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

Hilmar Lapp hlapp at gnf.org
Tue Nov 16 15:43:22 EST 2004 

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
>>
>> _______________________________________________
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>>
>>
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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
>
> _______________________________________________
> 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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