load_format_module /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO.pm:260 STACK: Bio::OntologyIO::new /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO.pm:170 STACK: Bio::Ontology::OntologyStore::get_ontology /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OntologyStore.pm:225 STACK: Bio::SeqFeature::Annotated::primary_tag /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:654 STACK: Bio::SeqFeature::Annotated::from_feature /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:287 STACK: Bio::SeqFeature::Annotated::_initialize /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:247 STACK: Bio::SeqFeature::Annotated::new /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:210 STACK: t/SeqFeatAnnotated.t:42 ----------------------------------------------------------- For more information about the OntologyIO system please see the docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_ontology" on an undefined value at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OntologyStore.pm line 229. # Looks like you planned 26 tests but only ran 5. # Looks like your test died just after 5. t/SeqFeatAnnotated..............dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 6-26 Failed 21/26 tests, 19.23% okay
- DB.t. Now fixed in Subversion.
...
ok 105 - use Bio::DB::EntrezGene;
ok 106
Not a HASH reference at /Users/cjfields/src/core/bioperl-live/Bio/SeqIO/entrezgene.pm line 372, <IN> line 2.
# Looks like you planned 116 tests but only ran 106.
# Looks like your test died just after 106.
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 10/116 subtests
Test Summary Report
-------------------
t/DB.t (Wstat: 65280 Tests: 106 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 116 tests but ran 106.
Files=1, Tests=106, 25 wallclock secs ( 0.03 usr 0.01 sys + 1.61 cusr 0.36 csys = 2.01 CPU)
Result: FAIL
Failed 1/1 test programs. 0/106 subtests failed.
- entrezgene.t Now fixed in Subversion.
...
ok 643
ok 644
ok 645
ok 646
ok 647
ok 648 - correct number of loops for T15
Not a HASH reference at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line 491, <IN> line 15.
# Looks like you planned 1422 tests but only ran 648.
# Looks like your test died just after 648.
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 774/1422 subtests
Test Summary Report
-------------------
t/entrezgene.t (Wstat: 65280 Tests: 648 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 1422 tests but ran 648.
Files=1, Tests=648, 2 wallclock secs ( 0.10 usr 0.02 sys + 1.35 cusr 0.05 csys = 1.52 CPU)
Result: FAIL
Failed 1/1 test programs. 0/648 subtests failed.
Other issues (all perl versions)
- Repeated
"Encountered CODE ref, using dummy placeholder at /usr/local/lib/perl5/5.10.0/darwin-2level/Data/Dumper.pm line 190."warnings. May be specific to my perl build. [I'm seeing the same error on a PPC Mac. -Dave Messina 16:22, 19 December 2007 (EST)] This appears to be a problem in Module::Build.- Confirmed as due to changes in Module::Build
- Now fixed in Subversion.
- MySQL tests for Bio::DB::SeqFeature not run b/c one can't configure connection variables ala Bio::DB::GFF tests. Now fixed in Subversion.
- Tests were run with a new CVS checkout with all prereqs and bioperl-ext modules installed.
Test Summary Report
-------------------
t/Annotation.t (Wstat: 0 Tests: 112 Failed: 0)
TODO passed: 96
t/BioGraphics.t (Wstat: 256 Tests: 35 Failed: 1)
Failed test number(s): 4
Non-zero exit status: 1
t/DB.t (Wstat: 65280 Tests: 106 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 116 tests but ran 106.
t/DBCUTG.t (Wstat: 1024 Tests: 33 Failed: 4)
Failed test number(s): 29-31, 33
Non-zero exit status: 4
t/RNA_SearchIO.t (Wstat: 2048 Tests: 496 Failed: 8)
Failed test number(s): 291, 338, 372-374, 395, 455, 486
Non-zero exit status: 8
t/Spidey.t (Wstat: 65280 Tests: 3 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 26 tests but ran 3.
t/entrezgene.t (Wstat: 65280 Tests: 648 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 1422 tests but ran 648.
Files=255, Tests=17416, 381 wallclock secs ( 3.29 usr 1.58 sys + 137.04 cusr 13.41 csys = 155.32 CPU)
Result: FAIL
Failed 7/255 test programs. 14/17416 subtests failed.
- RNA_SearchIO.t tests need to be updated to reflect recent changes to Bio::SearchIO-related modules. Now fixed in Subversion.
- DBCUTG.t: Now fixed in Subversion.
...
ok 26
ok 27
ok 28
Use of uninitialized value $sp in substitution (s///) at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 240.
Use of uninitialized value $sp in concatenation (.) or string at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 244.
Use of uninitialized value $name in pattern match (m//) at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 151.
Use of uninitialized value in concatenation (.) or string at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 256.
--------------------- WARNING ---------------------
MSG: probable parsing error - should be 21 entries for 20aa + stop codon
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: cds_count value is undefined, returning 0
---------------------------------------------------
not ok 29
# Failed test at t/DBCUTG.t line 68.
# '0'
# >
# '600'
not ok 30
# Failed test at t/DBCUTG.t line 69.
# '0'
# >
# '1'
--------------------- WARNING ---------------------
MSG: coding gc values aren't defined, returning 0
---------------------------------------------------
not ok 31
# Failed test at t/DBCUTG.t line 70.
Use of uninitialized value $got in numeric lt (<) at t/DBCUTG.t line 71.
ok 32
--------------------- WARNING ---------------------
MSG: probable parsing error - should be 21 entries for 20aa + stop codon
---------------------------------------------------
not ok 33
# Failed test at t/DBCUTG.t line 79.
# got: 'unknown'
# expected: 'Homo sapiens'
# Looks like you failed 4 tests of 33.
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/33 subtests
Test Summary Report
-------------------
t/DBCUTG.t (Wstat: 1024 Tests: 33 Failed: 4)
Failed test number(s): 29-31, 33
Non-zero exit status: 4
Files=1, Tests=33, 3 wallclock secs ( 0.02 usr 0.01 sys + 0.44 cusr 0.09 csys = 0.56 CPU)
Result: FAIL
Failed 1/1 test programs. 4/33 subtests failed.
- Spidey.t Now fixed in Subversion.
...
1..26
ok 1 - use Bio::Tools::Spidey::Results;
ok 2
ok 3
Can't call method "sub_SeqFeature" on an undefined value at t/Spidey.t line 24, <GEN1> line 170.
# Looks like you planned 26 tests but only ran 3.
# Looks like your test died just after 3.
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 23/26 subtests
Test Summary Report
-------------------
t/Spidey.t (Wstat: 65280 Tests: 3 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 26 tests but ran 3.
Files=1, Tests=3, 0 wallclock secs ( 0.01 usr 0.00 sys + 0.19 cusr 0.03 csys = 0.23 CPU)
Result: FAIL
Failed 1/1 test programs. 0/3 subtests failed.
bioperl-db
No apparent issues: all tests pass using DBI and DBD::mysql, Mac OS X Leopard, and the latest BioSQL checkout.
