[Bioperl-l] Failed Test Installing BioPerl-1.6.901

[dumps]

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
> 
> 

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