Attachment 77678 Details for Bug 111817 – py-biopython-1.43_1.42.patch

[patch] py-biopython-1.43_1.42.patch

py-biopython-1.43_1.42.patch (text/x-patch), 12.17 KB, created by P.BandieraPaiva on 2007-05-02 20:33:36 UTC

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Creator: P.BandieraPaiva

Created: 2007-05-02 20:33:36 UTC

Size: 12.17 KB

patch

obsolete

>diff -ruN /usr/ports/biology/py-biopython/Makefile /home/paiva/src/py-biopython/Makefile
>--- /usr/ports/biology/py-biopython/Makefile	Tue Oct 31 11:25:21 2006
>+++ /home/paiva/src/py-biopython/Makefile	Wed May  2 16:20:11 2007
>@@ -1,12 +1,12 @@
>-# New ports collection makefile for:	py-biopython
>-# Date created:		28 July 2000
>-# Whom:	      		Johann Visagie <johann@egenetics.com>
>+# New ports collection makefile for:    py-biopython
>+# Date created:         28 July 2000
>+# Whom:                 Johann Visagie <johann@egenetics.com>
> #
> # $FreeBSD: ports/biology/py-biopython/Makefile,v 1.22 2006/10/31 13:25:21 miwi Exp $
> #
> 
> PORTNAME=	biopython
>-PORTVERSION=	1.42
>+PORTVERSION=	1.43
> CATEGORIES=	biology python
> MASTER_SITES=	http://www.biopython.org/DIST/
> PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
>diff -ruN /usr/ports/biology/py-biopython/distinfo /home/paiva/src/py-biopython/distinfo
>--- /usr/ports/biology/py-biopython/distinfo	Tue Oct 31 11:25:21 2006
>+++ /home/paiva/src/py-biopython/distinfo	Tue Apr 17 21:33:14 2007
>@@ -1,3 +1,3 @@
>-MD5 (biopython-1.42.tar.gz) = 6d9bf58d0fcfa5a3b2053ad419069ff3
>-SHA256 (biopython-1.42.tar.gz) = ba4d00fdf7de67196ecba317dee09a14850b40596bd83d73e458c5f19fc9fc58
>-SIZE (biopython-1.42.tar.gz) = 3933507
>+MD5 (biopython-1.43.tar.gz) = 3c275b321bb1db7d8bda764913aaedcd
>+SHA256 (biopython-1.43.tar.gz) = eb424da9efddbf376c31660786ecb34ff893ea752bf7300f4a06d1b8c6ba175b
>+SIZE (biopython-1.43.tar.gz) = 3867907
>diff -ruN /usr/ports/biology/py-biopython/pkg-plist /home/paiva/src/py-biopython/pkg-plist
>--- /usr/ports/biology/py-biopython/pkg-plist	Tue Oct 31 11:25:21 2006
>+++ /home/paiva/src/py-biopython/pkg-plist	Wed Apr 18 17:15:10 2007
>@@ -323,6 +323,9 @@
> %%PYTHON_SITELIBDIR%%/Bio/GenBank/Record.py
> %%PYTHON_SITELIBDIR%%/Bio/GenBank/Record.pyc
> %%PYTHON_SITELIBDIR%%/Bio/GenBank/Record.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/GenBank/Scanner.py
>+%%PYTHON_SITELIBDIR%%/Bio/GenBank/Scanner.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/GenBank/Scanner.pyo
> %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.pyo
>@@ -389,6 +392,16 @@
> %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.py
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.py
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/_CKDTree.so
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.py
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyo
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyo
>@@ -642,6 +655,9 @@
> %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.py
> %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.pyc
> %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PDB/PSEA.py
>+%%PYTHON_SITELIBDIR%%/Bio/PDB/PSEA.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PDB/PSEA.pyo
> %%PYTHON_SITELIBDIR%%/Bio/PDB/Polypeptide.py
> %%PYTHON_SITELIBDIR%%/Bio/PDB/Polypeptide.pyc
> %%PYTHON_SITELIBDIR%%/Bio/PDB/Polypeptide.pyo
>@@ -793,9 +809,33 @@
> %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.py
> %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyc
> %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/ClustalIO.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/ClustalIO.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/ClustalIO.pyo
> %%PYTHON_SITELIBDIR%%/Bio/SeqIO/FASTA.py
> %%PYTHON_SITELIBDIR%%/Bio/SeqIO/FASTA.pyc
> %%PYTHON_SITELIBDIR%%/Bio/SeqIO/FASTA.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/FastaIO.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/FastaIO.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/FastaIO.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/InsdcIO.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/InsdcIO.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/InsdcIO.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/Interfaces.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/Interfaces.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/Interfaces.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/NexusIO.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/NexusIO.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/NexusIO.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/StockholmIO.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/StockholmIO.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/StockholmIO.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyo
> %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyo
>@@ -1154,91 +1194,92 @@
> %%PYTHON_SITELIBDIR%%/Martel/setup.py
> %%PYTHON_SITELIBDIR%%/Martel/setup.pyc
> %%PYTHON_SITELIBDIR%%/Martel/setup.pyo
>-@dirrm %%PYTHON_SITELIBDIR%%/Martel
>-@dirrm %%PYTHON_SITELIBDIR%%/BioSQL
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/config
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/Search
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/WWW
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/SwissProt
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/SubsMat
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Statistics
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Sequencing
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Saf
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Nexus
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/NMR
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/MultiProc
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/MEME
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Kabat
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/InterPro
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/HMM
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Selection
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Repair
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Mutation
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Application
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/CAPS
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Compass
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Data
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Data
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Compass
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/CAPS
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Application
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais
>-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Mutation
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Repair
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Selection
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/HMM
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/InterPro
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KDTree
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Kabat
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/MEME
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/MultiProc
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NMR
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Nexus
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Saf
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Sequencing
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Statistics
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SubsMat
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SwissProt
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/WWW
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/Search
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/config
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers
> @dirrm %%PYTHON_SITELIBDIR%%/Bio
>+@dirrm %%PYTHON_SITELIBDIR%%/BioSQL
>+@dirrm %%PYTHON_SITELIBDIR%%/Martel

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Attachments on bug 111817: 77676 | 77677 | 77678 | 77679