R help - Apr 2009 - Compiling Fortran Subroutines as R Shared Objects on Mac OS-X

Hello,

I am trying to compile some F77 subroutines as shared objects for R on my Mac.
--> Mac OS-X Version 10.4.11 (Tiger Intel Mac)


I have done this (successfully) before on Sun Solaris and Linux Fedora systems
using the following command.
> R CMD SHLIB myfile.f
I have g77 installed from this page.
http://hpc.sourceforge.net/

I am using R 2.8.1, and I have installed all 4 additional packages including
gfortran.

When I try to compile my subroutines (which worked on two other systems), I get
the following error.  (I have also tried a very simple subroutine and produced
the same error message.)

chad-r-bhattis-computer:~/MyR/Examples/Fortran/Test1 chadrbhatti$ R CMD SHLIB
two.f
gfortran -arch i386   -fPIC  -g -O2 -c two.f -o two.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
-mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/usr/local/lib -o two.so two.o  -lgfortran
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
/usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) object:
/usr/local/lib/libgfortran.dylib malformed object (unknown load command 4)
/usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) object:
/usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load command 4)
make: *** [two.so] Error 1
chad-r-bhattis-computer:~/MyR/Examples/Fortran/Test1 chadrbhatti$ which g77
/usr/local/bin/g77
chad-r-bhattis-computer:~/MyR/Examples/Fortran/Test1 chadrbhatti$ which
gfortran/usr/local/bin/gfortran



Would anyone happen to understand this error?  The words "malformed
object" and "cpusubtype" concern me.

Note:  I am much more of a Unix user than administrator.  I have very limited
administrator knowledge and vocabulary.

I appreciate any help.

Many Thanks,

Chad R. Bhatti

Chad R. Bhatti wrote:
> 
> 
> Hello,
> 
> I am trying to compile some F77 subroutines as shared objects for R on my
> Mac.
> --> Mac OS-X Version 10.4.11 (Tiger Intel Mac)
> 
> <SNIP>
> 
> chad-r-bhattis-computer:~/MyR/Examples/Fortran/Test1 chadrbhatti$ R CMD
> SHLIB two.f
> gfortran -arch i386   -fPIC  -g -O2 -c two.f -o two.o
> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names
> -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/usr/local/lib -o two.so two.o  -lgfortran
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> object: /usr/local/lib/libgfortran.dylib malformed object (unknown load
> command 4)
> /usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3)
> object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load
> command 4)
> make: *** [two.so] Error 1
> chad-r-bhattis-computer:~/MyR/Examples/Fortran/Test1 chadrbhatti$ which
> g77
> /usr/local/bin/g77
> chad-r-bhattis-computer:~/MyR/Examples/Fortran/Test1 chadrbhatti$ which
> gfortran/usr/local/bin/gfortran
> 
> 
Hi Chad,

I have an Intel mac running OS X 10.5 and I have compiled and used several
Fortran 77 and Fortran 90 subroutines, including MINPACK and MINOS, using R
CMD SHLIB.

I guess the first question I have, is have you installed the developer tools
from the OSX cd (the installer is located in the 'Optional Installs'
folder)? Pardon if this seems obvious, but it may explain the complaint
about the libgcc shared library.

Second, sometimes the options used in gfortran commands executed by R CMD
SHLIB can cause problems (specifically the -fPIC or -fno-common flags),
especially if modules or common blocks are involved in the fortran routines.
To get around this you can try running the compiler on the Fortran code
yourself and then R CMD SHLIB on the object code like so:

gfortran -c *.f
R CMD SHLIB -o myLib.so *.o

I'm no UNIX wizard myself, but the way you're trying to do things seems
like
the correct way and should work, I have absolutely no idea why it is
complaining about cpu architecture if you have an Intel based machine.

-Charlie


-----
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
-- 
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