Hi, Not sure my previous message ever got through, in any case I've solved the issue by installing a newer gfortran from http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 Note that the tools suggested at http://cran.r-project.org/bin/macosx/tools/ are limited to version 4.2.3, while the link at http://r.research.att.com/tools/ (also for 4.2.3) is dead.
Regards, baptiste On 24 May 2015 at 10:55, Baptiste Auguie <[email protected]> wrote: > Hi, > > I've been unsuccessful in installing my own packages 'planar' and 'cda' > from source, since I updated my MacBook Pro to Yosemite. I have the latest > stable binary of R from CRAN, re-installed the latest Xcode via AppStore, > got gfortran from http://r.research.att.com/, and I still get a > compilation error. My guess is that I have inadvertently carried over an > older version of gcc from the previous OS, and R is looking for a different > one. The error message for planar goes like this, > > R CMD INSTALL planar > * installing to library > ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’ > * installing *source* package ‘planar’ ... > ** package ‘planar’ successfully unpacked and MD5 sums checked > ** libs > 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 > planar.so collection.o gaussian_beam.o hcubature.o multilayer.o > -L/Library/Frameworks/R.framework/Resources/lib -lRlapack > -L/Library/Frameworks/R.framework/Resources/lib -lRblas > -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 -lquadmath > clang: error: linker command failed with exit code 1 (use -v to see > invocation) > make: *** [planar.so] Error 1 > ERROR: compilation failed for package ‘planar’ > * removing > ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/planar’ > * restoring previous > ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/planar’ > > ------------------------- > > Indeed, the directory "/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2" > does not exist. The closest thing seems to be > "/usr/local/lib/gcc/i686-apple-darwin8", > > > ls -R /usr/local/lib/gcc | tree > |-------i686-apple-darwin8 > |---------4.2.3 > |-----------finclude > |-----------x86_64 > |-------powerpc-apple-darwin8 > |---------4.2.3 > |-----------finclude > |-----------ppc64 > > Could it be enough to set a few compilation flags to point R to the right > gcc libraries? (not sure how) > > Best regards, > > baptiste > > ----- session info ----- > > > sessionInfo() > R version 3.2.0 Patched (2015-05-21 r68393) > Platform: x86_64-apple-darwin13.4.0 (64-bit) > Running under: OS X 10.10.3 (Yosemite) > > locale: > [1] en_NZ.UTF-8/en_NZ.UTF-8/en_NZ.UTF-8/C/en_NZ.UTF-8/en_NZ.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_3.2.0 > > > Sys.getenv() > __CF_USER_TEXT_ENCODING 0x1F5:0x0:0x0 > Apple_PubSub_Socket_Render > > /private/tmp/com.apple.launchd.2pqH8flWmK/Render > DISPLAY > /private/tmp/com.apple.launchd.e31xJhIRZF/org.macosforge.xquartz:0 > DYLD_FALLBACK_LIBRARY_PATH > > /Users/baptiste/lib:/usr/local/lib:/usr/lib::/Library/Frameworks/R.framework/Resources/lib > EDITOR vi > GIT_ASKPASS rpostback-askpass > HOME /Users/baptiste > LANG en_NZ.UTF-8 > LC_CTYPE en_NZ.UTF-8 > LN_S ln -s > LOGNAME baptiste > MAKE make > PAGER /usr/bin/less > PATH > /usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/bin:/opt/X11/bin > PDFLATEX /usr/texbin/pdflatex > R_BROWSER /usr/bin/open > R_BZIPCMD /usr/bin/bzip2 > R_DOC_DIR /Library/Frameworks/R.framework/Resources/doc > R_GZIPCMD /usr/bin/gzip > R_HOME /Library/Frameworks/R.framework/Resources > R_INCLUDE_DIR > /Library/Frameworks/R.framework/Resources/include > R_LIBS_SITE > R_LIBS_USER ~/Library/R/3.2/library > R_PAPERSIZE a4 > R_PDFVIEWER /usr/bin/open > R_PLATFORM x86_64-apple-darwin13.4.0 > R_PRINTCMD lpr > R_QPDF > /Library/Frameworks/R.framework/Resources/bin/qpdf > R_RD4PDF times,inconsolata,hyper > R_SESSION_TMPDIR > /var/folders/nh/4719qghd3bz60tc_n28062840000gn/T//RtmpNqgTMe > R_SHARE_DIR /Library/Frameworks/R.framework/Resources/share > R_SYSTEM_ABI osx,gcc,gxx,gfortran,? > R_TEXI2DVICMD /usr/local/bin/texi2dvi > R_UNZIPCMD /usr/bin/unzip > R_ZIPCMD /usr/bin/zip > RMARKDOWN_MATHJAX_PATH > /Applications/RStudio.app/Contents/Resources/resources/mathjax-23 > RS_RPOSTBACK_PATH > /Applications/RStudio.app/Contents/MacOS/rpostback > RS_SHARED_SECRET 8dfae406-353d-44e7-bf9a-12efa87271a8 > RSTUDIO 1 > RSTUDIO_PANDOC /Applications/RStudio.app/Contents/MacOS/pandoc > RSTUDIO_SESSION_PORT 33826 > RSTUDIO_USER_IDENTITY baptiste > SED /usr/bin/sed > SHELL /bin/bash > SSH_AUTH_SOCK > /private/tmp/com.apple.launchd.v82zIG6NDp/Listeners > TAR /usr/bin/tar > TMPDIR > /var/folders/nh/4719qghd3bz60tc_n28062840000gn/T/ > USER baptiste > XPC_FLAGS 0x0 > XPC_SERVICE_NAME 0 > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
