From owner-freebsd-questions@FreeBSD.ORG Tue Feb 6 20:12:09 2007 Return-Path: X-Original-To: questions@freebsd.org Delivered-To: freebsd-questions@FreeBSD.ORG Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id 76EEE16A401 for ; Tue, 6 Feb 2007 20:12:09 +0000 (UTC) (envelope-from joey@mingrone.org) Received: from wr-out-0506.google.com (wr-out-0506.google.com [64.233.184.233]) by mx1.freebsd.org (Postfix) with ESMTP id 2DE6B13C441 for ; Tue, 6 Feb 2007 20:12:06 +0000 (UTC) (envelope-from joey@mingrone.org) Received: by wr-out-0506.google.com with SMTP id 69so1720481wra for ; Tue, 06 Feb 2007 12:12:05 -0800 (PST) Received: by 10.90.99.20 with SMTP id w20mr10951881agb.1170791049926; Tue, 06 Feb 2007 11:44:09 -0800 (PST) Received: by 10.90.53.9 with HTTP; Tue, 6 Feb 2007 11:44:09 -0800 (PST) Message-ID: Date: Tue, 6 Feb 2007 15:44:09 -0400 From: "Joey Mingrone" To: questions@freebsd.org, "Eric van Gyzen" In-Reply-To: <45C7B175.50603@vangyzen.net> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline References: <45C7B175.50603@vangyzen.net> Cc: Subject: Re: FreeBSD Port: R-2.4.1 X-BeenThere: freebsd-questions@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: User questions List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 06 Feb 2007 20:12:09 -0000 Hey Eric, all, That was the first install attempt of R on this box. There was no previous installation. Also, I tried again with portinstall -Rf R, which, I believe, reinstalled all the dependencies, but with the same outcome. For the line that failed I also went into the directory: /usr/ports/math/R/work/R-2.4.1/src/main and changed the original command which was cc -std=gnu99 -export-dynamic -L/usr/local/lib -o R.bin Rmain.o -L../../lib -lR to gcc42 -std=gnu99 -export-dynamic -L/usr/local/lib -o R.bin Rmain.o -L../../lib -lR -lgcc_s and the command worked (note I changed cc to gcc42 and added -lgcc_s) Any other ideas? Joey On 2/5/07, Eric van Gyzen wrote: > Joey, > > Try removing any existing R installation before building 2.4.1. > > Also, reinstall all of R's dependencies -- blas and its dependents are > now built with gfortran 4.2.0. > > Eric > > Joey Mingrone wrote: > > Hi: > > > > I'm trying to install the R port, but get linking errors during the > > installation. I've included the text below. > > > > Here's what my uname -a says: > > > > FreeBSD karlsruhe.mingrone.org 6.1-RELEASE-p11 FreeBSD 6.1-RELEASE-p11 > > #0: Wed Dec 20 08:25:54 AST 2006 > > root@karlsruhe.mingrone.org:/usr/obj/usr/src/sys/KARLSRUHE_MINGRONE_ORG_2006-12-20 > > > > i386 > > > > Thanks for any help you can provide and please let me know if there is > > any other information you need. > > > > Joey > > > > > > cc -std=gnu99 -I. -I../../src/include -I../../src/include > > -I/usr/local/include -DHAVE_CONFIG_H -D__NO_MATH_INLINES -fpic -O2 > > -fno-strict-aliasing -pipe -c util.c -o util.o > > cc -std=gnu99 -I. -I../../src/include -I../../src/include > > -I/usr/local/include -DHAVE_CONFIG_H -D__NO_MATH_INLINES -fpic -O2 > > -fno-strict-aliasing -pipe -c version.c -o version.o > > cc -std=gnu99 -I. -I../../src/include -I../../src/include > > -I/usr/local/include -DHAVE_CONFIG_H -D__NO_MATH_INLINES -fpic -O2 > > -fno-strict-aliasing -pipe -c vfonts.c -o vfonts.o > > gfortran42 -D__NO_MATH_INLINES -fpic -g -O2 -c xxxpr.f -o xxxpr.o > > cc -std=gnu99 -shared -L/usr/local/lib -o libR.so CConverters.o > > CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o > > apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o > > colors.o complex.o connections.o context.o cov.o cum.o dcf.o > > datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o dstruct.o > > duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o > > gevents.o gram.o gram-ex.o graphics.o identical.o internet.o > > iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o > > match.o memory.o model.o names.o objects.o optim.o optimize.o > > options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o > > print.o printarray.o printvector.o printutils.o qsort.o random.o > > regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o > > serialize.o size.o sort.o source.o split.o sprintf.o startup.o > > subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o > > version.o vfonts.o xxxpr.o `ls ../appl/*.o ../nmath/*.o ../unix/*.o > > 2>/dev/null|grep -v /ext-` -lblas > > -L/usr/local/lib/gcc-4.2.0/gcc/i386-portbld-freebsd6.1/4.2.0 > > -L/usr/local/lib/gcc-4.2.0 -lgfortran -lm -lgcc_s > > /usr/local/lib/libintl.so /usr/local/lib/libiconv.so -Wl,-rpath > > -Wl,/usr/local/lib -lreadline -lpcre -lbz2 -lz -lm -liconv > > mkdir /usr/ports/math/R/work/R-2.4.1/bin/exec > > mkdir /usr/ports/math/R/work/R-2.4.1/lib > > cc -std=gnu99 -I. -I../../src/include -I../../src/include > > -I/usr/local/include -DHAVE_CONFIG_H -D__NO_MATH_INLINES -fpic -O2 > > -fno-strict-aliasing -pipe -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/gcc-4.2.0/libgfortran.so.2: undefined reference to > > `__mulxc3@GCC_4.0.0' > > /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to > > `__mulsc3@GCC_4.0.0' > > /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to > > `__divsc3@GCC_4.0.0' > > /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to > > `__muldc3@GCC_4.0.0' > > /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to > > `__divdc3@GCC_4.0.0' > > /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to > > `__divxc3@GCC_4.0.0' > > *** Error code 1 > > > > Stop in /usr/ports/math/R/work/R-2.4.1/src/main. > > *** Error code 1 > > > > Stop in /usr/ports/math/R/work/R-2.4.1/src/main. > > *** Error code 1 > > > > Stop in /usr/ports/math/R/work/R-2.4.1/src. > > *** Error code 1 > > > > Stop in /usr/ports/math/R/work/R-2.4.1. > > *** Error code 1 > > > > Stop in /usr/ports/math/R. > > ** Command failed [exit code 1]: /usr/bin/script -qa > > /tmp/portinstall.44120.0 env make > > ** Fix the problem and try again. > > ** Listing the failed packages (*:skipped / !:failed) > > ! math/R (linker error) > > ---> Packages processed: 0 done, 0 ignored, 0 skipped and 1 failed > > >