Howdy,
I am attempting to install the fields_6.7.6 package under R-3.0.0 on OS X
10.7.5. I think the install process is calling the wrong gfortran compiler.
The compiler being called is /usr/local/gfortran/bin/gfortran, which is "GNU
Fortran (GCC) 4.4.0 20090321 (experimental) [trunk revision 144983]". I've
installed the gfortran-4.2.3.pkg package from
http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg.
The /Library/Frameworks/R.framework/Versions/3.0/Resources/etc/Makeconf file
specifies:
FC = gfortran-4.2 -arch x86_64
and
F77 = gfortran-4.2 -arch x86_64
The text output from install.packages() shows lots of -c compilation using this
wrong gfortran, then attempts to link with llvm-gcc-4.2. The linking step
complains about the .o files being architecture i386, which is probably wrong
output from the gfortran-4.4.0 compiler:
> /usr/local/gfortran/bin/gfortran -fPIC -g -O2 -c sortm.f -o sortm.o
> llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/usr/local/gfortran/lib/ -o fields.so css.o
> csstr.o cvrf.o dchold.o dcopy.o ddfind.o ddot.o derrb.o dlv.o dmaket.o
> drdfun.o dsetup.o evlpoly.o evlpoly2.o expfn.o ifind.o igpoly.o inpoly.o
> mltdrb.o mltdtd.o multeb.o multrb.o radbas.o radfn2.o radfun.o rcss.o rcssr.o
> rcsswt.o sortm.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64
> -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3
> -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> ld: warning: ld: warning: ignoring file css.o, file was built for i386 which
> is not the architecture being linked (x86_64): css.oignoring file csstr.o,
> file was built for i386 which is not the architecture being linked (x86_64):
> csstr.o
There's no Makefile in the fields package, so FC and F77 are not being
overridden by the package itself, I believe. The FC and F77 variables from R's
Makeconf are not being respected, and I've tried to specify alternative
gfortran compilers with syntax like:
install.packages("fields",type="source",repos="http://cran.us.r-project.org",clean=TRUE,configure.vars=list(F77="gfortran-4.2
-arch x86_64",FC="gfortran-4.2 -arch x86_64"))
Nothing I do seems to tell the fields package to use the proper gfortran
compiler. I have no environment variables like FC or F77 defined. I have to
admit that I do have four different gfortran versions installed on this
machine: in addition to the R pkg version and the gfortran-4.4.0, there's a
fink /sw/bin/gfortran 4.6.2, and a /usr/bin/gfortran-4.2 which claims to come
from Apple (GNU Fortran (GCC) 4.2.1 (Apple Inc. build 5566)). I'm up to date
with Xcode.
Any advice about how to do this correctly would be much appreciated!
Thanks,
Andy
--
Andy Jacobson
[email protected]
NOAA Earth System Research Lab
Global Monitoring Division
325 Broadway R/GMD1
Boulder, Colorado 80305
303/578-2237
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