[Bioperl-l] Re: 1.5.0-RC1 available for download
Jason Stajich
jason.stajich at duke.edu
Tue Nov 16 15:52:54 EST 2004
The cvs export command is dropping the $ $ which bound the '$Revision$'
not the $Revision variable. You need to provide a delimiter to the q
operator.
I've fixed it by putting square brackets [] around the Revision
declaration.
bioperl-run needs some more testing and fixing before the release.
Shouldn't take too long but need people to run the tests, and fix the
warnings. Some tests seem to be lacking code which handles the cases
when the application being used is not present.
-jason
On Nov 16, 2004, at 3:43 PM, Hilmar Lapp wrote:
> Aaron,
>
> are you sure that you cannot use $ as the quote character?
>
> In Brian's message, the '$Revision' line was missing the closing $
> which may have been the only error.
>
> -hilmar
>
> On Nov 16, 2004, at 9:37 AM, Aaron J. Mackey wrote:
>
>> 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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
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>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>> --
>> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
> --
> -------------------------------------------------------------
> Hilmar Lapp email: lapp at gnf.org
> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> -------------------------------------------------------------
>
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> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/
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