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

[Brian Osborne]

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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