GCC on Lion and above
On Apr 24, 2012, at 3:06 PM, Timothy Bates 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
That is wrong - you should never see gcc from /usr/local - that is some entirely different compiler (unless you're experimenting with non-Apple compilers but then you may as well just compile Fortran ..).
but gfortran -bash: gfortran: command not found
As Kasper pointed out, you may need to use gfortran-4.2 or create a symlink from gfortran to gfortran-4.2 (and probably use gcc-4.2 although either should work). Cheers, Simon
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$
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