[Debian-med-packaging] Another issue in test suite of new version of bioperl.

[Andreas Tille]

Hi again,

I updated bioperl in Git[1] to the just released new upstream version
and found another strange issue in the test suite:


...
t/SeqIO/Splicedseq.t .................
1..27
ok 1 - use Bio::Seq;
...
ok 25

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: WebDBSeqI Request Error:
500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (Temporary failure in name resolution)
Content-Type: text/plain
Client-Date: Tue, 05 Feb 2019 09:47:24 GMT
Client-Warning: Internal response

Can't connect to eutils.ncbi.nlm.nih.gov:443 (Temporary failure in name resolution)

Temporary failure in name resolution at /usr/share/perl5/LWP/Protocol/http.pm line 50, <GEN2> line 53.

STACK: Error::throw
STACK: Bio::Root::Root::throw /build/bioperl-1.7.3/blib/lib/Bio/Root/Root.pm:445
STACK: Bio::DB::WebDBSeqI::_stream_request /build/bioperl-1.7.3/blib/lib/Bio/DB/WebDBSeqI.pm:780
STACK: Bio::DB::WebDBSeqI::get_seq_stream /build/bioperl-1.7.3/blib/lib/Bio/DB/WebDBSeqI.pm:473
STACK: Bio::DB::WebDBSeqI::get_Stream_by_id /build/bioperl-1.7.3/blib/lib/Bio/DB/WebDBSeqI.pm:294
STACK: Bio::DB::WebDBSeqI::get_Seq_by_id /build/bioperl-1.7.3/blib/lib/Bio/DB/WebDBSeqI.pm:159
STACK: t/SeqIO/Splicedseq.t:97
-----------------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: id 'AF032048.1' does not exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /build/bioperl-1.7.3/blib/lib/Bio/Root/Root.pm:445
STACK: Bio::DB::WebDBSeqI::get_Seq_by_id /build/bioperl-1.7.3/blib/lib/Bio/DB/WebDBSeqI.pm:173
STACK: t/SeqIO/Splicedseq.t:97
-----------------------------------------------------------
ok 26 # skip Warning: Problem accessing GenBank entry AF032048.1 to test spliced_seq on remote DBs
ok 27 # skip Warning: Problem accessing GenBank entry AF032048.1 to test spliced_seq on remote DBs
ok 26 # skip Warning: Problem accessing GenBank entry AF032048t/SeqIO/Splicedseq.t .................
1..27

...


t/SeqIO/Splicedseq.t              (Wstat: 0 Tests: 29 Failed: 2)
  Failed tests:  26-27
  Parse errors: Tests out of sequence.  Found (26) but expected (28)
                Tests out of sequence.  Found (27) but expected (29)
                Bad plan.  You planned 27 tests but ran 29.


The code inside t/SeqIO/Splicedseq.t says (including line numbers):

 89 SKIP: {
 90     test_skip(-tests => 3,
 91               -requires_modules    => [qw(Bio::DB::GenBank
 92                                           LWP::UserAgent )],
 93               -requires_networking => 1);
 94     my $db_in;
 95     eval {
 96         ok $db_in = Bio::DB::GenBank->new();
 97         my $seq_obj = $db_in->get_Seq_by_id('AF032048.1');
 98     };
 99     if ($@) {
100         print "$@\n";
101         skip  "Warning: Problem accessing GenBank entry AF032048.1 "
102             . "to test spliced_seq on remote DBs", 2;
103     }
104 
105     my $len_w_db;
106     warning_is { $len_w_db = length($feats[1]->spliced_seq(-db => $db_in)->seq) }
107                [],
108                "no warnings if GenBank db provided for remote sequence";
109     ok($len_w_db == 374, "correct length if remote sequence is provided")
110 }

Shouldn't line 97 which is causing the failures above be skipped due to
the SKIP statement in line 89?

Kind regards

      Andreas.

-- 
http://fam-tille.de