Hi Tim I encountered this recently. If you do gcc --version you'll notice that you get the llvm, whereas gcc-4.2 --version gives you the "right"s standard GCC. So essentially, when you compile, you need to make sure you use gcc-4.2 and gfortran-4.2 both of which are in /usr/bin. Note that gcc-4.2 and gcc are two different beasts. All of this can usually be done by doing something like CC=/usr/bin/gcc-4.2 ./configure
Kasper Output: gcc --version i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00) gcc-4.2 --version i686-apple-darwin11-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) On Tue, Apr 24, 2012 at 3:06 PM, Timothy Bates <[email protected]> wrote: > 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$ > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
