Hi Tom, Yes, that is fine. Those modules are provided by BioPerl. They were also in the GBrowse cvs to patch older versions of BioPerl but that is no longer necessary as the new version of BioPerl is sufficient.
Scott On Wed, 2008-02-27 at 17:02 -0800, Tom Conlin wrote: > Hi Scott > I am just looking at gbrowse again after a year or two and thought I would > freshen my instaltion. Should the current 'stable' cvs branch > > cvs -d :pserver:[EMAIL PROTECTED]:/cvsroot/gmod co -r stable > Generic-Genome-Browser > > be missing these lib files? > > comm -23 ./old_libs ./new_libs > > ./Bio/DB/GFF/Adaptor/ace.pm > ./Bio/DB/GFF/Adaptor/berkeleydb.pm > ./Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm > ./Bio/DB/GFF/Adaptor/biofetch.pm > ./Bio/DB/GFF/Adaptor/biofetch_oracle.pm > ./Bio/DB/GFF/Adaptor/dbi.pm > ./Bio/DB/GFF/Adaptor/dbi/caching_handle.pm > ./Bio/DB/GFF/Adaptor/dbi/iterator.pm > ./Bio/DB/GFF/Adaptor/dbi/mysql.pm > ./Bio/DB/GFF/Adaptor/dbi/mysqlace.pm > ./Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm > ./Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm > ./Bio/DB/GFF/Adaptor/dbi/oracle.pm > ./Bio/DB/GFF/Adaptor/dbi/oracleace.pm > ./Bio/DB/GFF/Adaptor/dbi/pg.pm > ./Bio/DB/GFF/Adaptor/memory.pm > ./Bio/DB/GFF/Adaptor/memory/feature_serializer.pm > ./Bio/DB/GFF/Adaptor/memory/iterator.pm > ./Bio/DB/GFF/Aggregator.pm > ./Bio/DB/GFF/Featname.pm > ./Bio/DB/GFF/Feature.pm > ./Bio/DB/GFF/Homol.pm > ./Bio/DB/GFF/RelSegment.pm > ./Bio/DB/GFF/Segment.pm > ./Bio/DB/GFF/Typename.pm > ./Bio/Graphics/Browser/CAlign.pm > > > the missing Bio/DB/GFF/Adaptor/ is what concerns me at the moment. > > embryonix [Bio/DB/GFF]% ll > total 24 > drwxr-sr-x 5 tomc fishadmin 512 Feb 27 14:49 ../ > drwxr-sr-x 2 tomc fishadmin 512 Feb 27 14:49 CVS/ > drwxr-sr-x 4 tomc fishadmin 512 Feb 27 14:49 ./ > drwxr-sr-x 3 tomc fishadmin 512 Feb 27 14:49 Aggregator/ > -rw-r--r-- 1 tomc fishadmin 2624 Dec 21 13:52 SyntenyBlock.pm > -rw-r--r-- 1 tomc fishadmin 4413 Dec 21 13:52 SyntenyIO.pm > > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. [EMAIL PROTECTED] GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-gbrowse mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
