From owner-freebsd-python@FreeBSD.ORG Fri Sep 21 19:08:52 2012 Return-Path: Delivered-To: freebsd-python@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id E3DD1106566B for ; Fri, 21 Sep 2012 19:08:52 +0000 (UTC) (envelope-from mauricio@arareko.net) Received: from nm26.bullet.mail.bf1.yahoo.com (nm26.bullet.mail.bf1.yahoo.com [98.139.212.185]) by mx1.freebsd.org (Postfix) with SMTP id 29BAC8FC0A for ; Fri, 21 Sep 2012 19:08:51 +0000 (UTC) Received: from [98.139.212.153] by nm26.bullet.mail.bf1.yahoo.com with NNFMP; 21 Sep 2012 19:05:31 -0000 Received: from [98.139.215.230] by tm10.bullet.mail.bf1.yahoo.com with NNFMP; 21 Sep 2012 19:05:31 -0000 Received: from [127.0.0.1] by omp1070.mail.bf1.yahoo.com with NNFMP; 21 Sep 2012 19:05:31 -0000 X-Yahoo-Newman-Property: ymail-3 X-Yahoo-Newman-Id: 813498.3148.bm@omp1070.mail.bf1.yahoo.com Received: (qmail 48298 invoked by uid 60001); 21 Sep 2012 19:05:31 -0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=yahoo.com; s=s1024; t=1348254331; bh=MLdJJFXBA/IAPV3cc8Zx3kTwi6lt0jHK+ML6iee1r8U=; h=X-YMail-OSG:Received:X-RocketYMMF:X-Mailer:References:Message-ID:Date:From:Reply-To:Subject:To:In-Reply-To:MIME-Version:Content-Type; b=XuWfGB1xxZxGflDFcINJglIlDBcnHJrD6eYWDB9/LGJ1wZXph8fud5TZeHXnKZExiPav08oMVXPx6+lBhRaa/vlnYccPWVDmxEG/b2ROuBkDpR4ha22Pi4ik0iLIwkD6vFA1Z5ugSDmgdvX3D98IvTCmSZZazyJeVBoeoT/HWp0= X-YMail-OSG: Co0sD7sVM1kElRbCeHjLcabbUUE8Qd358iKEQMXwZZ5hfM7 BOCDd29Q5t95QN0j38YQ_qgkOlcg1t8mB9p9zv0khRB1kAc2NqN7KifjFjwO gOLEdAlrqO9dAWTHgHhKC1H8BcdygUPzC6mBmyb4e0SCJV1CHOP3kg5R8Nkm iOXgEqdV1OjF2ZULILdBDvTM1aA518SbwANXVlf77_wAMgL4mhI5SPVDqQ7R yIZdtbKtV.OBwLDngwLvNxVWOo_NqH7dsNraeaQzdnCCO7CZnj1oMAWZiT4g 5tYhK0urTw3I5USA1NW5K1randT6x1MpJwayWo488WNwJxpLXfCpsSnZmtbP FmUn7TNAnFybaBYRGf9Ji3cbUUVSARI5PiCphhCKDBmNMxmAKOQUKMBKS5zs MOGi0q7lpborbojapMmxYz4YqIOSZSvSt_0zV.f_.bL381llRAbAQ62Riwv1 7r9VFuAHH3KE6I2VHqEV7YasonadzzSSUHpm0fvAXLz_H9K0Ht3DQizFRMKA eMg8saEpbhb9h3tbfMQRhhvJmG7zSqEHOzUjdNbRi.ZBxZSlRMH64G81lGbt bggaB1mgUmnms3ei.dwT8gGkRYKBOqqOtUeXYbCoc6OH5zSc1Xt5bzek83Q2 aDTVITOmtlfYN_Cjh5kEQOUxi5E802jM_ Received: from [201.103.231.228] by web31813.mail.mud.yahoo.com via HTTP; Fri, 21 Sep 2012 12:05:31 PDT X-RocketYMMF: arareko X-Mailer: YahooMailWebService/0.8.121.434 References: <201209171230.q8HCUkXG021906@freefall.freebsd.org> Message-ID: <1348254331.43020.YahooMailNeo@web31813.mail.mud.yahoo.com> Date: Fri, 21 Sep 2012 12:05:31 -0700 (PDT) From: Mauricio Herrera Cuadra To: "rm@FreeBSD.org" , "freebsd-python@FreeBSD.org" In-Reply-To: <201209171230.q8HCUkXG021906@freefall.freebsd.org> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Content-Filtered-By: Mailman/MimeDel 2.1.5 Cc: Subject: Re: ports/171115: [Update]biology/py-biopython:update to 1.60 X-BeenThere: freebsd-python@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Mauricio Herrera Cuadra List-Id: FreeBSD-specific Python issues List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Sep 2012 19:08:53 -0000 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 =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 =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 =0A=0A=0A=0A=0A=0A___________= _____________________=0A From: "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