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:=0A=0A[root@freebsd9-vm]= /usr/ports/biology/py-biopython # patch < biopython-1.60.diff.txt =0AHmm..= .=A0 Looks like a unified diff to me...=0AThe text leading up to this was:= =0A--------------------------=0A|Index: Makefile=0A|=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0A|--- Makefile=A0=A0=A0 (revision 304395)= =0A|+++ Makefile=A0=A0=A0 (working copy)=0A--------------------------=0APat= ching file Makefile using Plan A...=0AHunk #1 failed at 1.=0A1 out of 1 hun= ks failed--saving rejects to Makefile.rej=0AHmm...=A0 The next patch looks = like a unified diff to me...=0AThe text leading up to this was:=0A---------= -----------------=0A|Index: pkg-descr=0A|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=0A|--- pkg-descr=A0=A0=A0 (revision 304395)=0A|+++ pkg-d= escr=A0=A0=A0 (working copy)=0A--------------------------=0APatching file p= kg-descr using Plan A...=0AHunk #1 succeeded at 12.=0AHmm...=A0 The next pa= tch looks like a unified diff to me...=0AThe text leading up to this was:= =0A--------------------------=0A|Index: distinfo=0A|=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0A|--- distinfo=A0=A0=A0 (revision 304395)= =0A|+++ distinfo=A0=A0=A0 (working copy)=0A--------------------------=0APat= ching file distinfo using Plan A...=0AHunk #1 succeeded at 1.=0AHmm...=A0 T= he next patch looks like a unified diff to me...=0AThe text leading up to t= his was:=0A--------------------------=0A|Index: pkg-plist=0A|=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0A|--- pkg-plist=A0=A0=A0 (revision= 304395)=0A|+++ pkg-plist=A0=A0=A0 (working copy)=0A-----------------------= ---=0APatching file pkg-plist using Plan A...=0AHunk #1 succeeded at 1.=0AH= unk #2 succeeded at 103.=0AHunk #3 succeeded at 358.=0AHunk #4 succeeded at= 451.=0AHunk #5 succeeded at 482.=0AHunk #6 succeeded at 509.=0AHunk #7 suc= ceeded at 570.=0AHunk #8 succeeded at 658.=0AHunk #9 succeeded at 686.=0AHu= nk #10 succeeded at 707.=0AHunk #11 succeeded at 861.=0AHunk #12 succeeded = at 1017.=0AHunk #13 succeeded at 1033.=0AHunk #14 succeeded at 1055.=0Adone= =0A=0A=0A[root@freebsd9-vm] /usr/ports/biology/py-biopython # cat Makefile.= rej =0A***************=0A*** 1,29 ****=0A- # New ports collection makefile = for:=A0=A0=A0 py-biopython=0A- # Date created:=A0=A0=A0 =A0=A0=A0 28 July 2= 000=0A- # Whom:=A0=A0=A0 =A0=A0=A0 =A0=A0=A0 Johann Visagie <johann@egeneti= cs.com>=0A- #=0A=A0 # $FreeBSD$=0A- #=0A=A0 =0A=A0 PORTNAME=3D=A0=A0=A0 bio= python=0A- PORTVERSION=3D=A0=A0=A0 1.59=0A=A0 CATEGORIES=3D=A0=A0=A0 biolog= y python=0A=A0 MASTER_SITES=3D=A0=A0=A0 http://www.biopython.org/DIST/=0A= =A0 PKGNAMEPREFIX=3D=A0=A0=A0 ${PYTHON_PKGNAMEPREFIX}=0A=A0 =0A=A0 MAINTAIN= ER=3D=A0=A0=A0 mauricio@arareko.net=0A- COMMENT=3D=A0=A0=A0 A collection of= Python modules for bioinformatics=0A=A0 =0A=A0 BUILD_DEPENDS=3D=A0=A0=A0 $= {PYNUMPY}=0A=A0 RUN_DEPENDS=3D=A0=A0=A0 ${PYNUMPY}=0A=A0 =0A- USE_PYTHON=3D= =A0=A0=A0 =A0=A0=A0 2.5-2.7=0A=A0 USE_PYDISTUTILS=3D=A0=A0=A0 easy_install= =0A=A0 PYEASYINSTALL_ARCHDEP=3D=A0=A0=A0 yes=0A=A0 =0A=A0 .if !defined(WITH= OUT_REPORTLAB)=0A- BUILD_DEPENDS+=3D=A0=A0=A0 ${PYTHON_SITELIBDIR}/reportla= b/__init__.py:${PORTSDIR}/print/py-reportlab=0A- RUN_DEPENDS+=3D=A0=A0=A0 $= {PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab=0A= =A0 .endif=0A=A0 =0A=A0 .include <bsd.port.mk>=0A--- 1,23 ----=0A=A0 # $Fre= eBSD$=0A=A0 =0A=A0 PORTNAME=3D=A0=A0=A0 biopython=0A+ PORTVERSION=3D=A0=A0= =A0 1.60=0A=A0 CATEGORIES=3D=A0=A0=A0 biology python=0A=A0 MASTER_SITES=3D= =A0=A0=A0 http://www.biopython.org/DIST/=0A=A0 PKGNAMEPREFIX=3D=A0=A0=A0 ${= PYTHON_PKGNAMEPREFIX}=0A=A0 =0A=A0 MAINTAINER=3D=A0=A0=A0 mauricio@arareko.= net=0A+ COMMENT=3D=A0=A0=A0 Collection of Python modules for bioinformatics= =0A=A0 =0A=A0 BUILD_DEPENDS=3D=A0=A0=A0 ${PYNUMPY}=0A=A0 RUN_DEPENDS=3D=A0= =A0=A0 ${PYNUMPY}=0A=A0 =0A+ USE_PYTHON=3D=A0=A0=A0 =A0=A0=A0 -2.7=0A=A0 US= E_PYDISTUTILS=3D=A0=A0=A0 easy_install=0A=A0 PYEASYINSTALL_ARCHDEP=3D=A0=A0= =A0 yes=0A=A0 =0A=A0 .if !defined(WITHOUT_REPORTLAB)=0A+ RUN_DEPENDS+=3D=A0= =A0=A0 ${PYTHON_PKGNAMEPREFIX}reportlab>0:${PORTSDIR}/print/py-reportlab=0A= =A0 .endif=0A=A0 =0A=A0 .include <bsd.port.mk>=0A=0A=0A=0A=0A=0A___________= _____________________=0A From: "rm@FreeBSD.org" <rm@FreeBSD.org>=0ATo: maur= icio@arareko.net; rm@FreeBSD.org; freebsd-python@FreeBSD.org; rm@FreeBSD.or= g =0ASent: Monday, September 17, 2012 7:30 AM=0ASubject: Re: ports/171115: = [Update]biology/py-biopython:update to 1.60=0A =0ASynopsis: [Update]biology= /py-biopython:update to 1.60=0A=0AResponsible-Changed-From-To: freebsd-pyth= on->rm=0AResponsible-Changed-By: rm=0AResponsible-Changed-When: Mon Sep 17 = 12:30:45 UTC 2012=0AResponsible-Changed-Why: =0ATake. Hi Mauricio. Here is = 'assembled' patch (that was mangled by gnats)=0Afrom Wen plus some of my ch= anges: 1. trim Makefile header 2. remove=0Aundefined article from COMMENT 3= . change USE_PYTHON to just -2.7 4.=0Aremove reportlab from BUILD_DEPENDS 5= . remove deprecated Authors: field=0Afrom pkg-descr 6. tab -> space change = in pkg-descr:WWW. Here is the=0Apatch: http://people.freebsd.org/~rm/biopyt= hon-1.60.diff.txt and here is=0Athe buildlog: http://people.freebsd.org/~rm= /py27-biopython-1.60.log.=0AWould you approve?=0A=0Ahttp://www.freebsd.org/= cgi/query-pr.cgi?pr=3D171115
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