svn commit: r371237 - in head/biology: artemis biococoa crux emboss fasta3 fastdnaml garlic hmmer iolib jalview libsbml mafft mopac mummer ncbi-toolkit p5-AcePerl p5-Bio-ASN1-EntrezGene p5-Bio-Das ...

Baptiste Daroussin bapt at FreeBSD.org
Mon Oct 20 07:10:58 UTC 2014 

Author: bapt
Date: Mon Oct 20 07:10:48 2014
New Revision: 371237
URL: https://svnweb.freebsd.org/changeset/ports/371237
QAT: https://qat.redports.org/buildarchive/r371237/

Log:
  Cleanup plist

Modified:
  head/biology/artemis/pkg-plist
  head/biology/biococoa/pkg-plist
  head/biology/crux/pkg-plist
  head/biology/emboss/pkg-plist
  head/biology/fasta3/pkg-plist
  head/biology/fastdnaml/pkg-plist
  head/biology/garlic/pkg-plist
  head/biology/hmmer/pkg-plist
  head/biology/iolib/pkg-plist
  head/biology/jalview/pkg-plist
  head/biology/libsbml/pkg-plist
  head/biology/mafft/pkg-plist
  head/biology/mopac/pkg-plist
  head/biology/mummer/pkg-plist
  head/biology/ncbi-toolkit/pkg-plist
  head/biology/p5-AcePerl/pkg-plist
  head/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
  head/biology/p5-Bio-Das-Lite/pkg-plist
  head/biology/p5-Bio-Das/pkg-plist
  head/biology/p5-Bio-GFF3/pkg-plist
  head/biology/p5-Bio-Glite/pkg-plist
  head/biology/p5-Bio-Graphics/pkg-plist
  head/biology/p5-Bio-MAGETAB/pkg-plist
  head/biology/p5-Bio-NEXUS/pkg-plist
  head/biology/p5-Bio-Phylo/pkg-plist
  head/biology/p5-Bio-SCF/pkg-plist
  head/biology/p5-bioperl-run/pkg-plist
  head/biology/p5-bioperl/pkg-plist
  head/biology/paml/pkg-plist
  head/biology/phylip/pkg-plist
  head/biology/platon/pkg-plist
  head/biology/protomol/pkg-plist
  head/biology/ruby-bio/pkg-plist
  head/biology/seqan/pkg-plist
  head/biology/tinker/pkg-plist
  head/biology/ugene/pkg-plist

Modified: head/biology/artemis/pkg-plist
==============================================================================
--- head/biology/artemis/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/artemis/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -1778,34 +1778,3 @@ artemis-%%PORTVERSION%%/uk/ac/sanger/art
 artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util/WorkingGZIPInputStream.java
 bin/act
 bin/art
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/ibatis
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/util
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/sequence
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/plot
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/j2ssh
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/io
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/editor
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder/gff
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder/cv
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/genebuilder
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/filetree
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components/database
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/components
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis/chado
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger/artemis
- at dirrm artemis-%%PORTVERSION%%/uk/ac/sanger
- at dirrm artemis-%%PORTVERSION%%/uk/ac
- at dirrm artemis-%%PORTVERSION%%/uk
- at dirrm artemis-%%PORTVERSION%%/type
- at dirrm artemis-%%PORTVERSION%%/seqdb
- at dirrm artemis-%%PORTVERSION%%/nsdb/NucFeaturePackage
- at dirrm artemis-%%PORTVERSION%%/nsdb/LocationPackage
- at dirrm artemis-%%PORTVERSION%%/nsdb/EmblPackage
- at dirrm artemis-%%PORTVERSION%%/nsdb
- at dirrm artemis-%%PORTVERSION%%/lib/j2ssh
- at dirrm artemis-%%PORTVERSION%%/lib/ibatis
- at dirrm artemis-%%PORTVERSION%%/lib
- at dirrm artemis-%%PORTVERSION%%/images
- at dirrm artemis-%%PORTVERSION%%/etc
- at dirrm artemis-%%PORTVERSION%%/artemis_sqlmap
- at dirrm artemis-%%PORTVERSION%%

Modified: head/biology/biococoa/pkg-plist
==============================================================================
--- head/biology/biococoa/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/biococoa/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -63,8 +63,3 @@ GNUstep/Local/Library/Headers/BioCocoa
 GNUstep/Local/Library/Libraries/libBioCocoa.so
 GNUstep/Local/Library/Libraries/libBioCocoa.so.2
 GNUstep/Local/Library/Libraries/libBioCocoa.so.2.2.2
- at dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Resources
- at dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2/Headers
- at dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/2
- at dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions
- at dirrmtry GNUstep/Local/Library/Frameworks/BioCocoa.framework

Modified: head/biology/crux/pkg-plist
==============================================================================
--- head/biology/crux/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/crux/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -54,19 +54,3 @@ lib/Crux/parsers/Fasta.pickle
 %%PYTHON_SITELIBDIR%%/Crux/__init__.py
 %%PYTHON_SITELIBDIR%%/Crux/__init__.so
 %%PYTHON_SITELIBDIR%%/Parsing.so
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include/Crux
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/include
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/Tree
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/Mc3
- at dirrm %%PYTHON_SITELIBDIR%%/Crux/DistMatrix
- at dirrm %%PYTHON_SITELIBDIR%%/Crux
- at dirrm lib/Crux/parsers
- at dirrm lib/Crux/lib
- at dirrm lib/Crux

Modified: head/biology/emboss/pkg-plist
==============================================================================
--- head/biology/emboss/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/emboss/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -2314,51 +2314,3 @@ lib/libnucleus.so.6.0.5
 %%PORTDOCS%%%%DOCSDIR%%/programs/text/wosstopic.txt
 %%PORTDOCS%%%%DOCSDIR%%/programs/text/xmlget.txt
 %%PORTDOCS%%%%DOCSDIR%%/programs/text/xmltext.txt
- at dirrm bin
- at dirrm include/ezlib
- at dirrm include/eplplot
- at dirrm include/epcre
- at dirrm include/eexpat
- at dirrm include
- at dirrm lib
- at dirrm %%DATADIR%%/acd
- at dirrm %%DATADIR%%/data/AAINDEX
- at dirrm %%DATADIR%%/data/CODONS
- at dirrm %%DATADIR%%/data/JASPAR_CNE
- at dirrm %%DATADIR%%/data/JASPAR_CORE
- at dirrm %%DATADIR%%/data/JASPAR_FAM
- at dirrm %%DATADIR%%/data/JASPAR_PHYLOFACTS
- at dirrm %%DATADIR%%/data/JASPAR_PBM
- at dirrm %%DATADIR%%/data/JASPAR_PBM_HLH
- at dirrm %%DATADIR%%/data/JASPAR_PBM_HOMEO
- at dirrm %%DATADIR%%/data/JASPAR_POLII
- at dirrm %%DATADIR%%/data/JASPAR_SPLICE
- at dirrm %%DATADIR%%/data/OBO
- at dirrm %%DATADIR%%/data/PRINTS
- at dirrm %%DATADIR%%/data/PROSITE
- at dirrm %%DATADIR%%/data/REBASE
- at dirrm %%DATADIR%%/data/TAXONOMY
- at dirrm %%DATADIR%%/data
- at dirrm %%DATADIR%%/index
- at dirrm %%DATADIR%%/jemboss/images
- at dirrm %%DATADIR%%/jemboss/lib/axis
- at dirrm %%DATADIR%%/jemboss/lib
- at dirrm %%DATADIR%%/jemboss/resources
- at dirrm %%DATADIR%%/jemboss/utils
- at dirrm %%DATADIR%%/jemboss
- at dirrm %%DATADIR%%/test/data
- at dirrm %%DATADIR%%/test/embl
- at dirrm %%DATADIR%%/test/genbank
- at dirrm %%DATADIR%%/test/pir
- at dirrm %%DATADIR%%/test/swiss
- at dirrm %%DATADIR%%/test/swnew
- at dirrm %%DATADIR%%/test/testdb
- at dirrm %%DATADIR%%/test
- at dirrmtry %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
- at dirrmtry share

Modified: head/biology/fasta3/pkg-plist
==============================================================================
--- head/biology/fasta3/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/fasta3/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -118,6 +118,3 @@ man/man1/tfasty35.1.gz
 %%DATADIR%%/pam250.mat
 %%DATADIR%%/rna.mat
 %%DATADIR%%/vtml160.mat
- at dirrm %%DATADIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%

Modified: head/biology/fastdnaml/pkg-plist
==============================================================================
--- head/biology/fastdnaml/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/fastdnaml/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -32,4 +32,3 @@ bin/fastdnaml/usertree
 bin/fastdnaml/usertrees
 bin/fastdnaml/weights
 bin/fastdnaml/weights_categories
- at dirrm bin/fastdnaml

Modified: head/biology/garlic/pkg-plist
==============================================================================
--- head/biology/garlic/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/garlic/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -1,7 +1,6 @@
 bin/garlic
 share/garlic/.garlicrc
 share/garlic/residues.pdb
- at dirrm share/garlic
 %%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/ascorbic_acid1.jpg
 %%PORTDOCS%%%%DOCSDIR%%/ascorbic_acid2.jpg
@@ -258,30 +257,6 @@ share/garlic/residues.pdb
 %%PORTDOCS%%%%DOCSDIR%%/whatis/favicon.ico
 %%PORTDOCS%%%%DOCSDIR%%/whatis/garlic.gif
 %%PORTDOCS%%%%DOCSDIR%%/whatis/index.html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/whatis
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorial
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/techinfo
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/support
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/scripts
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/refcard
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/precompiled_packages
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/options
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/mouse/.xvpics
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/mouse
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/license
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/install
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/gallery
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/features
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/download
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/data
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/cookbook
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/controls
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/config
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/competition
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/commands
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/changes
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/bugfixes
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
 %%PORTDOCS%%%%EXAMPLESDIR%%/adrenaline.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/22porins.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/backup-hyd.script
@@ -325,4 +300,3 @@ share/garlic/residues.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/trp.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/two-positive.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/water.pdb
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%

Modified: head/biology/hmmer/pkg-plist
==============================================================================
--- head/biology/hmmer/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/hmmer/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -43,5 +43,3 @@ man/man1/phmmer.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%

Modified: head/biology/iolib/pkg-plist
==============================================================================
--- head/biology/iolib/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/iolib/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -110,4 +110,3 @@ man/man3/write_reading.3.gz
 man/man3/write_scf.3.gz
 man/man3/write_scf_header.3.gz
 man/man4/Read.4.gz
- at dirrmtry include/io_lib

Modified: head/biology/jalview/pkg-plist
==============================================================================
--- head/biology/jalview/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/jalview/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -14,4 +14,3 @@ bin/jalview
 %%DATADIR%%/castor-0.9.6-xml.jar
 %%DATADIR%%/axis.jar
 %%DATADIR%%/xml-apis.jar
- at dirrm %%DATADIR%%

Modified: head/biology/libsbml/pkg-plist
==============================================================================
--- head/biology/libsbml/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/libsbml/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -492,37 +492,3 @@ lib/libsbml.so.5.10.2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twoalgebraicrules.xml
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-3/twodimensional.xml
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/xslt/layout/layout2svg.xsl
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/xslt
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-3
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-2
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/r
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++/layout
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml
- at dirrm include/sbml/xml
- at dirrm include/sbml/validator
- at dirrm include/sbml/util
- at dirrm include/sbml/units
- at dirrm include/sbml/math
- at dirrm include/sbml/extension
- at dirrm include/sbml/conversion
- at dirrm include/sbml/compress
- at dirrm include/sbml/common
- at dirrm include/sbml/annotation
- at dirrm include/sbml

Modified: head/biology/mafft/pkg-plist
==============================================================================
--- head/biology/mafft/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/mafft/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -66,6 +66,3 @@ man/man1/mafft.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi
- at dirrmtry libexec/mafft
-%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
-%%PORTEXAMPLES%%@dirrmtry %%EXAMPLESDIR%%

Modified: head/biology/mopac/pkg-plist
==============================================================================
--- head/biology/mopac/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/mopac/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -6,4 +6,3 @@ lib/libmopac7.so.0
 lib/libmopac7.so.0.0.0
 libdata/pkgconfig/libmopac7.pc
 libexec/mopac7
- at dirrm include/mopac7

Modified: head/biology/mummer/pkg-plist
==============================================================================
--- head/biology/mummer/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/mummer/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -23,4 +23,3 @@ bin/show-tiling
 %%PORTDOCS%%%%DOCSDIR%%/INSTALL
 %%PORTDOCS%%%%DOCSDIR%%/LICENSE
 %%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%@dirrm %%DOCSDIR%%

Modified: head/biology/ncbi-toolkit/pkg-plist
==============================================================================
--- head/biology/ncbi-toolkit/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/ncbi-toolkit/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -811,12 +811,3 @@ man/man1/vecscreen.1.gz
 %%DATADIR%%/sgmlbb.ent
 %%DATADIR%%/taxlist.txt
 %%DATADIR%%/validrules.prt
- at dirrmtry %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
- at dirrm lib/ncbi
- at dirrm include/ncbi/connect
- at dirrm include/ncbi

Modified: head/biology/p5-AcePerl/pkg-plist
==============================================================================
--- head/biology/p5-AcePerl/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-AcePerl/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -144,16 +144,3 @@ bin/ace.pl
 %%PERL5_MAN3%%/Ace::Sequence::Multi.3.gz
 %%PERL5_MAN3%%/Ace::Sequence::Transcript.3.gz
 man/man1/ace.pl.1.gz
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/GFF
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace

Modified: head/biology/p5-Bio-ASN1-EntrezGene/pkg-plist
==============================================================================
--- head/biology/p5-Bio-ASN1-EntrezGene/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-ASN1-EntrezGene/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -7,10 +7,3 @@
 %%PERL5_MAN3%%/Bio::ASN1::EntrezGene::Indexer.3.gz
 %%PERL5_MAN3%%/Bio::ASN1::Sequence.3.gz
 %%PERL5_MAN3%%/Bio::ASN1::Sequence::Indexer.3.gz
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/ASN1/EntrezGene
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/ASN1
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
- at dirrmtry %%SITE_PERL%%/Bio/ASN1/EntrezGene
- at dirrmtry %%SITE_PERL%%/Bio/ASN1/Sequence
- at dirrmtry %%SITE_PERL%%/Bio/ASN1
- at dirrmtry %%SITE_PERL%%/Bio

Modified: head/biology/p5-Bio-Das-Lite/pkg-plist
==============================================================================
--- head/biology/p5-Bio-Das-Lite/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-Das-Lite/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -1,4 +1,2 @@
 %%SITE_PERL%%/Bio/Das/Lite.pm
 %%PERL5_MAN3%%/Bio::Das::Lite.3.gz
- at dirrmtry %%SITE_PERL%%/Bio/Das
- at dirrmtry %%SITE_PERL%%/Bio

Modified: head/biology/p5-Bio-Das/pkg-plist
==============================================================================
--- head/biology/p5-Bio-Das/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-Das/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -51,10 +51,3 @@
 %%PERL5_MAN3%%/Bio::Das::Type.3.gz
 %%PERL5_MAN3%%/Bio::Das::TypeHandler.3.gz
 %%PERL5_MAN3%%/Bio::Das::Util.3.gz
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Das
- at dirrmtry %%SITE_PERL%%/Bio/Das/Request
- at dirrmtry %%SITE_PERL%%/Bio/Das/HTTP
- at dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/MySQL
- at dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage/CSV
- at dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer/SQLStorage
- at dirrmtry %%SITE_PERL%%/Bio/Das/AGPServer

Modified: head/biology/p5-Bio-GFF3/pkg-plist
==============================================================================
--- head/biology/p5-Bio-GFF3/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-GFF3/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -11,10 +11,3 @@ bin/gff3_from_fasta
 %%PERL5_MAN3%%/Bio::GFF3::Transform::FromFasta.3.gz
 %%PERL5_MAN3%%/Bio::GFF3::Transform::SyncDirectives.3.gz
 man/man1/gff3_from_fasta.1.gz
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/GFF3
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
- at dirrm %%SITE_PERL%%/Bio/GFF3/Transform
- at dirrm %%SITE_PERL%%/Bio/GFF3/LowLevel/Parser
- at dirrm %%SITE_PERL%%/Bio/GFF3/LowLevel
- at dirrm %%SITE_PERL%%/Bio/GFF3
- at dirrmtry %%SITE_PERL%%/Bio

Modified: head/biology/p5-Bio-Glite/pkg-plist
==============================================================================
--- head/biology/p5-Bio-Glite/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-Glite/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -1,6 +1,3 @@
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Glite/.packlist
 %%SITE_PERL%%/Bio/Glite.pm
 %%PERL5_MAN3%%/Bio::Glite.3.gz
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Glite
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
- at dirrmtry %%SITE_PERL%%/Bio

Modified: head/biology/p5-Bio-Graphics/pkg-plist
==============================================================================
--- head/biology/p5-Bio-Graphics/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-Graphics/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -216,7 +216,3 @@ man/man1/contig_draw.pl.1.gz
 man/man1/feature_draw.pl.1.gz
 man/man1/frend.pl.1.gz
 man/man1/search_overview.pl.1.gz
- at dirrmtry %%SITE_PERL%%/Bio/Graphics/FeatureFile
- at dirrmtry %%SITE_PERL%%/Bio/Graphics/Glyph
- at dirrmtry %%SITE_PERL%%/Bio/Graphics/Wiggle
- at dirrmtry %%SITE_PERL%%/Bio/Graphics

Modified: head/biology/p5-Bio-MAGETAB/pkg-plist
==============================================================================
--- head/biology/p5-Bio-MAGETAB/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-MAGETAB/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -117,10 +117,3 @@ bin/unload_magetab_namespace.pl
 %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::IDF.3.gz
 %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::SDRF.3.gz
 %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::Tabfile.3.gz
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/MAGETAB
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
- at dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Reader
- at dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Writer
- at dirrm %%SITE_PERL%%/Bio/MAGETAB/Util
- at dirrm %%SITE_PERL%%/Bio/MAGETAB
- at dirrmtry %%SITE_PERL%%/Bio

Modified: head/biology/p5-Bio-NEXUS/pkg-plist
==============================================================================
--- head/biology/p5-Bio-NEXUS/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-NEXUS/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -61,9 +61,3 @@ bin/nextool.pl
 man/man1/nex2text_tree.pl.1.gz
 man/man1/nexplot.pl.1.gz
 man/man1/nextool.pl.1.gz
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
- at dirrm %%SITE_PERL%%/Bio/NEXUS/Util
- at dirrm %%SITE_PERL%%/Bio/NEXUS/Tools
- at dirrm %%SITE_PERL%%/Bio/NEXUS
- at dirrmtry %%SITE_PERL%%/Bio

Modified: head/biology/p5-Bio-Phylo/pkg-plist
==============================================================================
--- head/biology/p5-Bio-Phylo/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-Phylo/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -239,28 +239,3 @@
 %%PERL5_MAN3%%/Bio::Phylo::Util::OptionalInterface.3.gz
 %%PERL5_MAN3%%/Bio::Phylo::Util::StackTrace.3.gz
 %%PERL5_MAN3%%/Bio::PhyloRole.3.gz
- at dirrm %%SITE_PERL%%/Bio/Phylo/Util/CONSTANT
- at dirrm %%SITE_PERL%%/Bio/Phylo/Util
- at dirrm %%SITE_PERL%%/Bio/Phylo/Unparsers
- at dirrm %%SITE_PERL%%/Bio/Phylo/Treedrawer
- at dirrm %%SITE_PERL%%/Bio/Phylo/Taxa
- at dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Service
- at dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS/Resource
- at dirrm %%SITE_PERL%%/Bio/Phylo/PhyloWS
- at dirrm %%SITE_PERL%%/Bio/Phylo/Parsers
- at dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/Meta
- at dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Element
- at dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM/Document
- at dirrm %%SITE_PERL%%/Bio/Phylo/NeXML/DOM
- at dirrm %%SITE_PERL%%/Bio/Phylo/NeXML
- at dirrm %%SITE_PERL%%/Bio/Phylo/Models/Substitution/Dna
- at dirrm %%SITE_PERL%%/Bio/Phylo/Models/Substitution
- at dirrm %%SITE_PERL%%/Bio/Phylo/Models
- at dirrm %%SITE_PERL%%/Bio/Phylo/Mediators
- at dirrm %%SITE_PERL%%/Bio/Phylo/Matrices/Datatype
- at dirrm %%SITE_PERL%%/Bio/Phylo/Matrices
- at dirrm %%SITE_PERL%%/Bio/Phylo/Forest
- at dirrm %%SITE_PERL%%/Bio/Phylo
- at dirrmtry %%SITE_PERL%%/Bio
- at dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Phylo
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio

Modified: head/biology/p5-Bio-SCF/pkg-plist
==============================================================================
--- head/biology/p5-Bio-SCF/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-Bio-SCF/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -3,7 +3,3 @@
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF/SCF.so
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF/.packlist
 %%PERL5_MAN3%%/Bio::SCF.3.gz
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/SCF
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/Bio/SCF
- at dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/Bio

Modified: head/biology/p5-bioperl-run/pkg-plist
==============================================================================
--- head/biology/p5-bioperl-run/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-bioperl-run/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -261,25 +261,3 @@ bin/bp_run_protdist
 %%PORTDOCS%%%%DOCSDIR%%/Changes
 %%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
 %%PORTDOCS%%%%DOCSDIR%%/README
- at dirrmtry %%SITE_PERL%%/Bio/DB/ESoap
- at dirrmtry %%SITE_PERL%%/Bio/DB/SoapEUtilities/FetchAdaptor
- at dirrmtry %%SITE_PERL%%/Bio/DB/SoapEUtilities
- at dirrmtry %%SITE_PERL%%/Bio/Installer
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Alignment
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Analysis
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BEDTools
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BWA
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/BlastPlus
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Bowtie
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Maq
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Njtree
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phast
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Phylo
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/Samtools
- at dirrmtry %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus
-%%PORTDOCS%%@dirrmtry %%DOCSDIR%%

Modified: head/biology/p5-bioperl/pkg-plist
==============================================================================
--- head/biology/p5-bioperl/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/p5-bioperl/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -1937,159 +1937,3 @@ man/man1/bp_unflatten_seq.pl.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl
- at dirrm %%SITE_PERL%%/Bio/Align
- at dirrm %%SITE_PERL%%/Bio/AlignIO/Handler
- at dirrm %%SITE_PERL%%/Bio/AlignIO
- at dirrm %%SITE_PERL%%/Bio/Annotation
- at dirrm %%SITE_PERL%%/Bio/Assembly/IO
- at dirrm %%SITE_PERL%%/Bio/Assembly/Tools
- at dirrm %%SITE_PERL%%/Bio/Assembly
- at dirrm %%SITE_PERL%%/Bio/Cluster
- at dirrm %%SITE_PERL%%/Bio/ClusterIO
- at dirrm %%SITE_PERL%%/Bio/CodonUsage
- at dirrm %%SITE_PERL%%/Bio/Coordinate/Result
- at dirrm %%SITE_PERL%%/Bio/Coordinate
- at dirrm %%SITE_PERL%%/Bio/DB/Expression
- at dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB
- at dirrm %%SITE_PERL%%/Bio/DB/Flat
- at dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/berkeleydb
- at dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/dbi
- at dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor/memory
- at dirrm %%SITE_PERL%%/Bio/DB/GFF/Adaptor
- at dirrm %%SITE_PERL%%/Bio/DB/GFF/Aggregator
- at dirrm %%SITE_PERL%%/Bio/DB/GFF/Util
- at dirrm %%SITE_PERL%%/Bio/DB/GFF
- at dirrm %%SITE_PERL%%/Bio/DB/HIV
- at dirrm %%SITE_PERL%%/Bio/DB/Query
- at dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store/DBI
- at dirrm %%SITE_PERL%%/Bio/DB/SeqFeature/Store
- at dirrm %%SITE_PERL%%/Bio/DB/SeqFeature
- at dirrm %%SITE_PERL%%/Bio/DB/SeqVersion
- at dirrm %%SITE_PERL%%/Bio/DB/TFBS
- at dirrm %%SITE_PERL%%/Bio/DB/Taxonomy
- at dirrm %%SITE_PERL%%/Bio/DB
- at dirrm %%SITE_PERL%%/Bio/Das
- at dirrm %%SITE_PERL%%/Bio/Draw
- at dirrm %%SITE_PERL%%/Bio/Event
- at dirrm %%SITE_PERL%%/Bio/Factory
- at dirrm %%SITE_PERL%%/Bio/Index
- at dirrm %%SITE_PERL%%/Bio/LiveSeq/IO
- at dirrm %%SITE_PERL%%/Bio/LiveSeq
- at dirrm %%SITE_PERL%%/Bio/Location
- at dirrm %%SITE_PERL%%/Bio/Map
- at dirrm %%SITE_PERL%%/Bio/MapIO
- at dirrm %%SITE_PERL%%/Bio/Matrix/IO
- at dirrm %%SITE_PERL%%/Bio/Matrix/PSM/IO
- at dirrm %%SITE_PERL%%/Bio/Matrix/PSM
- at dirrm %%SITE_PERL%%/Bio/Matrix
- at dirrm %%SITE_PERL%%/Bio/MolEvol
- at dirrm %%SITE_PERL%%/Bio/Nexml
- at dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine
- at dirrm %%SITE_PERL%%/Bio/Ontology
- at dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
- at dirrm %%SITE_PERL%%/Bio/OntologyIO
- at dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH
- at dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM
- at dirrm %%SITE_PERL%%/Bio/Phenotype
- at dirrm %%SITE_PERL%%/Bio/PhyloNetwork
- at dirrm %%SITE_PERL%%/Bio/PopGen/IO
- at dirrm %%SITE_PERL%%/Bio/PopGen/Simulation
- at dirrm %%SITE_PERL%%/Bio/PopGen
- at dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme
- at dirrm %%SITE_PERL%%/Bio/Restriction/IO
- at dirrm %%SITE_PERL%%/Bio/Restriction
- at dirrm %%SITE_PERL%%/Bio/Root
- at dirrm %%SITE_PERL%%/Bio/Search/HSP
- at dirrm %%SITE_PERL%%/Bio/Search/Hit
- at dirrm %%SITE_PERL%%/Bio/Search/Iteration
- at dirrm %%SITE_PERL%%/Bio/Search/Result
- at dirrm %%SITE_PERL%%/Bio/Search/Tiling
- at dirrm %%SITE_PERL%%/Bio/Search
- at dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
- at dirrm %%SITE_PERL%%/Bio/SearchIO/XML
- at dirrm %%SITE_PERL%%/Bio/SearchIO
- at dirrm %%SITE_PERL%%/Bio/Seq/Meta
- at dirrm %%SITE_PERL%%/Bio/Seq
- at dirrm %%SITE_PERL%%/Bio/SeqEvolution
- at dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
- at dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA
- at dirrm %%SITE_PERL%%/Bio/SeqFeature/Tools
- at dirrm %%SITE_PERL%%/Bio/SeqFeature
- at dirrm %%SITE_PERL%%/Bio/SeqIO/Handler
- at dirrm %%SITE_PERL%%/Bio/SeqIO/game
- at dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
- at dirrm %%SITE_PERL%%/Bio/SeqIO
- at dirrm %%SITE_PERL%%/Bio/Structure/IO
- at dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
- at dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE
- at dirrm %%SITE_PERL%%/Bio/Structure/SecStr
- at dirrm %%SITE_PERL%%/Bio/Structure
- at dirrm %%SITE_PERL%%/Bio/Symbol
- at dirrm %%SITE_PERL%%/Bio/Taxonomy
- at dirrm %%SITE_PERL%%/Bio/Tools/Alignment
- at dirrm %%SITE_PERL%%/Bio/Tools/Analysis/DNA
- at dirrm %%SITE_PERL%%/Bio/Tools/Analysis/Protein
- at dirrm %%SITE_PERL%%/Bio/Tools/Analysis
- at dirrm %%SITE_PERL%%/Bio/Tools/EMBOSS
- at dirrm %%SITE_PERL%%/Bio/Tools/HMMER
- at dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy
- at dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML
- at dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Phylip
- at dirrm %%SITE_PERL%%/Bio/Tools/Phylo
- at dirrm %%SITE_PERL%%/Bio/Tools/Prediction
- at dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor
- at dirrm %%SITE_PERL%%/Bio/Tools/Primer
- at dirrm %%SITE_PERL%%/Bio/Tools/Run/WrapperBase
- at dirrm %%SITE_PERL%%/Bio/Tools/Run
- at dirrm %%SITE_PERL%%/Bio/Tools/SeqPattern
- at dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset
- at dirrm %%SITE_PERL%%/Bio/Tools/SiRNA
- at dirrm %%SITE_PERL%%/Bio/Tools/Signalp
- at dirrm %%SITE_PERL%%/Bio/Tools/Sim4
- at dirrm %%SITE_PERL%%/Bio/Tools/Spidey
- at dirrm %%SITE_PERL%%/Bio/Tools
- at dirrm %%SITE_PERL%%/Bio/Tree/Draw
- at dirrm %%SITE_PERL%%/Bio/Tree
- at dirrm %%SITE_PERL%%/Bio/TreeIO
- at dirrm %%SITE_PERL%%/Bio/Variation/IO
- at dirrm %%SITE_PERL%%/Bio/Variation
- at dirrm %%DATADIR%%/models
- at dirrm %%DATADIR%%/scripts/Bio-DB-GFF
- at dirrm %%DATADIR%%/scripts/Bio-DB-SeqFeature-Store
- at dirrm %%DATADIR%%/scripts/DB
- at dirrm %%DATADIR%%/scripts/DB-HIV
- at dirrm %%DATADIR%%/scripts/das
- at dirrm %%DATADIR%%/scripts/index
- at dirrm %%DATADIR%%/scripts/popgen
- at dirrm %%DATADIR%%/scripts/searchio
- at dirrm %%DATADIR%%/scripts/seq
- at dirrm %%DATADIR%%/scripts/seqstats
- at dirrm %%DATADIR%%/scripts/taxa
- at dirrm %%DATADIR%%/scripts/tree
- at dirrm %%DATADIR%%/scripts/utilities
- at dirrm %%DATADIR%%/scripts
- at dirrm %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/align
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/cluster
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/contributed
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/db
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/liveseq
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/popgen
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/quality
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/searchio
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sirna
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/structure
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tk
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tools
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tree
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%

Modified: head/biology/paml/pkg-plist
==============================================================================
--- head/biology/paml/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/paml/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -8,4 +8,3 @@ bin/yn00
 %%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
-%%PORTDOCS%%@dirrm %%DOCSDIR%%

Modified: head/biology/phylip/pkg-plist
==============================================================================
--- head/biology/phylip/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/phylip/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -41,4 +41,3 @@ lib/libdrawtree.so
 %%DATADIR%%/font4
 %%DATADIR%%/font5
 %%DATADIR%%/font6
- at dirrm %%DATADIR%%

Modified: head/biology/platon/pkg-plist
==============================================================================
--- head/biology/platon/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/platon/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -72,13 +72,3 @@ bin/pluton
 %%DOCSDIR%%/s913a.res
 %%DOCSDIR%%/sucrose.spf
 %%PORTDOCS%%%%DOCSDIR%%/platon_html.tar.gz
- at dirrm %%DOCSDIR%%/TEST/ABSORB_EXAMPLE
- at dirrm %%DOCSDIR%%/TEST/ABSTOMPA_EXAMPLE
- at dirrm %%DOCSDIR%%/TEST/ABSTOMPA_TEST
- at dirrm %%DOCSDIR%%/TEST/ADDSYM_EXAMPLE
- at dirrm %%DOCSDIR%%/TEST/ASYM_EXAMPLE
- at dirrm %%DOCSDIR%%/TEST/MULABS_EXAMPLE
- at dirrm %%DOCSDIR%%/TEST/PSICOR_EXAMPLE
- at dirrm %%DOCSDIR%%/TEST/SQUEEZE_EXAMPLE
- at dirrm %%DOCSDIR%%/TEST
- at dirrm %%DOCSDIR%%

Modified: head/biology/protomol/pkg-plist
==============================================================================
--- head/biology/protomol/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/protomol/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -112,17 +112,3 @@ bin/xyzviz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.spce.par
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.spce.psf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/water_648/water648.tip3.par
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/coulomb_309
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_water_184x
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/argon_400
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/bpti_water_1101
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/bpti_water_14281
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/butane_4
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/alanine_dipeptide_23
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/decalanine_66
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/electrons_22
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/methane_ethane_xxx
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/testset
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/water_216
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/water_648
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%

Modified: head/biology/ruby-bio/pkg-plist
==============================================================================
--- head/biology/ruby-bio/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/ruby-bio/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -330,65 +330,3 @@ bin/br_bioflat
 bin/br_biogetseq
 bin/br_pmfetch
 etc/bioinformatics/seqdatabase.ini.sample
- at dirrm etc/bioinformatics
- at dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/single_strand
- at dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range/sequence_range
- at dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/range
- at dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme/double_stranded
- at dirrm %%RUBY_SITELIBDIR%%/bio/util/restriction_enzyme
- at dirrm %%RUBY_SITELIBDIR%%/bio/util/color_scheme
- at dirrm %%RUBY_SITELIBDIR%%/bio/util
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby/generators
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins/bioruby
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor/plugins
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails/vendor
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/rails
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell/plugin
- at dirrm %%RUBY_SITELIBDIR%%/bio/shell
- at dirrm %%RUBY_SITELIBDIR%%/bio/sequence
- at dirrm %%RUBY_SITELIBDIR%%/bio/io/flatfile
- at dirrm %%RUBY_SITELIBDIR%%/bio/io/biosql/config
- at dirrm %%RUBY_SITELIBDIR%%/bio/io/biosql
- at dirrm %%RUBY_SITELIBDIR%%/bio/io
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/sanger_chromatogram
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/phyloxml
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/pdb
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/kegg
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/genbank
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/fastq
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/fasta
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/embl
- at dirrm %%RUBY_SITELIBDIR%%/bio/db/biosql
- at dirrm %%RUBY_SITELIBDIR%%/bio/db
- at dirrm %%RUBY_SITELIBDIR%%/bio/data
- at dirrm %%RUBY_SITELIBDIR%%/bio/compat
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/tmhmm
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/targetp
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/spidey
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/sosui
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/sim4
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/psort
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/phylip
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/yn00
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/codeml
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml/baseml
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/paml
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/meme/mast
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/meme
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/mafft
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/iprscan
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/hmmer
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/genscan
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/gcg
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/fasta
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/clustalw
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/blat
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/blast
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl/bl2seq
- at dirrm %%RUBY_SITELIBDIR%%/bio/appl
- at dirrm %%RUBY_SITELIBDIR%%/bio
- at dirrm %%RUBY_EXAMPLESDIR%%/bio
- at dirrm %%RUBY_DOCDIR%%/bio/ja
- at dirrm %%RUBY_DOCDIR%%/bio

Modified: head/biology/seqan/pkg-plist
==============================================================================
--- head/biology/seqan/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/seqan/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -2109,37 +2109,3 @@ include/seqan/version.h
 %%DATADIR%%/gapped_params/results_N73_H.dat
 %%DATADIR%%/gapped_params/results_N74_H.dat
 %%DATADIR%%/gapped_params/results_N75_H.dat
- at dirrm %%DATADIR%%/gapped_params
- at dirrm %%DATADIR%%/docs
- at dirrm %%DATADIR%%
- at dirrm include/seqan/system
- at dirrm include/seqan/store
- at dirrm include/seqan/statistics
- at dirrm include/seqan/sequence_journaled
- at dirrm include/seqan/sequence
- at dirrm include/seqan/seeds2
- at dirrm include/seqan/seeds
- at dirrm include/seqan/score
- at dirrm include/seqan/refinement
- at dirrm include/seqan/random
- at dirrm include/seqan/platform
- at dirrm include/seqan/pipe
- at dirrm include/seqan/parallel
- at dirrm include/seqan/modifier
- at dirrm include/seqan/misc
- at dirrm include/seqan/map
- at dirrm include/seqan/index
- at dirrm include/seqan/graph_types
- at dirrm include/seqan/graph_msa
- at dirrm include/seqan/graph_align
- at dirrm include/seqan/graph_algorithms
- at dirrm include/seqan/find_motif
- at dirrm include/seqan/find2
- at dirrm include/seqan/find
- at dirrm include/seqan/file
- at dirrm include/seqan/consensus
- at dirrm include/seqan/chaining
- at dirrm include/seqan/blast
- at dirrm include/seqan/basic
- at dirrm include/seqan/align
- at dirrm include/seqan

Modified: head/biology/tinker/pkg-plist
==============================================================================
--- head/biology/tinker/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/tinker/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -607,9 +607,3 @@ bin/xyzsybyl
 %%DATADIR%%/test/water.run
 %%DATADIR%%/test/water.xyz
 %%DATADIR%%/tinker.txt
- at dirrm %%DATADIR%%/test
- at dirrm %%DATADIR%%/params
- at dirrm %%DATADIR%%/bench
- at dirrm %%DATADIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%

Modified: head/biology/ugene/pkg-plist
==============================================================================
--- head/biology/ugene/pkg-plist	Mon Oct 20 07:03:48 2014	(r371236)
+++ head/biology/ugene/pkg-plist	Mon Oct 20 07:10:48 2014	(r371237)
@@ -1430,74 +1430,3 @@ share/pixmaps/ugene.xpm
 %%DATADIR%%/workflow_samples/users/Get the second half of sequence.usa
 %%DATADIR%%/workflow_samples/users/LinkData Fetch.usa
 %%DATADIR%%/workflow_samples/users/QualityFilter.usa
- at dirrm %%DATADIR%%/workflow_samples/users
- at dirrm %%DATADIR%%/workflow_samples/Transcriptomics
- at dirrm %%DATADIR%%/workflow_samples/Scenarios
- at dirrm %%DATADIR%%/workflow_samples/NGS/tuxedo
- at dirrm %%DATADIR%%/workflow_samples/NGS/cistrome
- at dirrm %%DATADIR%%/workflow_samples/NGS
- at dirrm %%DATADIR%%/workflow_samples/HMMER
- at dirrm %%DATADIR%%/workflow_samples/Data merging
- at dirrm %%DATADIR%%/workflow_samples/Data marking
- at dirrm %%DATADIR%%/workflow_samples/Custom elements
- at dirrm %%DATADIR%%/workflow_samples/Conversions
- at dirrm %%DATADIR%%/workflow_samples/Alignment
- at dirrm %%DATADIR%%/workflow_samples
- at dirrm %%DATADIR%%/weight_matrix
- at dirrm %%DATADIR%%/snp_scripts
- at dirrm %%DATADIR%%/sitecon_models/prokaryotic
- at dirrm %%DATADIR%%/sitecon_models/eukaryotic
- at dirrm %%DATADIR%%/sitecon_models
- at dirrm %%DATADIR%%/samples/Swiss-Prot
- at dirrm %%DATADIR%%/samples/Stockholm
- at dirrm %%DATADIR%%/samples/SCF
- at dirrm %%DATADIR%%/samples/Raw
- at dirrm %%DATADIR%%/samples/PDB
- at dirrm %%DATADIR%%/samples/Newick
- at dirrm %%DATADIR%%/samples/MSF
- at dirrm %%DATADIR%%/samples/MMDB
- at dirrm %%DATADIR%%/samples/HMM
- at dirrm %%DATADIR%%/samples/Genbank
- at dirrm %%DATADIR%%/samples/GFF
- at dirrm %%DATADIR%%/samples/FASTQ
- at dirrm %%DATADIR%%/samples/FASTA
- at dirrm %%DATADIR%%/samples/EMBL
- at dirrm %%DATADIR%%/samples/CLUSTALW
- at dirrm %%DATADIR%%/samples/Assembly
- at dirrm %%DATADIR%%/samples/ACE
- at dirrm %%DATADIR%%/samples/ABIF
- at dirrm %%DATADIR%%/samples
- at dirrm %%DATADIR%%/query_samples
- at dirrm %%DATADIR%%/primer3
- at dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/PNAS08
- at dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/NBT06
- at dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/GR09
- at dirrm %%DATADIR%%/position_weight_matrix/UniPROBE/Cell08
- at dirrm %%DATADIR%%/position_weight_matrix/UniPROBE
- at dirrm %%DATADIR%%/position_weight_matrix/JASPAR/vertebrates
- at dirrm %%DATADIR%%/position_weight_matrix/JASPAR/urochordates
- at dirrm %%DATADIR%%/position_weight_matrix/JASPAR/plants
- at dirrm %%DATADIR%%/position_weight_matrix/JASPAR/nematodes
- at dirrm %%DATADIR%%/position_weight_matrix/JASPAR/insects
- at dirrm %%DATADIR%%/position_weight_matrix/JASPAR/fungi
- at dirrm %%DATADIR%%/position_weight_matrix/JASPAR
- at dirrm %%DATADIR%%/position_weight_matrix
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
- at dirrm %%DATADIR%%/genome_lengths
- at dirrm %%DATADIR%%/enzymes
- at dirrm %%DATADIR%%/custom_annotations
- at dirrm %%DATADIR%%/cmdline
- at dirrm %%DATADIR%%/biostruct3d_plugin
- at dirrm %%DATADIR%%/back_translation/Yeast
- at dirrm %%DATADIR%%/back_translation/Viruses
- at dirrm %%DATADIR%%/back_translation/Vertebrates
- at dirrm %%DATADIR%%/back_translation/Rodents
- at dirrm %%DATADIR%%/back_translation/Primates
- at dirrm %%DATADIR%%/back_translation/Plants
- at dirrm %%DATADIR%%/back_translation/Mammalia
- at dirrm %%DATADIR%%/back_translation/Invertebrates
- at dirrm %%DATADIR%%/back_translation/Bacteria
- at dirrm %%DATADIR%%/back_translation
- at dirrm %%DATADIR%%
- at dirrm lib/ugene/plugins
- at dirrm lib/ugene

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