[Bioperl-l] Re: 1.5.0-RC1 available for download

[Nathan Haigh]

On WinXP I see these failed tests:

Failed Test         Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t\Biblio.t           255 65280    24   22  91.67%  2 4-24
t\Biblio_biofetch.t  255 65280    11   11 100.00%  1-11
t\Biblio_eutils.t    255 65280     5    5 100.00%  1-5
t\DBCUTG.t           255 65280    24    0   0.00%  ??
t\Domcut.t           255 65280    25    0   0.00%  ??
t\ELM.t              255 65280    14    0   0.00%  ??
t\GOR4.t             255 65280    13    0   0.00%  ??
t\HNN.t              255 65280    13    0   0.00%  ??
t\MeSH.t             255 65280    26    0   0.00%  ??
t\MitoProt.t         255 65280     8    0   0.00%  ??
t\NetPhos.t          255 65280    14    0   0.00%  ??
t\OntologyStore.t                  6    4  66.67%  3-6
t\Scansite.t         255 65280    12    0   0.00%  ??
t\SeqFeature.t                   192    1   0.52%  74
t\Sopma.t            255 65280    15    0   0.00%  ??
t\Taxonomy.t                       8    3  37.50%  2-3 8
t\Unflattener2.t                  11    2  18.18%  7 10
16 subtests skipped.
Failed 17/193 test scripts, 91.19% okay. 48/8889 subtests failed, 99.46% okay.

Similar to those errors already mentioned by Brian.

Nathan

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Brian Osborne
> Sent: 14 November 2004 03:06
> To: Aaron J. Mackey; Bioperl
> Subject: RE: [Bioperl-l] Re: 1.5.0-RC1 available for download
> 
> Aaron,
> 
> On Cygwin I see a whole slew of new failed tests:
> 
> Failed Test         Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------------
> ---
> t/Biblio.t           255 65280    24   38 158.33%  4-24
> t/Biblio_biofetch.t  255 65280    11    0   0.00%  ??
> t/Biblio_eutils.t    255 65280     5    0   0.00%  ??
> t/DBCUTG.t             2   512    24    0   0.00%  ??
> t/Domcut.t           255 65280    25    0   0.00%  ??
> t/ELM.t              255 65280    14    0   0.00%  ??
> t/GOR4.t             255 65280    13    0   0.00%  ??
> t/HNN.t              255 65280    13    0   0.00%  ??
> t/MeSH.t             255 65280    26    0   0.00%  ??
> t/MitoProt.t         255 65280     8    0   0.00%  ??
> t/NetPhos.t          255 65280    14    0   0.00%  ??
> t/Scansite.t         255 65280    12    0   0.00%  ??
> t/Sopma.t            255 65280    15    0   0.00%  ??
> t/Unflattener2.t                  11    2  18.18%  7 10
> 24 subtests skipped.
> make: *** [test_dynamic] Error 14
> 
> 
> Most of them seem to be due to the same problem, blocks like this:
> 
> 95 BEGIN {
> 96    $Revision = qSimpleAnalysisI.pm,v 1.4 2003/06/04 08:36:35 heikki Exp;
> 97 }
> 
> 
> 129 ~/tmp/bioperl-1.5.0-RC1>perl -I. -w t/Scansite.t
> 1..12
> Number found where operator expected at Bio/SimpleAnalysisI.pm line 96, near
> "v
> 1.4"
>         (Do you need to predeclare v?)
> Number found where operator expected at Bio/SimpleAnalysisI.pm line 96, near
> "1.
> 4 2003"
>         (Missing operator before  2003?)
> Number found where operator expected at Bio/SimpleAnalysisI.pm line 96, near
> "04
>  08"
>         (Missing operator before  08?)
> Bareword found where operator expected at Bio/SimpleAnalysisI.pm line 96,
> near "
> 35 heikki"
>         (Missing operator before heikki?)
> syntax error at Bio/SimpleAnalysisI.pm line 96, near "v 1.4"
> Illegal octal digit '8' at Bio/SimpleAnalysisI.pm line 96, at end of line
> BEGIN not safe after errors--compilation aborted at Bio/SimpleAnalysisI.pm
> line
> 97.
> Compilation failed in require at Bio/Tools/Analysis/SimpleAnalysisBase.pm
> line 7
> 7.
> BEGIN failed--compilation aborted at
> Bio/Tools/Analysis/SimpleAnalysisBase.pm li
> ne 77.
> Compilation failed in require at Bio/Tools/Analysis/Protein/Scansite.pm line
> 138
> .
> BEGIN failed--compilation aborted at Bio/Tools/Analysis/Protein/Scansite.pm
> line
>  138.
> Compilation failed in require at t/Scansite.t line 50.
> 
> Brian O.
> 
> 
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Aaron J. Mackey
> Sent: Thursday, November 11, 2004 9:33 AM
> To: Bioperl
> Subject: [Bioperl-l] Re: 1.5.0-RC1 available for download
> 
> 
> And you can now get them via http, directly from the bioperl.org/DIST/
> directory:
> 
>    http://bioperl.org/DIST/bioperl-1.5.0-RC1.tar.gz
>    http://bioperl.org/DIST/bioperl-run-1.5.0-RC1.tar.gz
>    http://bioperl.org/DIST/bioperl-ext-1.5.0-RC1.tar.gz
> 
> -Aaron
> 
> On Nov 11, 2004, at 9:16 AM, Aaron J. Mackey wrote:
> 
> >
> > The somewhat-anxiously anticipated 1.5.0 release candidates are
> > starting to roll off the shelves.  Since I don't seem to have access
> > to the download directory at bioperl.org, they are currently available
> > via FTP (active, not passive) at:
> >
> >
> > ftp://roos-compbio.bio.upenn.edu/bioperl/bioperl-release-1.5.0-
> > RC1.tar.gz
> >
> > ftp://roos-compbio.bio.upenn.edu/bioperl/bioperl-run-release-1.5.0-
> > RC1.tar.gz
> >
> > ftp://roos-compbio.bio.upenn.edu/bioperl/bioperl-ext-release-1.5.0-
> > RC1.tar.gz
> >
> > Regarding -run and -ext versioning, I've bumped them all to be in sync
> > with bioperl-live; I remember there was some discussion of this long
> > ago, but please remind me if there's some critical reason for this not
> > to occur.
> >
> > Thanks, enjoy, and gimme feedback (I already know that Unflattener2.t
> > will fail 2 tests; these have already been fixed, and will be in the
> > next RC, and/or final)
> >
> > -Aaron
> >
> > --
> > Aaron J. Mackey, Ph.D.
> > Dept. of Biology, Goddard 212
> > University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> > 415 S. University Avenue         office: 215-898-1205
> > Philadelphia, PA  19104-6017     fax:    215-746-6697
> >
> >
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
> 
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> 
> 
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