> On May 25, 2015, at 3:16 AM, Baptiste Auguie <baptiste.aug...@gmail.com> > wrote: > > 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.
Not dead for me. Note that it says: "Make sure you add /usr/local/bin to your PATH in order to use this compiler. This can be done, e.g. by export PATH=$PATH:/usr/local/bin" The link offered was: http://r.research.att.com/gfortran-4.2.3.dmg -- David. > > Regards, > > baptiste > > On 24 May 2015 at 10:55, Baptiste Auguie <baptiste.aug...@gmail.com> 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 > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac