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Message-Id: <201007010746.o617kKEL014709@www.freebsd.org>
Date: Thu, 1 Jul 2010 07:46:20 GMT
From: Ju Pengfei <jupengfei@gmail.com>
To: freebsd-gnats-submit@FreeBSD.org
Subject: [update] biology/py-biopython
X-Send-Pr-Version: www-3.1
X-GNATS-Notify: mauricio@arareko.net

>Number:         148274
>Category:       ports
>Synopsis:       [update] biology/py-biopython
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    wen
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Thu Jul 01 07:50:04 UTC 2010
>Closed-Date:    Fri Jul 02 02:58:55 UTC 2010
>Last-Modified:  Fri Jul  2 03:00:08 UTC 2010
>Originator:     Ju Pengfei
>Release:        8.0-RELEASE-p3
>Organization:
Ju Pengfei
>Environment:
>Description:
update to 1.54.

Changes:
removed lang/py-mx-base from BUILD_DEPENDS;
lang/py-mx-base is no longer used at all.
(ref: http://biopython.org/DIST/docs/install/Installation.html#htoc17)
>How-To-Repeat:

>Fix:
apply this patch, please.
thanks.

Patch attached with submission follows:

diff -ruN py-biopython.bak/Makefile py-biopython/Makefile
--- py-biopython.bak/Makefile	2010-01-06 08:29:25.000000000 +0800
+++ py-biopython/Makefile	2010-07-01 15:13:26.000000000 +0800
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.53
+PORTVERSION=	1.54
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/DIST/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -14,8 +14,7 @@
 MAINTAINER=	mauricio@arareko.net
 COMMENT=	A collection of Python modules for bioinformatics
 
-BUILD_DEPENDS=	${PYNUMPY} \
-		${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
+BUILD_DEPENDS=	${PYNUMPY}
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
 USE_PYTHON=	2.4+
diff -ruN py-biopython.bak/distinfo py-biopython/distinfo
--- py-biopython.bak/distinfo	2010-01-06 08:29:25.000000000 +0800
+++ py-biopython/distinfo	2010-07-01 10:38:07.000000000 +0800
@@ -1,3 +1,3 @@
-MD5 (biopython-1.53.tar.gz) = df1004ec64b9b593c0e690c14a20667a
-SHA256 (biopython-1.53.tar.gz) = 0db8bf8d37641fdfc6a8aac248de3d8cb4111e55484deb43f67e8d7ad082013f
-SIZE (biopython-1.53.tar.gz) = 4284683
+MD5 (biopython-1.54.tar.gz) = d4c4ce5a3e1bb401928ca3dc3d1b08cd
+SHA256 (biopython-1.54.tar.gz) = 6f704698d68af75b3601b2a862386682b2317038b8bbaf2eb2ad68c1e1a4dc35
+SIZE (biopython-1.54.tar.gz) = 6445527
diff -ruN py-biopython.bak/pkg-plist py-biopython/pkg-plist
--- py-biopython.bak/pkg-plist	2010-01-06 08:29:25.000000000 +0800
+++ py-biopython/pkg-plist	2010-07-01 15:25:17.000000000 +0800
@@ -1,19 +1,3 @@
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py
-%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py
-%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py
-%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo
-@dirrm %%PYTHON_SITELIBDIR%%/BioSQL
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.py
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyo
@@ -189,6 +173,8 @@
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/HomoloGene.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd
@@ -219,29 +205,88 @@
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/PIR_General.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/PRF_General.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/SP_General.mod.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/XHTMLtablesetup.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivearticle.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-classes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-mixes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-models.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-modules.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/articlemeta.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/backmatter.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/chars.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/common.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/default-classes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/default-mixes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/display.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eInfo_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eLink_020511.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eLink_090910.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/ePost_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSearch_020511.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSpell.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSummary_041029.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/egquery.dtd
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pmc-1.dtd
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/elink_020122.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/format.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/htmltable.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsa.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsb.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsc.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsn.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamso.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsr.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isobox.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isocyr1.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isocyr2.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isodia.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk1.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk2.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk3.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk4.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isolat1.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isolat2.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isomfrk.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isomopf.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isomscr.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isonum.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isopub.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isotech.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/journalmeta.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/link.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/list.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/math.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mathml2-qname-1.mod
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mathml2.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mathmlsetup.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mmlalias.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mmlextra.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/modules.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_011101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_011101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_090101.dtd
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmserials_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/notat.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/para.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/phrase.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pmc-1.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_020114.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/references.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/section.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/taxon.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/xmlspecchars.ent
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.py
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyo
@@ -498,12 +543,12 @@
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.py
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.py
-%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.py
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.py
+%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyo
@@ -692,6 +737,36 @@
 %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyo
@@ -710,15 +785,18 @@
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py
-%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc
-%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.py
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyo
@@ -789,9 +867,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.py
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyo
@@ -810,6 +885,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.py
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.py
 %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyo
@@ -825,12 +903,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.py
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.py
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyo
@@ -855,6 +927,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyo
@@ -864,6 +939,12 @@
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyo
@@ -897,15 +978,15 @@
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.py
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.py
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyo
@@ -939,12 +1020,12 @@
 %%PYTHON_SITELIBDIR%%/Bio/Translate.py
 %%PYTHON_SITELIBDIR%%/Bio/Translate.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Translate.pyo
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.py
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyc
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyo
+%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyo
@@ -981,6 +1062,21 @@
 %%PYTHON_SITELIBDIR%%/Bio/utils.py
 %%PYTHON_SITELIBDIR%%/Bio/utils.pyc
 %%PYTHON_SITELIBDIR%%/Bio/utils.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Align/Applications
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
@@ -1035,6 +1131,7 @@
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Phylo
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop
@@ -1056,3 +1153,4 @@
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise
 @dirrm %%PYTHON_SITELIBDIR%%/Bio
+@dirrm %%PYTHON_SITELIBDIR%%/BioSQL


>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->wen 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Thu Jul 1 07:50:39 UTC 2010 
Responsible-Changed-Why:  
wen@ wants his PRs (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=148274 
State-Changed-From-To: open->feedback 
State-Changed-By: edwin 
State-Changed-When: Thu Jul 1 07:50:42 UTC 2010 
State-Changed-Why:  
Awaiting maintainers feedback (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=148274 

From: Edwin Groothuis <edwin@FreeBSD.org>
To: mauricio@arareko.net
Cc: bug-followup@FreeBSD.org
Subject: Re: ports/148274: [update] biology/py-biopython
Date: Thu, 1 Jul 2010 07:50:41 UT

 Maintainer of biology/py-biopython,
 
 Please note that PR ports/148274 has just been submitted.
 
 If it contains a patch for an upgrade, an enhancement or a bug fix
 you agree on, reply to this email stating that you approve the patch
 and a committer will take care of it.
 
 The full text of the PR can be found at:
     http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/148274
 
 -- 
 Edwin Groothuis via the GNATS Auto Assign Tool
 edwin@FreeBSD.org

From: Mauricio Herrera Cuadra <mauricio@arareko.net>
To: bug-followup@FreeBSD.org
Cc: Edwin Groothuis <edwin@FreeBSD.org>
Subject: Re: ports/148274: [update] biology/py-biopython
Date: Thu, 1 Jul 2010 07:32:26 -0700 (PDT)

 --0-1800490649-1277994746=:56974
 Content-Type: text/plain; charset=us-ascii
 
 Patch works fine. Approved. Thanks! :)
 
 
 
 ________________________________
 From: Edwin Groothuis <edwin@FreeBSD.org>
 To: mauricio@arareko.net
 Cc: bug-followup@FreeBSD.org
 Sent: Thu, July 1, 2010 2:50:41 AM
 Subject: Re: ports/148274: [update] biology/py-biopython
 
 Maintainer of biology/py-biopython,
 
 Please note that PR ports/148274 has just been submitted.
 
 If it contains a patch for an upgrade, an enhancement or a bug fix
 you agree on, reply to this email stating that you approve the patch
 and a committer will take care of it.
 
 The full text of the PR can be found at:
     http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/148274
 
 -- 
 Edwin Groothuis via the GNATS Auto Assign Tool
 edwin@FreeBSD.org
 
 --0-1800490649-1277994746=:56974
 Content-Type: text/html; charset=us-ascii
 
 <html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Patch works fine. Approved. Thanks! :)</div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: lucida console,sans-serif; font-size: 10pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Edwin Groothuis &lt;edwin@FreeBSD.org&gt;<br><b><span  style="font-weight: bold;">To:</span></b> mauricio@arareko.net<br><b><span style="font-weight: bold;">Cc:</span></b> bug-followup@FreeBSD.org<br><b><span style="font-weight: bold;">Sent:</span></b> Thu, July 1, 2010 2:50:41 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: ports/148274: [update] biology/py-biopython<br></font><br>Maintainer of biology/py-biopython,<br><br>Please note that PR ports/148274 has just been
  submitted.<br><br>If it contains a patch for an upgrade, an enhancement or a bug fix<br>you agree on, reply to this email stating that you approve the patch<br>and a committer will take care of it.<br><br>The full text of the PR can be found at:<br>&nbsp; &nbsp; <a href="http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/148274" target="_blank">http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/148274</a><br><br>-- <br>Edwin Groothuis via the GNATS Auto Assign Tool<br><a ymailto="mailto:edwin@FreeBSD.org" hre f="mailto:edwin@FreeBSD.org">edwin@FreeBSD.org</a><br></div></div>
 </div></body></html>
 --0-1800490649-1277994746=:56974--
State-Changed-From-To: feedback->closed 
State-Changed-By: wen 
State-Changed-When: Fri Jul 2 02:58:55 UTC 2010 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=148274 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/148274: commit references a PR
Date: Fri,  2 Jul 2010 02:58:42 +0000 (UTC)

 wen         2010-07-02 02:57:19 UTC
 
   FreeBSD ports repository
 
   Modified files:
     biology/py-biopython Makefile distinfo pkg-plist 
   Log:
   - Update to 1.54
   
   PR:             ports/148274
   Submitted by:   Ju Pengfei <jupengfei@gmail.com>
   Approved by:    maintainer
   Feature safe:   yes
   
   Revision  Changes    Path
   1.30      +2 -3      ports/biology/py-biopython/Makefile
   1.20      +3 -3      ports/biology/py-biopython/distinfo
   1.19      +141 -43   ports/biology/py-biopython/pkg-plist
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>Unformatted:
