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Re: FreeBSD Port: R-2.4.1



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 <eric_(_at_)_vangyzen_(_dot_)_net> 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_(_at_)_karlsruhe_(_dot_)_mingrone_(_dot_)_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_(_at_)_GCC_4_(_dot_)_0_(_dot_)_0'
> /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to
> `__mulsc3_(_at_)_GCC_4_(_dot_)_0_(_dot_)_0'
> /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to
> `__divsc3_(_at_)_GCC_4_(_dot_)_0_(_dot_)_0'
> /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to
> `__muldc3_(_at_)_GCC_4_(_dot_)_0_(_dot_)_0'
> /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to
> `__divdc3_(_at_)_GCC_4_(_dot_)_0_(_dot_)_0'
> /usr/local/lib/gcc-4.2.0/libgfortran.so.2: undefined reference to
> `__divxc3_(_at_)_GCC_4_(_dot_)_0_(_dot_)_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
>

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