[Bioperl-microarray] RE: [Bioperl-l] Release Announcement: bioperl-microarray 0.1

[Allen Day]

Malcolm,

There is a prerequisite of bioperl-1.2.3, which was released a few days
ago.  It is this distribution, and not any earlier, which contains your
missing files.  You can also use the CVS version of bioperl-live.

-Allen



On Fri, 19 Sep 2003, Cook, Malcolm wrote:

> Hooray!
> 
> But...
> 
> Installation woes:
> 
> Trying to installing with CPAN I got errors until I first did:
> 
> install enum
> install Class::MakeMethods
> 
> After that I still fail tests:
> 
> PERL_DL_NONLAZY=1 /n/site/inst/Linux-i686/sys/bin/perl
> "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib',
> 'blib/arch')" t/*.t
> t/affy_u133a_cel.......
>  
> 
> t/affy_u133a_cel.......ok 1/39
>  
> 
> t/affy_u133a_cel.......ok 2/39
>  
> 
> t/affy_u133a_cel.......ok 3/39
>  
> 
> t/affy_u133a_cel.......ok 4/39
>  
> 
> t/affy_u133a_cel.......ok 5/39
>                   Bio/Expression/MicroarrayIO/affymetrix.pm: couldn't
> load affymetrix - for more details on
>                   supported formats please see the MicroarrayIO docs
>                   Exception Can't locate Bio/Expression/FeatureGroup.pm
> in @INC (@INC contains: t .
> /n/site/inst/Linux-i686/sys/.cpan/build/bioperl-microarray-0.1/blib/lib
> /n/site/inst/Linux-i686/sys/.cpan/build/bioperl-microarray-0.1/blib/arch
> /n/site/inst/Linux-i686/bioinfo/seals/lib/perl
> /n/site/inst/Linux-i686/sys/lib/perl5/5.8.0/i686-linux
> /n/site/inst/Linux-i686/sys/lib/perl5/5.8.0
> /n/site/inst/Linux-i686/sys/lib/perl5/site_perl/5.8.0/i686-linux
> /n/site/inst/Linux-i686/sys/lib/perl5/site_perl/5.8.0
> /n/site/inst/Linux-i686/sys/lib/perl5/site_perl) at
> Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm line 57.
> 
> 
> And indeed looking into my install directory I don't see
> FeatureGroup.pm, only:
> 
> ls ./Bio/Expression
> Microarray  MicroarrayI.pm  MicroarrayIO  MicroarrayIO.pm
> 
> I'm eager for another try ...
> 
> Thanks,
> 
> Malcolm Cook
> Stowers Institute for Medical Research 
> 
> -----Original Message-----
> From: Allen Day [mailto:allenday at ucla.edu] 
> Sent: Thursday, September 18, 2003 8:13 PM
> To: bioperl-microarray at bioperl.org
> Cc: Bioperl; Bioperl Announce
> Subject: [Bioperl-l] Release Announcement: bioperl-microarray 0.1
> 
> 
> The Bioperl developers are pleased to announce a 0.1 release of
> bioperl-microarray, a Bioperl extension package dedicated to
> manipulation 
> of microarray data.
> 
> The package is implemented using IO conventions Bioperl developers
> should 
> already be familiar with. Data types currently supported are:
> 
>   Affymetrix GeneChip CEL files (read and write)
>   Affymetrix GeneChip CDF files (read)
>   Affymetrix GeneChip Microarray Suite 5.0 normalized files (read)
>   Affymetrix GeneChip dChip normalized files (read)
> 
> Data types for which support is planned in a 0.2 release include:
> 
>   Bio::MAGE objects and MAGE-ML (read and write)
>   Affymetrix SNPChip genotype files (read)
>   GenePix GPR files (read)
> 
> Release packages are available from:
>   http://www.bioperl.org/DIST/
>     http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.bz2 
>     http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.gz
>     http://www.bioperl.org/DIST/bioperl-microarray-0.1.zip
> 
>   as well as from CPAN:
>     http://search.cpan.org/author/ALLENDAY/
> 
> Documentation available from:
>   http://doc.bioperl.org/bioperl-microarray/
> 
> Subscribe to the bioperl-microarray mailing list at:
>   http://bioperl.org/mailman/listinfo/bioperl-microarray/
> 
> Report bugs at:
>   http://bugzilla.bioperl.org/
> 
> 
> -Allen
> --------------------
> Allen Day
> Human Genetics, UCLA
> 
> 
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