I downgraded my gfortran to 4.8 and things seem to be working again. Thanks for the hint. Bryan
> On Jan 12, 2015, at 3:36 PM, Bryan Hanson <[email protected]> wrote: > > 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
