[Bioperl-l] Re: 1.5.0-RC1 available for download
Aaron J. Mackey
amackey at pcbi.upenn.edu
Tue Nov 16 12:37:16 EST 2004
Whomever thought this was cute, was wrong:
% grep -r 'q\$Id' live ext run
live/Bio/AnalysisI.pm: $Revision = q$Id: AnalysisI.pm,v 1.5
2003/06/04 08:36:35 heikki Exp $;
live/Bio/Biblio/IO/medline2ref.pm: $Revision = q$Id:
medline2ref.pm,v 1.11 2003/06/04 08:36:36 heikki Exp $;
live/Bio/Biblio/IO/medlinexml.pm: $Revision = q$Id: medlinexml.pm,v
1.6 2003/06/04 08:36:36 heikki Exp $;
live/Bio/Biblio/IO/pubmed2ref.pm: $Revision = q$Id: pubmed2ref.pm,v
1.3 2003/06/04 08:36:36 heikki Exp $;
live/Bio/Biblio/IO/pubmedxml.pm: $Revision = q$Id: pubmedxml.pm,v
1.5 2003/06/04 08:36:36 heikki Exp $;
live/Bio/Biblio.pm: $Revision = q$Id: Biblio.pm,v 1.11 2004/07/13
11:44:37 bosborne Exp $;
live/Bio/DB/Biblio/biofetch.pm: $Revision = q$Id: biofetch.pm,v 1.6
2003/06/04 08:36:37 heikki Exp $;
live/Bio/DB/Biblio/soap.pm: $Revision = q$Id: soap.pm,v 1.6
2003/06/04 08:36:37 heikki Exp $;
live/Bio/DB/BiblioI.pm: $Revision = q$Id: BiblioI.pm,v 1.6
2003/06/04 08:36:37 heikki Exp $;
live/Bio/Factory/AnalysisI.pm: $Revision = q$Id: AnalysisI.pm,v 1.2
2003/06/04 08:36:39 heikki Exp $;
live/Bio/SimpleAnalysisI.pm: $Revision = q$Id: SimpleAnalysisI.pm,v
1.4 2003/06/04 08:36:35 heikki Exp $;
live/Bio/WebAgent.pm: $Revision = q$Id: WebAgent.pm,v 1.4 2003/06/04
08:36:35 heikki Exp $;
run/Bio/Tools/Run/Analysis/soap.pm: $Revision = q$Id: soap.pm,v 1.8
2003/06/04 08:48:26 heikki Exp $;
run/Bio/Tools/Run/Analysis.pm: $Revision = q$Id: Analysis.pm,v 1.6
2003/06/04 08:48:26 heikki Exp $;
run/Bio/Tools/Run/AnalysisFactory/soap.pm: $Revision = q$Id:
soap.pm,v 1.3 2003/06/04 08:48:26 heikki Exp $;
run/Bio/Tools/Run/AnalysisFactory.pm: $Revision = q$Id:
AnalysisFactory.pm,v 1.6 2003/06/04 08:48:26 heikki Exp $;
run/blib/lib/Bio/Tools/Run/Analysis/soap.pm: $Revision = q$Id:
soap.pm,v 1.8 2003/06/04 08:48:26 heikki Exp $;
run/blib/lib/Bio/Tools/Run/Analysis.pm: $Revision = q$Id:
Analysis.pm,v 1.6 2003/06/04 08:48:26 heikki Exp $;
run/blib/lib/Bio/Tools/Run/AnalysisFactory/soap.pm: $Revision =
q$Id: soap.pm,v 1.3 2003/06/04 08:48:26 heikki Exp $;
run/blib/lib/Bio/Tools/Run/AnalysisFactory.pm: $Revision = q$Id:
AnalysisFactory.pm,v 1.6 2003/06/04 08:48:26 heikki Exp $;
run/scripts/panalysis.PLS: $Revision = q$Id: panalysis.PLS,v 1.5
2003/11/25 18:09:56 bosborne Exp $;
run/scripts/papplmaker.PLS: $Revision = q$Id: papplmaker.PLS,v 1.3
2003/05/30 15:43:22 jason Exp $;
can someone please replace these q$Id ... $; with q[$Id .. $] or
something similar?
Thanks,
-Aaron
On Nov 13, 2004, at 10:06 PM, Brian Osborne wrote:
> 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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--
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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