Date: Fri, 21 Sep 2012 12:05:31 -0700 (PDT) From: Mauricio Herrera Cuadra <mauricio@arareko.net> To: "rm@FreeBSD.org" <rm@FreeBSD.org>, "freebsd-python@FreeBSD.org" <freebsd-python@FreeBSD.org> Subject: Re: ports/171115: [Update]biology/py-biopython:update to 1.60 Message-ID: <1348254331.43020.YahooMailNeo@web31813.mail.mud.yahoo.com> In-Reply-To: <201209171230.q8HCUkXG021906@freefall.freebsd.org> References: <201209171230.q8HCUkXG021906@freefall.freebsd.org>
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The patch is still wonky, please review the output: [root@freebsd9-vm] /usr/ports/biology/py-biopython # patch < biopython-1.60.diff.txt Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |Index: Makefile |=================================================================== |--- Makefile (revision 304395) |+++ Makefile (working copy) -------------------------- Patching file Makefile using Plan A... Hunk #1 failed at 1. 1 out of 1 hunks failed--saving rejects to Makefile.rej Hmm... The next patch looks like a unified diff to me... The text leading up to this was: -------------------------- |Index: pkg-descr |=================================================================== |--- pkg-descr (revision 304395) |+++ pkg-descr (working copy) -------------------------- Patching file pkg-descr using Plan A... Hunk #1 succeeded at 12. Hmm... The next patch looks like a unified diff to me... The text leading up to this was: -------------------------- |Index: distinfo |=================================================================== |--- distinfo (revision 304395) |+++ distinfo (working copy) -------------------------- Patching file distinfo using Plan A... Hunk #1 succeeded at 1. Hmm... The next patch looks like a unified diff to me... The text leading up to this was: -------------------------- |Index: pkg-plist |=================================================================== |--- pkg-plist (revision 304395) |+++ pkg-plist (working copy) -------------------------- Patching file pkg-plist using Plan A... Hunk #1 succeeded at 1. Hunk #2 succeeded at 103. Hunk #3 succeeded at 358. Hunk #4 succeeded at 451. Hunk #5 succeeded at 482. Hunk #6 succeeded at 509. Hunk #7 succeeded at 570. Hunk #8 succeeded at 658. Hunk #9 succeeded at 686. Hunk #10 succeeded at 707. Hunk #11 succeeded at 861. Hunk #12 succeeded at 1017. Hunk #13 succeeded at 1033. Hunk #14 succeeded at 1055. done [root@freebsd9-vm] /usr/ports/biology/py-biopython # cat Makefile.rej *************** *** 1,29 **** - # New ports collection makefile for: py-biopython - # Date created: 28 July 2000 - # Whom: Johann Visagie <johann@egenetics.com> - # # $FreeBSD$ - # PORTNAME= biopython - PORTVERSION= 1.59 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= mauricio@arareko.net - COMMENT= A collection of Python modules for bioinformatics BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} - USE_PYTHON= 2.5-2.7 USE_PYDISTUTILS= easy_install PYEASYINSTALL_ARCHDEP= yes .if !defined(WITHOUT_REPORTLAB) - BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab - RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab .endif .include <bsd.port.mk> --- 1,23 ---- # $FreeBSD$ PORTNAME= biopython + PORTVERSION= 1.60 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= mauricio@arareko.net + COMMENT= Collection of Python modules for bioinformatics BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} + USE_PYTHON= -2.7 USE_PYDISTUTILS= easy_install PYEASYINSTALL_ARCHDEP= yes .if !defined(WITHOUT_REPORTLAB) + RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}reportlab>0:${PORTSDIR}/print/py-reportlab .endif .include <bsd.port.mk> ________________________________ From: "rm@FreeBSD.org" <rm@FreeBSD.org> To: mauricio@arareko.net; rm@FreeBSD.org; freebsd-python@FreeBSD.org; rm@FreeBSD.org Sent: Monday, September 17, 2012 7:30 AM Subject: Re: ports/171115: [Update]biology/py-biopython:update to 1.60 Synopsis: [Update]biology/py-biopython:update to 1.60 Responsible-Changed-From-To: freebsd-python->rm Responsible-Changed-By: rm Responsible-Changed-When: Mon Sep 17 12:30:45 UTC 2012 Responsible-Changed-Why: Take. Hi Mauricio. Here is 'assembled' patch (that was mangled by gnats) from Wen plus some of my changes: 1. trim Makefile header 2. remove undefined article from COMMENT 3. change USE_PYTHON to just -2.7 4. remove reportlab from BUILD_DEPENDS 5. remove deprecated Authors: field from pkg-descr 6. tab -> space change in pkg-descr:WWW. Here is the patch: http://people.freebsd.org/~rm/biopython-1.60.diff.txt and here is the buildlog: http://people.freebsd.org/~rm/py27-biopython-1.60.log. Would you approve? http://www.freebsd.org/cgi/query-pr.cgi?pr=171115help
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