[med-svn] r1842 - in trunk/packages/libgo-perl/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Sat May 10 01:32:35 UTC 2008
Author: plessy
Date: 2008-05-10 01:32:34 +0000 (Sat, 10 May 2008)
New Revision: 1842
Added:
trunk/packages/libgo-perl/trunk/debian/patches/fix-missing-manpages
Modified:
trunk/packages/libgo-perl/trunk/debian/control
trunk/packages/libgo-perl/trunk/debian/patches/fix-whatis-entries.patch
trunk/packages/libgo-perl/trunk/debian/patches/series
trunk/packages/libgo-perl/trunk/debian/rules
Log:
More work on missing manpages.
Modified: trunk/packages/libgo-perl/trunk/debian/control
===================================================================
--- trunk/packages/libgo-perl/trunk/debian/control 2008-05-09 05:09:16 UTC (rev 1841)
+++ trunk/packages/libgo-perl/trunk/debian/control 2008-05-10 01:32:34 UTC (rev 1842)
@@ -13,7 +13,6 @@
Package: libgo-perl
Architecture: all
-Section: science
Depends: ${perl:Depends}
Recommends: libdata-stag-perl
Suggests: xsltproc, libxml-perl, bioperl
Added: trunk/packages/libgo-perl/trunk/debian/patches/fix-missing-manpages
===================================================================
--- trunk/packages/libgo-perl/trunk/debian/patches/fix-missing-manpages (rev 0)
+++ trunk/packages/libgo-perl/trunk/debian/patches/fix-missing-manpages 2008-05-10 01:32:34 UTC (rev 1842)
@@ -0,0 +1,50 @@
+--- a/scripts/go-apply-xslt
++++ b/scripts/go-apply-xslt
+@@ -99,3 +99,19 @@
+ EOM
+ ;
+ }
++
++__END__
++
++=head1 NAME
++
++go-apply-xslt - apply GO XSL on OBO-XML
++
++=head1 DESCRIPTION
++
++Will apply a GO XSL transform (by name) on an OBO-XML file
++
++For a full list of XSLs available, see <http://www.godatabase.org/xml/xsl>
++
++=head1 SEE ALSO
++
++L<go-perl>(1)
+--- a/scripts/go-export-prolog.pl
++++ b/scripts/go-export-prolog.pl
+@@ -36,3 +36,5 @@
+ ;
+ }
+ $parser->parse (@fns);
++
++
+--- a/scripts/go2error_report
++++ b/scripts/go2error_report
+@@ -28,3 +28,17 @@
+ $parser->errhandler($errhandler);
+ $parser->parse($f);
+ }
++
++__END__
++
++=head1 NAME
++
++go2error_report - converts go/obo to error_report
++
++=head1 DESCRIPTION
++
++Converts a file in any valid go/obo format to error_report.
++
++=head1 SEE ALSO
++
++L<go-perl>(1)
Modified: trunk/packages/libgo-perl/trunk/debian/patches/fix-whatis-entries.patch
===================================================================
--- trunk/packages/libgo-perl/trunk/debian/patches/fix-whatis-entries.patch 2008-05-09 05:09:16 UTC (rev 1841)
+++ trunk/packages/libgo-perl/trunk/debian/patches/fix-whatis-entries.patch 2008-05-10 01:32:34 UTC (rev 1842)
@@ -171,3 +171,335 @@
=head1 SYNOPSIS
+--- a/GO/IO/Dotty.pm
++++ b/GO/IO/Dotty.pm
+@@ -4,7 +4,7 @@
+
+ =head1 NAME
+
+- GO::IO::Dotty;
++ GO::IO::Dotty - Dotty diagrams from GO graphs
+
+ =head1 SYNOPSIS
+
+--- a/GO/IO/OBDXML.pm
++++ b/GO/IO/OBDXML.pm
+@@ -18,7 +18,7 @@
+
+ =head1 NAME
+
+- GO::IO::OBDXML;
++ GO::IO::OBDXML - dump GO terms as xml
+
+ =head1 SYNOPSIS
+
+--- a/GO/IO/ObanOwl.pm
++++ b/GO/IO/ObanOwl.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::IO::ObanOwl;
++ GO::IO::ObanOwl - dump GO terms as xml
+
+ =head1 SYNOPSIS
+
+--- a/GO/IO/RDFXML.pm
++++ b/GO/IO/RDFXML.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::IO::RDFXML;
++ GO::IO::RDFXML - dump GO terms as xml
+
+ =head1 SYNOPSIS
+
+--- a/GO/IO/go_assoc.pm
++++ b/GO/IO/go_assoc.pm
+@@ -15,7 +15,7 @@
+
+ =head1 NAME
+
+- GO::IO::go_assoc;
++ GO::IO::go_assoc - dump GO terms as OBD XML
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Association.pm
++++ b/GO/Model/Association.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Association;
++ GO::Model::Association - association between a GO term and a gene product
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/CrossProduct.pm
++++ b/GO/Model/CrossProduct.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::CrossProduct;
++ GO::Model::CrossProduct - intersection between class/term and list of anonymous subclass
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/DB.pm
++++ b/GO/Model/DB.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::DB;
++ GO::Model::DB - DB class
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Evidence.pm
++++ b/GO/Model/Evidence.pm
+@@ -12,7 +12,7 @@
+
+ =head1 NAME
+
+- GO::Model::Evidence;
++ GO::Model::Evidence - evidence for an association
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/GeneProduct.pm
++++ b/GO/Model/GeneProduct.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::GeneProduct;
++ GO::Model::GeneProduct - gene product in a particular species
+
+ =head1 DESCRIPTION
+
+--- a/GO/Model/GraphIterator.pm
++++ b/GO/Model/GraphIterator.pm
+@@ -12,7 +12,7 @@
+
+ =head1 NAME
+
+- GO::Model::GraphIterator;
++ GO::Model::GraphIterator - Graph iterator
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/LogicalDefinition.pm
++++ b/GO/Model/LogicalDefinition.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::LogicalDefinition;
++ GO::Model::LogicalDefinition - logical definition
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Modification.pm
++++ b/GO/Model/Modification.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Modification;
++ GO::Model::Modification - cross reference to external database
+
+ =head1 DESCRIPTION
+
+--- a/GO/Model/Ontology.pm
++++ b/GO/Model/Ontology.pm
+@@ -12,7 +12,7 @@
+
+ =head1 NAME
+
+- GO::Model::Ontology;
++ GO::Model::Ontology - synonym for GO::Model::Graph
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Path.pm
++++ b/GO/Model/Path.pm
+@@ -12,7 +12,7 @@
+
+ =head1 NAME
+
+- GO::Model::Path;
++ GO::Model::Path - path between two nodes
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Property.pm
++++ b/GO/Model/Property.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Property;
++ GO::Model::Property - model property
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Relationship.pm
++++ b/GO/Model/Relationship.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Relationship
++ GO::Model::Relationship - relationship between two terms
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Restriction.pm
++++ b/GO/Model/Restriction.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Restriction;
++ GO::Model::Restriction - model restriction
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Root.pm
++++ b/GO/Model/Root.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Root
++ GO::Model::Root - base class for all GO::Model objects
+
+ =head1 DESCRIPTION
+
+--- a/GO/Model/Seq.pm
++++ b/GO/Model/Seq.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Seq;
++ GO::Model::Seq - biological sequence
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Species.pm
++++ b/GO/Model/Species.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Species;
++ GO::Model::Species - gene product in a particular species
+
+ =head1 DESCRIPTION
+
+--- a/GO/Model/Term.pm
++++ b/GO/Model/Term.pm
+@@ -12,7 +12,7 @@
+
+ =head1 NAME
+
+-GO::Model::Term - a term or concept in an ontology
++GO::Model::Term - a term or concept in an ontology
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/TreeIterator.pm
++++ b/GO/Model/TreeIterator.pm
+@@ -13,7 +13,7 @@
+
+ =head1 NAME
+
+- GO::Model::GraphIterator;
++ GO::Model::GraphIterator - wraps GO::Model::GraphIterator
+
+ =head1 SYNOPSIS
+
+--- a/GO/Model/Xref.pm
++++ b/GO/Model/Xref.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::Model::Xref;
++ GO::Model::Xref - cross reference to an external database
+
+ =head1 SYNOPSIS
+
+--- a/GO/Parsers/locuslink_parser.pm
++++ b/GO/Parsers/locuslink_parser.pm
+@@ -6,7 +6,7 @@
+
+ =head1 NAME
+
+-GO::Parsers::locuslink_parser -
++GO::Parsers::locuslink_parser - Parser for LocusLink
+
+ =head1 SYNOPSIS
+
+--- a/GO/Parsers/ncbi_taxonomy_parser.pm
++++ b/GO/Parsers/ncbi_taxonomy_parser.pm
+@@ -10,7 +10,7 @@
+
+ =head1 NAME
+
+- GO::Parsers::ncbi_taxonomy_parser
++ GO::Parsers::ncbi_taxonomy_parser - Parser for NCBI taxonomy
+
+ =head1 SYNOPSIS
+
+--- a/GO/Parsers/obj_emitter.pm
++++ b/GO/Parsers/obj_emitter.pm
+@@ -10,7 +10,7 @@
+
+ =head1 NAME
+
+-GO::Parsers::obj_emitter -
++GO::Parsers::obj_emitter - Private class
+
+ =head1 SYNOPSIS
+
+--- a/GO/ObjCache.pm
++++ b/GO/ObjCache.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+- GO::ObjCache;
++ GO::ObjCache - private method
+
+ =head1 DESCRIPTION
+
+--- a/GO/Utils.pm
++++ b/GO/Utils.pm
+@@ -20,6 +20,10 @@
+ use Carp;
+ use Data::Dumper;
+
++=head1 NAME
++
++GO::Utils - utilities for GO modules
++
+ =head2 rearrange()
+
+ Usage : n/a
+--- a/scripts/go-dag-summary.pl
++++ b/scripts/go-dag-summary.pl
+@@ -110,7 +110,7 @@
+
+ =head1 NAME
+
+-go-dag-summary
++go-dag-summary - summarises an ontology
+
+ =head1 SYNOPSIS
+
Modified: trunk/packages/libgo-perl/trunk/debian/patches/series
===================================================================
--- trunk/packages/libgo-perl/trunk/debian/patches/series 2008-05-09 05:09:16 UTC (rev 1841)
+++ trunk/packages/libgo-perl/trunk/debian/patches/series 2008-05-10 01:32:34 UTC (rev 1842)
@@ -1 +1,2 @@
fix-whatis-entries.patch
+fix-missing-manpages
Modified: trunk/packages/libgo-perl/trunk/debian/rules
===================================================================
--- trunk/packages/libgo-perl/trunk/debian/rules 2008-05-09 05:09:16 UTC (rev 1841)
+++ trunk/packages/libgo-perl/trunk/debian/rules 2008-05-10 01:32:34 UTC (rev 1842)
@@ -2,3 +2,7 @@
include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/perlmodule.mk
+
+binary-fixup/libgo-perl::
+ prename 's/\.pl//' $(CURDIR)/debian/libgo-perl/usr/bin/*
+ prename 's/\.pl//' $(CURDIR)/debian/libdgo-perl/usr/share/man/man1/*1p*
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