From allenday at ucla.edu Thu Sep 18 21:12:55 2003 From: allenday at ucla.edu (Allen Day) Date: Thu Sep 18 21:11:16 2003 Subject: [Bioperl-microarray] Release Announcement: bioperl-microarray 0.1 In-Reply-To: Message-ID: 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 From MEC at Stowers-Institute.org Fri Sep 19 10:06:39 2003 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Fri Sep 19 10:05:03 2003 Subject: [Bioperl-microarray] RE: [Bioperl-l] Release Announcement: bioperl-microarray 0.1 Message-ID: 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@ucla.edu] Sent: Thursday, September 18, 2003 8:13 PM To: bioperl-microarray@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 _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From allenday at ucla.edu Fri Sep 19 13:04:07 2003 From: allenday at ucla.edu (Allen Day) Date: Fri Sep 19 13:02:19 2003 Subject: [Bioperl-microarray] RE: [Bioperl-l] Release Announcement: bioperl-microarray 0.1 In-Reply-To: Message-ID: 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@ucla.edu] > Sent: Thursday, September 18, 2003 8:13 PM > To: bioperl-microarray@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 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From MEC at Stowers-Institute.org Fri Sep 19 10:03:32 2003 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Fri Sep 19 23:11:20 2003 Subject: [Bioperl-microarray] RE: [Bioperl-l] Release Announcement: bioperl-microarray 0.1 Message-ID: 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@ucla.edu] Sent: Thursday, September 18, 2003 8:13 PM To: bioperl-microarray@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 _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l