ports/127776: [Update]biology/py-biopython:update to 1.48

[Wen heping]

>Number:         127776
>Category:       ports
>Synopsis:       [Update]biology/py-biopython:update to 1.48
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Wed Oct 01 14:00:05 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     Wen heping
>Release:        FreeBSD 7.0 release
>Organization:
ChangAn Middle School
>Environment:
FreeBSD tinderbox.wenjing.com 7.0-RELEASE FreeBSD 7.0-RELEASE #0: Sun Feb 24 19:59:52 UTC 2008     root at logan.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  i386
>Description:
update to 1.48 from 1.47

>How-To-Repeat:

>Fix:


Patch attached with submission follows:

--- Makefile.orig	2008-10-01 23:47:52.000000000 +0800
+++ Makefile	2008-10-01 23:47:52.000000000 +0800
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.47
+PORTVERSION=	1.48
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/DIST/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
--- distinfo.orig	2008-10-01 23:47:52.000000000 +0800
+++ distinfo	2008-10-01 23:47:52.000000000 +0800
@@ -1,3 +1,3 @@
-MD5 (biopython-1.47.tar.gz) = d4906278f7f0d0054f20ea73565fdf43
-SHA256 (biopython-1.47.tar.gz) = a83544c3ed155acfa3f38929b44a890e77806799399193e48b8787efa89b6213
-SIZE (biopython-1.47.tar.gz) = 4114907
+MD5 (biopython-1.48.tar.gz) = b049e3af8128bea68e4e86b55c6d0996
+SHA256 (biopython-1.48.tar.gz) = cfb3a1774d1d4b01a66b3428cec7b4c943517b2485e0ca577a6b540818f29cb0
+SIZE (biopython-1.48.tar.gz) = 4149100
--- pkg-plist.orig	2008-10-01 23:47:52.000000000 +0800
+++ pkg-plist	2008-10-01 23:47:52.000000000 +0800
@@ -227,6 +227,12 @@
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.py
+%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Emboss/PrimerSearch.py
+%%PYTHON_SITELIBDIR%%/Bio/Emboss/PrimerSearch.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Emboss/PrimerSearch.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyo
@@ -914,12 +920,18 @@
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PirIO.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PirIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PirIO.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/TabIO.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/TabIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/TabIO.pyo
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyo
@@ -1001,18 +1013,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/WWW/ExPASy.py
-%%PYTHON_SITELIBDIR%%/Bio/WWW/ExPASy.pyc
-%%PYTHON_SITELIBDIR%%/Bio/WWW/ExPASy.pyo
-%%PYTHON_SITELIBDIR%%/Bio/WWW/InterPro.py
-%%PYTHON_SITELIBDIR%%/Bio/WWW/InterPro.pyc
-%%PYTHON_SITELIBDIR%%/Bio/WWW/InterPro.pyo
-%%PYTHON_SITELIBDIR%%/Bio/WWW/NCBI.py
-%%PYTHON_SITELIBDIR%%/Bio/WWW/NCBI.pyc
-%%PYTHON_SITELIBDIR%%/Bio/WWW/NCBI.pyo
-%%PYTHON_SITELIBDIR%%/Bio/WWW/SCOP.py
-%%PYTHON_SITELIBDIR%%/Bio/WWW/SCOP.pyc
-%%PYTHON_SITELIBDIR%%/Bio/WWW/SCOP.pyo
 %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyo
@@ -1031,9 +1031,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/biblio.py
-%%PYTHON_SITELIBDIR%%/Bio/biblio.pyc
-%%PYTHON_SITELIBDIR%%/Bio/biblio.pyo
 %%PYTHON_SITELIBDIR%%/Bio/builders/Search/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/builders/Search/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/builders/Search/__init__.pyo


>Release-Note:
>Audit-Trail:
>Unformatted: