From owner-freebsd-ports@FreeBSD.ORG Wed Jan 14 20:28:03 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 25C92106581B for ; Wed, 14 Jan 2009 20:28:03 +0000 (UTC) (envelope-from pj@smo.de) Received: from ilk.de (mx-out20.ilk.de [194.121.104.20]) by mx1.freebsd.org (Postfix) with ESMTP id A8BA88FC27 for ; Wed, 14 Jan 2009 20:28:02 +0000 (UTC) (envelope-from pj@smo.de) Received: from bologna.intern.smo.de (pool61.ka.ilk.net [212.86.194.61]) by ilk.de (8.13.4/8.13.4/ilk-relay) with ESMTP id n0EKS0TH029949; Wed, 14 Jan 2009 21:28:00 +0100 Received: from [192.168.153.208] (herdubreid.intern.smo.de [192.168.153.208]) by bologna.intern.smo.de (8.13.8+Sun/8.13.8) with ESMTP id n0EKJils010282; Wed, 14 Jan 2009 21:19:45 +0100 (CET) Message-ID: <496E4AFE.2060803@smo.de> Date: Wed, 14 Jan 2009 21:28:46 +0100 From: Philipp Ost User-Agent: Mozilla/5.0 (X11; U; FreeBSD i386; en-US; rv:1.7.13) Gecko/20090111 X-Accept-Language: de, en-us, en MIME-Version: 1.0 To: bf2006a@yahoo.com References: <365052.26421.qm@web39107.mail.mud.yahoo.com> In-Reply-To: <365052.26421.qm@web39107.mail.mud.yahoo.com> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Cc: ports@freebsd.org, Glen Barber 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 20:28:06 -0000 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