bio-db-refseq's People
bio-db-refseq's Issues
Current tests not working
The database tests are actually silently failing but marked as passing:
[cjfields@ChristophersAir Bio-DB-RefSeq (master)]$ prove -lrv t/
t/RefSeq.t ..
1..8
ok 1 - use Bio::DB::RefSeq;
ok 2
ok 3 # skip Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!
ok 4 # skip Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!
ok 5 # skip Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!
ok 6 # skip Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!
ok 7 # skip Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!
ok 8 # skip Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!
ok
All tests successful.
Files=1, Tests=8, 3 wallclock secs ( 0.02 usr 0.00 sys + 0.22 cusr 0.04 csys = 0.28 CPU)
Result: PASS
This stems from the database name changing to refseqn
for nucleotide and refseqp
for protein. This will require a little effort in getting this up to speed, whereas the alternative database interface Bio::DB::Biofetch already has this in place. Questions are (1) is it worth keeping this up to date if another interface is already working, and (2) who wants to take this on?
RefSeq database switching:
We may need some fixes for switching between RefSeq databases when needed (e.g. looking up protein sequences). The default is too use refseqn
, but others exist (e.g. for protein sequences refseqp
).
Not sure if this should be labeled a bug, but definitely a feature request (so adding both).
Bio::DB::RefSeq install fails after exception message
Current tests fail
Tests on HEAD are failing:
10:09 $ dzil test
[DZ] building distribution under .build/zzQxhKieB9 for installation
[DZ] beginning to build Bio-DB-RefSeq
[@BioPerl/@Filter/ExtraTests] rewriting author test xt/author/pod-syntax.t
[@BioPerl/@Filter/ExtraTests] rewriting author test xt/author/pod-coverage.t
[@BioPerl/@Filter/ExtraTests] rewriting author test xt/author/mojibake.t
[@BioPerl/PkgVersion] no blank line for $VERSION after package Bio::DB::RefSeq statement in lib/Bio/DB/RefSeq.pm line 115
[DZ] guessing dist's main_module is lib/Bio/DB/RefSeq.pm
[DZ] writing Bio-DB-RefSeq in .build/zzQxhKieB9
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::DB::RefSeq
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/DB/RefSeq.pm blib/lib/Bio/DB/RefSeq.pm
PERL_DL_NONLAZY=1 "/Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/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 ...... ok
t/author-pod-coverage.t .. ok
t/author-pod-syntax.t .... ok
t/RefSeq.t ............... 1/16
# Failed test 'use Bio::DB::GenBank;'
# at t/RefSeq.t line 15.
# Tried to use 'Bio::DB::GenBank'.
# Error: Can't locate Bio/DB/GenBank.pm in @INC (you may need to install the Bio::DB::GenBank module) (@INC contains: /Users/cjfields/bioperl/Bio-DB-RefSeq/.build/zzQxhKieB9/blib/lib /Users/cjfields/bioperl/Bio-DB-RefSeq/.build/zzQxhKieB9/blib/arch /Users/cjfields/bioperl/bioperl-live/lib /Users/cjfields/bioperl/Bio-Coordinate/lib /Users/cjfields/bioperl/bioperl-run/lib /Users/cjfields/bioperl/bioperl-pipeline/lib /Users/cjfields/bioperl/Bio-EUtilities/lib /Users/cjfields/bioperl/Bio-SearchIO-blastxml/lib /Users/cjfields/bioperl/bioperl-live/lib /Users/cjfields/bioperl/Bio-Coordinate/lib /Users/cjfields/bioperl/bioperl-run/lib /Users/cjfields/bioperl/bioperl-pipeline/lib /Users/cjfields/bioperl/Bio-EUtilities/lib /Users/cjfields/bioperl/Bio-SearchIO-blastxml/lib /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/site_perl/5.24.1/darwin-2level /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/site_perl/5.24.1 /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/5.24.1/darwin-2level /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/5.24.1 .) at t/RefSeq.t line 15.
# BEGIN failed--compilation aborted at t/RefSeq.t line 15.
# Failed test 'use Bio::DB::EMBL;'
# at t/RefSeq.t line 16.
# Tried to use 'Bio::DB::EMBL'.
# Error: Can't locate Bio/DB/EMBL.pm in @INC (you may need to install the Bio::DB::EMBL module) (@INC contains: /Users/cjfields/bioperl/Bio-DB-RefSeq/.build/zzQxhKieB9/blib/lib /Users/cjfields/bioperl/Bio-DB-RefSeq/.build/zzQxhKieB9/blib/arch /Users/cjfields/bioperl/bioperl-live/lib /Users/cjfields/bioperl/Bio-Coordinate/lib /Users/cjfields/bioperl/bioperl-run/lib /Users/cjfields/bioperl/bioperl-pipeline/lib /Users/cjfields/bioperl/Bio-EUtilities/lib /Users/cjfields/bioperl/Bio-SearchIO-blastxml/lib /Users/cjfields/bioperl/bioperl-live/lib /Users/cjfields/bioperl/Bio-Coordinate/lib /Users/cjfields/bioperl/bioperl-run/lib /Users/cjfields/bioperl/bioperl-pipeline/lib /Users/cjfields/bioperl/Bio-EUtilities/lib /Users/cjfields/bioperl/Bio-SearchIO-blastxml/lib /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/site_perl/5.24.1/darwin-2level /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/site_perl/5.24.1 /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/5.24.1/darwin-2level /Users/cjfields/perl5/perlbrew/perls/perl-5.24.1/lib/5.24.1 .) at t/RefSeq.t line 16.
# BEGIN failed--compilation aborted at t/RefSeq.t line 16.
Can't locate object method "new" via package "Bio::DB::GenBank" (perhaps you forgot to load "Bio::DB::GenBank"?) at t/RefSeq.t line 28.
# Looks like your test exited with 255 just after 3.
t/RefSeq.t ............... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 15/16 subtests
Test Summary Report
-------------------
t/RefSeq.t (Wstat: 65280 Tests: 3 Failed: 2)
Failed tests: 2-3
Non-zero exit status: 255
Parse errors: Bad plan. You planned 16 tests but ran 3.
Files=5, Tests=8, 1 wallclock secs ( 0.02 usr 0.01 sys + 0.46 cusr 0.09 csys = 0.58 CPU)
Result: FAIL
Failed 1/5 test programs. 2/8 subtests failed.
make: *** [test_dynamic] Error 255
error running make test
✘-2 ~/bioperl/Bio-DB-RefSeq [master|✔]
It appears there may be several circular dependency issues here with tests which need to be resolved (Bio-DB-NCBIHelper and Bio-DB-EMBL)
Some smoke tests failing on CPAN tests for v1.7.3
Seems to be related to Module::Build
(and possibly Bio::Root::Build). Oddly occurs only in some perl versions and releases.
Overall tests: http://matrix.cpantesters.org/?dist=Bio-DB-RefSeq+1.7.3
Example: http://www.cpantesters.org/cpan/report/6c6024f0-6bf5-1014-9307-11f13f60cec8
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