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
