[R-SIG-Mac] GCC on Lion and above

[Timothy Bates]

Dear all (simon...)

I’ve installed what I think is the recommended gcc+fortran installer pkg for Lion:

http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg 

but get no fortran in my /usr/local/bin and compiling an R package that needs it (http://openmx.psyc.virginia.edu) fails... no fortran.

I _think_ i have followed the instructions on http://r.research.att.com/tools/#gcc42
        (it’s confusing that up-to-date OS instructions are buried down in the (long) list of possible packages to install: I would be happy to help reorg this...)


gcc is fine
which gcc
/usr/local/bin/gcc

but
 gfortran
-bash: gfortran: command not found


config info follows... sorry for the hassle
t

*** Config info ***

Xcode 4.4 with command line tools installed

echo $PATH

:/usr/local/bin:/usr/local/mysql/bin/:/Users/tim/bin:/Users/tim/Applications/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/bin:/usr/local/mysql/bin:/Users/tim/bin:/Users/tim/bin/plink



FYI, here’s the make trail from attempting to make OpenMx


spearman:Users tim$ cd ~/bin/OpenMx/; svn update; cd trunk/; make clean; make install; cd ..; svn status
At revision 2028.
rm -rf build/*
rm -rf models/passing/temp-files/*
rm -rf models/failing/temp-files/*
rm -rf build/*
rm -rf models/passing/temp-files/*
rm -rf models/failing/temp-files/*
cp DESCRIPTION DESCRIPTION.bak
sed '/Version:/d' DESCRIPTION.bak > DESCRIPTION
echo "Version: "999.0.0"-"2028 >> DESCRIPTION	
cd build; R CMD build ..
* checking for file ‘../DESCRIPTION’ ... OK
* preparing ‘OpenMx’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘OpenMx/docs/source/static/Rdoc’
Removed empty directory ‘OpenMx/docs/source/static/demo’
Removed empty directory ‘OpenMx/docs/source/static’
Removed empty directory ‘OpenMx/docs/source/templates’
Removed empty directory ‘OpenMx/inst/unit-tests’
Removed empty directory ‘OpenMx/models/failing/temp-files’
Removed empty directory ‘OpenMx/models/passing/temp-files’
Removed empty directory ‘OpenMx/testsuite’
* looking to see if a ‘data/datalist’ file should be added
* re-saving tabular files
* building ‘OpenMx_999.0.0-2028.tar.gz’

mv DESCRIPTION.bak DESCRIPTION
cd build; R CMD INSTALL "--configure-args=--enable-openmp" OpenMx_999.0.0-2028.tar.gz  
* installing to library ‘/Users/tim/Library/R/2.15/library’
* installing *source* package ‘OpenMx’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to support OpenMP... -fopenmp
checking whether gcc is installed... yes
checking build system type... i386-apple-darwin12.0.0
checking host system type... i386-apple-darwin12.0.0
checking for inst/npsol/osx/libnpsol.a... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: executing src/omxSymbolTable.h commands
config.status: executing src/omxSymbolTable.c commands
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -Wall -fopenmp -mmacosx-version-min=10.4  -fPIC  -g -O2  -c merge.c -o merge.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -Wall -fopenmp -mmacosx-version-min=10.4  -fPIC  -g -O2  -c npsolWrap.c -o npsolWrap.o
npsolWrap.c: In function ‘constraintFunction_’:
npsolWrap.c:798:19: warning: variable ‘size’ set but not used [-Wunused-but-set-variable]
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -Wall -fopenmp -mmacosx-version-min=10.4  -fPIC  -g -O2  -c omxAlgebra.c -o omxAlgebra.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -Wall -fopenmp -mmacosx-version-min=10.4  -fPIC  -g -O2  -c omxAlgebraFunctions.c -o omxAlgebraFunctions.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include   -Wall -fopenmp -mmacosx-version-min=10.4  -fPIC  -g -O2  -c omxAlgebraObjective.c -o omxAlgebraObjective.o
gfortran -arch i386   -fPIC  -g -O2  -c omxBLAS.f -o omxBLAS.o
make[1]: gfortran: No such file or directory
make[1]: *** [omxBLAS.o] Error 1
ERROR: compilation failed for package ‘OpenMx’
* removing ‘/Users/tim/Library/R/2.15/library/OpenMx’
* restoring previous ‘/Users/tim/Library/R/2.15/library/OpenMx’
make: *** [install] Error 1
?       typescript
?       .profile
?       trunk/demo/UnivariateTwinAnalysis_MatrixRaw_plusCov.R
?       trunk/build/OpenMx_999.0.0-2028.tar.gz
?       branches/three-matrix/src/.BC.szkLWC
?       branches/experimental/src/.BC.zDfeyx
spearman:OpenMx tim$