[Bioperl-l] Failed Test Installing BioPerl-1.6.901

[Chris Fields]

The last test fail is easy enough (lang difference, so bad test) but the 
first fail is a bit odd since it passes for almost everything.  I'll see 
if I can dig anything up.

chris

On 03/16/2012 12:56 PM, dumps wrote:
>
> Hi,
>
> I've experienced the same problem as Leon, yet on a SUSE 12.1 system
>
> "./Build test --test-files t/SeqIO/SeqIO.t --verbose"
>
> produced the following log
>
> t/SeqIO/SeqIO.t ..
> 1..45
> ok 1 - use Bio::SeqIO;
> ok 2
> ok 3 - ID for format gcg
> ok 4
> ok 5
> ok 6
> ok 7
> ok 8 - ID for format fasta
> ok 9
> ok 10
> ok 11
> ok 12 - accession.version
> ok 13
> ok 14
> ok 15
> ok 16
> ok 17
> ok 18
> ok 19 - ID for format pir
> ok 20
> ok 21
> ok 22
> ok 23
> ok 24
> ok 25 - ID for format tab
> ok 26
> ok 27
> ok 28
> ok 29
> ok 30
> ok 31 - ID for format ace
> ok 32
> ok 33
> ok 34
> ok 35
> ok 36 - use Algorithm::Diff;
> ok 37 - use IO::ScalarArray;
> ok 38 - use IO::String;
> ok 39
> ok 40
> ok 41
> not ok 42 - Must pass a file or file handle # TODO file/fh-based tests
> should be in Bio::Root::IO, see issue #3204
> #   Failed (TODO) test 'Must pass a file or file handle'
> #   at t/SeqIO/SeqIO.t line 120.
> # expecting: Regexp ((?-xism:No file, fh, or string argument provided))
> # found:
> # ------------- EXCEPTION -------------
> # MSG: Could not guess format from file/fh
> # STACK Bio::SeqIO::new Bio/SeqIO.pm:389
> # STACK Test::Exception::throws_ok t/SeqIO/SeqIO.t:119
> # STACK toplevel t/SeqIO/SeqIO.t:120
> # -------------------------------------
> ok 43 - Must pass a file or file handle
> ok 44 - Must pass a file or file handle
> not ok 45 - Must pass a real file
>
> #   Failed test 'Must pass a real file'
> #   at t/SeqIO/SeqIO.t line 135.
> # expecting: Regexp ((?-xism:Can not open 'foo.bar' for reading: No such
> file or directory))
> # found:
> # ------------- EXCEPTION -------------
> # MSG: Can not open 'foo.bar' for reading: Datei oder Verzeichnis nicht
> gefunden
> # STACK Bio::Tools::GuessSeqFormat::guess Bio/Tools/GuessSeqFormat.pm:462
> # STACK Bio::SeqIO::new Bio/SeqIO.pm:381
> # STACK Test::Exception::throws_ok t/SeqIO/SeqIO.t:134
> # STACK toplevel t/SeqIO/SeqIO.t:135
> # -------------------------------------
> # Looks like you failed 1 test of 45.
> Dubious, test returned 1 (wstat 256, 0x100)
> Failed 1/45 subtests
>
> Test Summary Report
> -------------------
> t/SeqIO/SeqIO.t (Wstat: 256 Tests: 45 Failed: 1)
>    Failed test:  45
>    Non-zero exit status: 1
> Files=1, Tests=45,  2 wallclock secs ( 0.05 usr  0.04 sys +  0.46 cusr  0.12
> csys =  0.67 CPU)
> Result: FAIL
> Failed 1/1 test programs. 1/45 subtests failed.
>
>
> Thanks
> Thomas
>
>
>
>
> Fields, Christopher J wrote:
>>
>> This unfortunately doesn't give us much to work on.  Can you give the
>> verbose test output?  Something like:
>>
>>     prove -lrv t/SeqIO/SeqIO.t
>>
>> or
>>
>>     ./Build test --test-files t/SeqIO/SeqIO.t --verbose
>>
>> chris
>>
>>
>