[Bioperl-l] All tests pass

[Jason Stajich]

These are all the same warnings on gets on UN*X systems which is nice to
see nothing different rearing its head in win32.

What exactly do you get for the subroutine redefined messages as I don't
see this at all on UN*X.


The XEMBL server is in fact down apparently or these tests are really
hosed.  Perhaps Martin can get a chance to check this out before the
release.

The SearchIO warnings are something that we've discussed before which need
Steve or myself to go in and retrofit his modules (the previous plan had
been to nuke them for the release but that won't happen now).

Alternatively we drop the one test which is cauing this (writing
HTMLBlast for Steve's objects) but people will get these types of
messages when attempting to dump out HTMLBlast reports using objects
created with the Bio::SearchIO:psiblast parser anyways so I guess it
ought to be fixed even though we're going to stop supporting this parser
soon.



-jason

On Sun, 15 Dec 2002, Paul Boutros wrote:

> Win2k
> Perl 5.6.1
> Fresh CVS
>
> Biblio_biofetch.t
> =================
> 1..11
> ok 1
> ok 2 # No network access - could not connect to Medline
> ok 3 # No network access - could not connect to Medline
> ok 4 # No network access - could not connect to Medline
> ok 5 # No network access - could not connect to Medline
> ok 6 # No network access - could not connect to Medline
> ok 7 # No network access - could not connect to Medline
> ok 8 # No network access - could not connect to Medline
> ok 9 # No network access - could not connect to Medline
> ok 10 # No network access - could not connect to Medline
> ok 11 # No network access - could not connect to Medline
> Note: network connection was present and active
>
> BioFetch_DB.t
> =============
> ok 16
> ok 17 # No network access - could not connect to embl
> ok 18 # No network access - could not connect to embl
> ok 19 # No network access - could not connect to embl
> ok 20 # No network access - could not connect to embl
> ok 21 # No network access - could not connect to embl
> ok 22 # No network access - could not connect to embl
> ok 23 # No network access - could not connect to embl
> ok 24 # No network access - could not connect to embl
> ok 25 # No network access - could not connect to embl
> ok 26 # No network access - could not connect to embl
> ok 27 # No network access - could not connect to embl
> Note: network connection was present and active
>
> EMBL_db.t
> =========
> ok 4
> ok 5 # could not connect to embl
> ok 6 # could not connect to embl
> ok 7 # could not connect to embl
> ok 8 # could not connect to embl
> ok 9 # could not connect to embl
> ok 10 # could not connect to embl
> ok 11 # could not connect to embl
> ok 12 # could not connect to embl
> ok 13 # could not connect to embl
> ok 14 # could not connect to embl
> ok 15 # could not connect to embl
>
> game.t
> ======
> Subroutine redefinition warnings
> ok 19
> ok 20
> Use of uninitialized value in pattern match (m//) at
> C:/Perl/site/lib/XML/Writer.pm line 307.
> Use of uninitialized value in print at C:/Perl/lib/IO/Handle.pm line 394.
> ok 21
>
> PHD.t
> =====
> Subroutine redefinition warnings
>
> Qual.t
> ======
> Subroutine redefinition warnings
>
> RefSeq.t
> ========
> 1..13
> ok 1
> ok 2
> ok 3
> sleeping for 3 seconds
> ok 4
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> ok 10
> ok 11
> ok 12 # Unable to RefSeq test - probably no network connection.
> ok 13 # Unable to RefSeq test - probably no network connection.
> Note: There is a network connection working
>
> Scf.t
> =====
> Subroutine redefinition warnings
>
> SearchIO.t
> ==========
> subroutine redefined warnings
>
> ok 476
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> ok 478
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> ok 480
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HitTableWriter.pm line 268, <GEN31> line 353.
> ok 482
> ok 483
> ok 484
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 192, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 192, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> ok 486
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> ok 488
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> ok 489
> ok 490
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> ok 491
> ok 492
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> ok 493
> ok 494
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in sprintf at
> Bio/SearchIO/Writer/HTMLResultWriter.pm line 259, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/HSP/BlastHSP.pm
> line 447, <GEN31> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/SearchUtils.pm
> line 154, <GEN37> line 353.
> Use of uninitialized value in addition (+) at Bio/Search/SearchUtils.pm
> line 154, <GEN37> line 353.
> Use of uninitialized value in numeric eq (==) at Bio/Search/SearchUtils.pm
> line 300, <GEN37> line 353.
> Use of uninitialized value in numeric eq (==) at Bio/Search/SearchUtils.pm
> line 300, <GEN37> line 353.
> Use of uninitialized value in concatenation (.) or string at
> Bio/Search/SearchUtils.pm line 227, <GEN37> line 353.
> Use of uninitialized value in concatenation (.) or string at
> Bio/Search/SearchUtils.pm line 228, <GEN37> line 353.
> Use of uninitialized value in concatenation (.) or string at
> Bio/Search/SearchUtils.pm line 229, <GEN37> line 353.
> Use of uninitialized value in concatenation (.) or string at
> Bio/Search/SearchUtils.pm line 227, <GEN37> line 353.
> Use of uninitialized value in concatenation (.) or string at
> Bio/Search/SearchUtils.pm line 228, <GEN37> line 353.
> Use of uninitialized value in concatenation (.) or string at
> Bio/Search/SearchUtils.pm line 229, <GEN37> line 353.
>
> Term.t
> ======
> Subroutine redefinition warnings
>
> UniGene.t
> =========
> subroutine redefined warnings
>
> Variation_IO.t
> ==============
> Subroutine redefinition warnings
>
> XEMBLE_db.t
> ===========
> 1..9
> Unrecognized escape \d passed through at C:/Perl/site/lib/XML/DOM.pm line
> 136.
> ok 1
> ok 2 # server may be down
> ok 3 # Server may be down
> ok 4 # Server may be down
> ok 5 # Server may be down
> ok 6 # Server may be down
> ok 7 # Server may be down
> ok 8 # Server may be down
> ok 9 # Server may be down
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu