From owner-freebsd-ports@FreeBSD.ORG Wed Jan 14 20:49:48 2009 Return-Path: Delivered-To: ports@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 30E3710656C7 for ; Wed, 14 Jan 2009 20:49:48 +0000 (UTC) (envelope-from rhurlin@gwdg.de) Received: from amailer.gwdg.de (amailer.gwdg.de [134.76.10.18]) by mx1.freebsd.org (Postfix) with ESMTP id B6AB78FC1A for ; Wed, 14 Jan 2009 20:49:47 +0000 (UTC) (envelope-from rhurlin@gwdg.de) Received: from p578b68b8.dip0.t-ipconnect.de ([87.139.104.184] helo=krabat.raven.hur) by mailer.gwdg.de with esmtpsa (TLSv1:AES256-SHA:256) (Exim 4.69) (envelope-from ) id 1LNCgG-0005wT-G4; Wed, 14 Jan 2009 21:49:40 +0100 Message-ID: <496E4FE5.6020001@gwdg.de> Date: Wed, 14 Jan 2009 21:49:41 +0100 From: Rainer Hurling User-Agent: Thunderbird 2.0.0.19 (X11/20090113) MIME-Version: 1.0 To: Philipp Ost References: <365052.26421.qm@web39107.mail.mud.yahoo.com> <496E4AFE.2060803@smo.de> In-Reply-To: <496E4AFE.2060803@smo.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Authenticated: Id:rhurlin X-Spam-Level: - X-Virus-Scanned: (clean) by exiscan+sophie Cc: ports@freebsd.org Subject: Re: math/R fails to build X-BeenThere: freebsd-ports@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Porting software to FreeBSD List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 14 Jan 2009 20:49:48 -0000 I have to set the following link, because R's configure is looking for pure name 'gfortran' # ln -s /usr/local/bin/gfortran43 /usr/local/bin/gfortran Hope this helps, Rainer On 14.01.2009 21:28 (UTC+1), Philipp Ost wrote: > bf wrote: >> --- On Tue, 1/13/09, Glen Barber wrote: >> >> >>> From: Glen Barber >>> Subject: Re: math/R fails to build >>> To: "Philipp Ost" >>> Cc: bf2006a@yahoo.com, ports@freebsd.org >>> Date: Tuesday, January 13, 2009, 8:03 PM >>> On Tue, Jan 13, 2009 at 5:10 PM, Philipp Ost >>> wrote: >>> >>>> Hi, >>>> >>>> math/R fails to build: >>>> # make >>>> [...] >>>> cc -std=gnu99 -I. -I../../src/include >>> >>> -I../../src/include >>> >>>> -I/usr/local/include -DHAVE_CONFIG_H -fpic -O2 >>> >>> -fno-strict-aliasing -pipe >>> >>>> -march=athlon-xp -c Rmain.c -o Rmain.o >>>> cc -std=gnu99 -export-dynamic -L/usr/local/lib -o >>> >>> R.bin Rmain.o -L../../lib >>> >>>> -lR >>>> /usr/local/lib/libblas.so.2: undefined reference to >>>> `_gfortran_runtime_error_at' >>>> *** Error code 1 >>>> >>>> Stop in /usr/ports/math/R/work/R-2.8.1/src/main. >>>> *** Error code 1 >>>> >>>> Stop in /usr/ports/math/R/work/R-2.8.1/src/main. >>>> *** Error code 1 >>>> >>>> Stop in /usr/ports/math/R/work/R-2.8.1/src. >>>> *** Error code 1 >>>> >>>> Stop in /usr/ports/math/R/work/R-2.8.1. >>>> *** Error code 1 >>>> >>>> Stop in /usr/ports/math/R. >>>> *** Error code 1 >>>> >>>> Stop in /usr/ports/math/R. >>>> # >>>> >>>> I run RELENG_7 as of 23 Dec. 2008 (on i386). >>>> >>>> Any hints? (Apart from rebuilding blas, which I did. >>> >>> It didn't solve the >>> >>>> problem) >>>> >>> >>> Is it a safe assumption that you have recently updated your >>> ports tree? > > Yes > > [...] > >> There were recently some changes to >> the organization of the Fortran-related >> ports on FreeBSD. The Fortran compiler >> was added to the list of runtime >> dependencies, as it should have been, >> and the default Fortran compiler was >> changed from gcc 4.2.x to 4.3.x. As >> Glen suggested, your problem may be >> related. Try updating your ports tree, >> and then rebuilding blas, lapack, >> and R, and see if it works. > [...] > > gcc43 is installed, ports tree is updated (as of ~20:00 MET today). I > did rebuild lapack and blas, then tried R again: > # make > [...] > cc -std=gnu99 -I. -I../../src/include -I../../src/include > -I/usr/local/include -DHAVE_CONFIG_H -fpic -O2 -fno-strict-aliasing > -pipe -march=athlon-xp -c Rmain.c -o Rmain.o > cc -std=gnu99 -export-dynamic -L/usr/local/lib -o R.bin Rmain.o > -L../../lib -lR > /usr/bin/ld: warning: libgfortran.so.2, needed by > /usr/local/lib/libR.so, not found (try using -rpath or -rpath-link) > /usr/local/lib/libblas.so.2: undefined reference to `_gfortran_st_write' > /usr/local/lib/libblas.so.2: undefined reference to > `_gfortran_transfer_character' > /usr/local/lib/libblas.so.2: undefined reference to > `_gfortran_st_write_done' > /usr/local/lib/libblas.so.2: undefined reference to > `_gfortran_runtime_error_at' > /usr/local/lib/libblas.so.2: undefined reference to > `_gfortran_transfer_integer' > /usr/local/lib/libblas.so.2: undefined reference to > `_gfortran_stop_numeric' > *** Error code 1 > > Stop in /usr/ports/math/R/work/R-2.8.1/src/main. > *** Error code 1 > > Stop in /usr/ports/math/R/work/R-2.8.1/src/main. > *** Error code 1 > > Stop in /usr/ports/math/R/work/R-2.8.1/src. > *** Error code 1 > > Stop in /usr/ports/math/R/work/R-2.8.1. > *** Error code 1 > > Stop in /usr/ports/math/R. > *** Error code 1 > > Stop in /usr/ports/math/R. > # > > Seems like blas is to blame... > > Here are some software version numbers: > blas-1.0_3 > lapack-3.1.1_2 > gcc-4.3.3_20090108 > R-2.8.0 > > I haven't done any other other updates in the meantime (perl et. al.). > If I have the time I will check and see if my 8.0-testbox has the same > problem (apart from being slow...). > > Thanks for your time and help, > Philipp > _______________________________________________ > freebsd-ports@freebsd.org mailing list > http://lists.freebsd.org/mailman/listinfo/freebsd-ports > To unsubscribe, send any mail to "freebsd-ports-unsubscribe@freebsd.org"