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

[Allen Day]

this is speculative, but maybe it is a perl version/platform-specific 
problem.

more importantly though, why would you want to use $ as a quote delimiter
when there are other, less potentially confusing, options available?  i
agree with aaron that is is not good.  at the very least it is bad style.

-allen

On Tue, 16 Nov 2004, 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
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at portal.open-bio.org
> >> 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
> >
>