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

[Cook, Malcolm]

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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