Date: Mon, 11 Sep 2000 16:46:05 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/21202: Update port: biology/py-biopython Message-ID: <E13YUqT-000EnA-00@fling.sanbi.ac.za>
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>Number: 21202 >Category: ports >Synopsis: Update port: biology/py-biopython >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Sep 11 07:50:01 PDT 2000 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 3.5-STABLE i386 >Organization: Electric Genetics >Environment: >Description: Update port biology/py-biopython from 0.90.d02 to 0.90.d03 The port now utilises the new variables defined bsd.python.mk >How-To-Repeat: >Fix: diff -ruN py-biopython.bak/Makefile py-biopython/Makefile --- py-biopython.bak/Makefile Mon Sep 11 11:50:57 2000 +++ py-biopython/Makefile Mon Sep 11 11:59:06 2000 @@ -6,22 +6,23 @@ # PORTNAME= biopython -PORTVERSION= 0.90.d02 +PORTVERSION= 0.90.d03 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/Download/ PKGNAMEPREFIX= py- -DISTNAME= biopython-0.90-d02 +DISTNAME= biopython-0.90-d03 MAINTAINER= johann@egenetics.com -BUILD_DEPENDS= python1.5:${PORTSDIR}/lang/python15 \ - ${LOCALBASE}/lib/python1.5/site-packages/Numeric/Numeric.py:${PORTSDIR}/math/numpy \ - ${LOCALBASE}/lib/python1.5/site-packages/distutils/core.py:${PORTSDIR}/misc/py-distutils +USE_PYTHON= yes + +BUILD_DEPENDS= ${PYDISTUTILS} \ + ${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/numpy do-build: - @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} python setup.py build) + @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py build) do-install: - @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} python setup.py install) + @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py install) .include <bsd.port.mk> diff -ruN py-biopython.bak/files/md5 py-biopython/files/md5 --- py-biopython.bak/files/md5 Mon Sep 11 11:50:57 2000 +++ py-biopython/files/md5 Thu Sep 7 13:16:11 2000 @@ -1 +1 @@ -MD5 (biopython-0.90-d02.tar.gz) = 56a53fa96765318cb053fc266e337ba9 +MD5 (biopython-0.90-d03.tar.gz) = 6eba4ef18fee09f47c127d44667a3d5c diff -ruN py-biopython.bak/pkg/PLIST py-biopython/pkg/PLIST --- py-biopython.bak/pkg/PLIST Mon Sep 11 11:50:57 2000 +++ py-biopython/pkg/PLIST Mon Sep 11 13:35:29 2000 @@ -1,124 +1,143 @@ -lib/python1.5/site-packages/Bio/__init__.py -lib/python1.5/site-packages/Bio/ParserSupport.py -lib/python1.5/site-packages/Bio/Seq.py -lib/python1.5/site-packages/Bio/Index.py -lib/python1.5/site-packages/Bio/PropertyManager.py -lib/python1.5/site-packages/Bio/File.py -lib/python1.5/site-packages/Bio/Sequence.py -lib/python1.5/site-packages/Bio/utils.py -lib/python1.5/site-packages/Bio/SeqRecord.py -lib/python1.5/site-packages/Bio/SwissProt/__init__.py -lib/python1.5/site-packages/Bio/SwissProt/KeyWList.py -lib/python1.5/site-packages/Bio/SwissProt/SProt.py -lib/python1.5/site-packages/Bio/Blast/__init__.py -lib/python1.5/site-packages/Bio/Blast/NCBIWWW.py -lib/python1.5/site-packages/Bio/Blast/Record.py -lib/python1.5/site-packages/Bio/Blast/NCBIStandalone.py -lib/python1.5/site-packages/Bio/Enzyme/__init__.py -lib/python1.5/site-packages/Bio/Enzyme/Enzyme.py -lib/python1.5/site-packages/Bio/Fasta/__init__.py -lib/python1.5/site-packages/Bio/Fasta/Fasta.py -lib/python1.5/site-packages/Bio/PDB/__init__.py -lib/python1.5/site-packages/Bio/Prosite/__init__.py -lib/python1.5/site-packages/Bio/Prosite/Prosite.py -lib/python1.5/site-packages/Bio/Prosite/Pattern.py -lib/python1.5/site-packages/Bio/Prosite/Prodoc.py -lib/python1.5/site-packages/Bio/Medline/Medline.py -lib/python1.5/site-packages/Bio/Medline/PubMed.py -lib/python1.5/site-packages/Bio/Medline/__init__.py -lib/python1.5/site-packages/Bio/Data/IUPACData.py -lib/python1.5/site-packages/Bio/Data/__init__.py -lib/python1.5/site-packages/Bio/Data/CodonTable.py -lib/python1.5/site-packages/Bio/Entrez/__init__.py -lib/python1.5/site-packages/Bio/Tools/mathfns.py -lib/python1.5/site-packages/Bio/Tools/__init__.py -lib/python1.5/site-packages/Bio/Tools/Transcribe.py -lib/python1.5/site-packages/Bio/Tools/listfns.py -lib/python1.5/site-packages/Bio/Tools/stringfns.py -lib/python1.5/site-packages/Bio/Tools/Translate.py -lib/python1.5/site-packages/Bio/Tools/Classification/__init__.py -lib/python1.5/site-packages/Bio/Tools/Classification/NaiveBayes.py -lib/python1.5/site-packages/Bio/Tools/Classification/SVM.py -lib/python1.5/site-packages/Bio/Tools/Classification/kNN.py -lib/python1.5/site-packages/Bio/WWW/__init__.py -lib/python1.5/site-packages/Bio/WWW/NCBI.py -lib/python1.5/site-packages/Bio/WWW/ExPASy.py -lib/python1.5/site-packages/Bio/WWW/SCOP.py -lib/python1.5/site-packages/Bio/Alphabet/__init__.py -lib/python1.5/site-packages/Bio/Alphabet/IUPAC.py -lib/python1.5/site-packages/Bio/Encodings/IUPACEncoding.py -lib/python1.5/site-packages/Bio/Encodings/__init__.py -lib/python1.5/site-packages/Bio/SeqIO/__init__.py -lib/python1.5/site-packages/Bio/SeqIO/FASTA.py -lib/python1.5/site-packages/Bio/PDB/__init__.pyc -lib/python1.5/site-packages/Bio/WWW/__init__.pyc -lib/python1.5/site-packages/Bio/WWW/NCBI.pyc -lib/python1.5/site-packages/Bio/WWW/ExPASy.pyc -lib/python1.5/site-packages/Bio/WWW/SCOP.pyc -lib/python1.5/site-packages/Bio/Data/IUPACData.pyc -lib/python1.5/site-packages/Bio/Data/__init__.pyc -lib/python1.5/site-packages/Bio/Data/CodonTable.pyc -lib/python1.5/site-packages/Bio/Encodings/IUPACEncoding.pyc -lib/python1.5/site-packages/Bio/Encodings/__init__.pyc -lib/python1.5/site-packages/Bio/__init__.pyc -lib/python1.5/site-packages/Bio/Blast/__init__.pyc -lib/python1.5/site-packages/Bio/Blast/NCBIWWW.pyc -lib/python1.5/site-packages/Bio/Blast/Record.pyc -lib/python1.5/site-packages/Bio/Blast/NCBIStandalone.pyc -lib/python1.5/site-packages/Bio/SeqIO/__init__.pyc -lib/python1.5/site-packages/Bio/SeqIO/FASTA.pyc -lib/python1.5/site-packages/Bio/ParserSupport.pyc -lib/python1.5/site-packages/Bio/Medline/Medline.pyc -lib/python1.5/site-packages/Bio/Medline/PubMed.pyc -lib/python1.5/site-packages/Bio/Medline/__init__.pyc -lib/python1.5/site-packages/Bio/Tools/mathfns.pyc -lib/python1.5/site-packages/Bio/Tools/__init__.pyc -lib/python1.5/site-packages/Bio/Tools/Transcribe.pyc -lib/python1.5/site-packages/Bio/Tools/listfns.pyc -lib/python1.5/site-packages/Bio/Tools/stringfns.pyc -lib/python1.5/site-packages/Bio/Tools/Translate.pyc -lib/python1.5/site-packages/Bio/Tools/Classification/__init__.pyc -lib/python1.5/site-packages/Bio/Tools/Classification/NaiveBayes.pyc -lib/python1.5/site-packages/Bio/Tools/Classification/SVM.pyc -lib/python1.5/site-packages/Bio/Tools/Classification/kNN.pyc -lib/python1.5/site-packages/Bio/Seq.pyc -lib/python1.5/site-packages/Bio/Index.pyc -lib/python1.5/site-packages/Bio/SwissProt/__init__.pyc -lib/python1.5/site-packages/Bio/SwissProt/KeyWList.pyc -lib/python1.5/site-packages/Bio/SwissProt/SProt.pyc -lib/python1.5/site-packages/Bio/Fasta/__init__.pyc -lib/python1.5/site-packages/Bio/Fasta/Fasta.pyc -lib/python1.5/site-packages/Bio/Alphabet/__init__.pyc -lib/python1.5/site-packages/Bio/Alphabet/IUPAC.pyc -lib/python1.5/site-packages/Bio/PropertyManager.pyc -lib/python1.5/site-packages/Bio/File.pyc -lib/python1.5/site-packages/Bio/Sequence.pyc -lib/python1.5/site-packages/Bio/utils.pyc -lib/python1.5/site-packages/Bio/Entrez/__init__.pyc -lib/python1.5/site-packages/Bio/Enzyme/__init__.pyc -lib/python1.5/site-packages/Bio/Enzyme/Enzyme.pyc -lib/python1.5/site-packages/Bio/SeqRecord.pyc -lib/python1.5/site-packages/Bio/Prosite/__init__.pyc -lib/python1.5/site-packages/Bio/Prosite/Prosite.pyc -lib/python1.5/site-packages/Bio/Prosite/Pattern.pyc -lib/python1.5/site-packages/Bio/Prosite/Prodoc.pyc -lib/python1.5/site-packages/Bio/Tools/Classification/cSVM.so -lib/python1.5/site-packages/Bio/Tools/clistfns.so -lib/python1.5/site-packages/Bio/Tools/cmathfns.so -lib/python1.5/site-packages/Bio/Tools/cstringfns.so -@dirrm lib/python1.5/site-packages/Bio/WWW -@dirrm 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+lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Lin.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Location.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Lin.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Location.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/__init__.pyc +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Prosite +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/PDB +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Entrez +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Encodings +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Data +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Rebase +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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