Hi Simon… I never compiled R myself, I just got R-devel-mavericks.pkg from http://r.research.att.com/ (this morning, though I had the same experience about 3 weeks ago, and gave up, hoping it was something which would go away…). I did update gcc back in December, this is what I have installed:
> gcc --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1 Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn) Target: x86_64-apple-darwin14.0.0 Thread model: posix which I notice has an even newer target. Bryan > On Jan 12, 2015, at 3:29 PM, Simon Urbanek <[email protected]> > wrote: > > Bryan, > > it means that you have a mismatch between the Fortran compiler used to build > R and the one you are using to build packages. Did you remove and/or update > Fortran between compiling R and the packages? > > Cheers, > Simon > > >> On Jan 12, 2015, at 2:20 PM, Bryan Hanson <[email protected]> wrote: >> >> I’m trying to get R 3.2 working fully so I can test my packages before >> sending to CRAN. R 3.2 appears to work OK in general terms. However, when >> I try to install some packages I need, I run into errors with the libraries >> that the install process desires. I get the same or very similar messages >> from several packages. Let’s use amap as an example: >> >> install.packages("amap", type = "source") >> […] >> ld: warning: directory not found for option >> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' >> ld: library not found for -lgfortran >> clang: error: linker command failed with exit code 1 (use -v to see >> invocation) >> make: *** [amap.so] Error 1 >> ERROR: compilation failed for package ‘amap’ >> * removing ‘/Users/bryanhanson/Library/R/3.2/library/amap’ >> * restoring previous ‘/Users/bryanhanson/Library/R/3.2/library/amap’ >> >> The full output is appended after this message. The problem here is clear >> in one sense: there no directory on my machine by that name, since on >> Yosemite it is darwin13.4.0 and gcc is at 4.9.2. xcode and xquartz have >> been updated. I don’t know if this is a problem with a symlink on my system >> or an issue with the amap package not yet being fully updated for R 3.2 or >> a problem with R 3.2 or a mangled gcc install. All suggestions welcome, >> there’s a good chance I’m being simple-minded here. >> >> Thank you. Bryan >> >> === dir listing >> >>> pwd >> /usr/local/lib/gcc/x86_64-apple-darwin13.4.0 >>> ls -l >> total 16 >> lrwxr-xr-x 1 bryanhanson wheel 67 Dec 12 14:29 4.8.2 -> >> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3 >> lrwxr-xr-x 1 bryanhanson wheel 67 Dec 12 14:22 4.8.3 -> >> ../../../Cellar/gcc48/4.8.3/lib/gcc/x86_64-apple-darwin13.4.0/4.8.3 >> drwxr-xr-x 66 bryanhanson wheel 2244 Dec 20 10:36 4.9.2 >> >> === SessionInfo() >> >> R Under development (unstable) (2015-01-11 r67421) >> Platform: x86_64-apple-darwin13.4.0 (64-bit) >> Running under: OS X 10.10.1 (Yosemite) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] sos_1.3-8 brew_1.0-6 >> >> loaded via a namespace (and not attached): >> [1] tools_3.2.0 >> >> === Full output from install.packages >> >> install.packages("amap", type = "source") >> Installing package into ‘/Users/bryanhanson/Library/R/3.2/library’ >> (as ‘lib’ is unspecified) >> trying URL 'http://cran.at.r-project.org/src/contrib/amap_0.8-14.tar.gz' >> Content type 'application/x-gzip' length 259358 bytes (253 KB) >> opened URL >> ================================================== >> downloaded 253 KB >> >> ******** >> ******** Loading Bryan's .Rprofile >> ******** >> Loading required package: brew >> ******** >> ******** Completed Bryan's .Rprofile GET TO WORK! >> ******** >> * installing *source* package ‘amap’ ... >> ** package ‘amap’ successfully unpacked and MD5 sums checked >> checking for gcc... gcc >> checking for C compiler default output file name... a.out >> checking whether the C compiler works... yes >> checking whether we are cross compiling... no >> checking for suffix of executables... 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 ANSI C... none needed >> checking for pthread_create in -lpthread... yes >> configure: creating ./config.status >> config.status: creating src/Makevars >> ** libs >> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG >> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2 >> -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c acprob.cpp -o >> acprob.o >> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG >> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2 >> -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c burt.c -o burt.o >> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG >> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2 >> -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c diss.c -o diss.o >> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG >> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2 >> -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c distance.cpp -o >> distance.o >> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG >> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2 >> -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c hclust.cpp -o >> hclust.o >> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG >> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2 >> -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c kmeans.cpp -o >> kmeans.o >> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG >> -I/usr/local/include/ -I/usr/local/include -I/usr/local/include/freetype2 >> -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c matrice.cpp -o >> matrice.o >> gfortran-4.8 -fPIC -g -O2 -c pop.f -o pop.o >> clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined >> dynamic_lookup -single_module -multiply_defined suppress >> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o amap.so >> acprob.o burt.o diss.o distance.o hclust.o kmeans.o matrice.o pop.o >> -lpthread -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran >> -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R >> -Wl,-framework -Wl,CoreFoundation >> ld: warning: directory not found for option >> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' >> ld: library not found for -lgfortran >> clang: error: linker command failed with exit code 1 (use -v to see >> invocation) >> make: *** [amap.so] Error 1 >> ERROR: compilation failed for package ‘amap’ >> * removing ‘/Users/bryanhanson/Library/R/3.2/library/amap’ >> * restoring previous ‘/Users/bryanhanson/Library/R/3.2/library/amap’ >> >> _______________________________________________ >> 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
