[Bioperl-l] Re: 1.5.0-RC1 available for download
amackey at pcbi.upenn.edu
amackey at pcbi.upenn.edu
Tue Nov 16 15:55:18 EST 2004
The issue is that on CVS export I'm using -kv to strip out the CVS keywords (to
be friendly to others who may wish to import the code into their own CVS
repositories). So "reusing" the CVS keyword-associated $'s for quoted
delimiters is cute, but (as evidenced below) causes problems.
-Aaron
Quoting Hilmar Lapp <hlapp at gnf.org>:
> 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
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp email: lapp at gnf.org
> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> -------------------------------------------------------------
>
More information about the Bioperl-l
mailing list