GCC on Lion and above
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
<timothy.c.bates at gmail.com> 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$
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