[R-SIG-Mac] failed compilation "ld: library not found for -lquadmath"

[Baptiste Auguie]

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 <baptiste.auguie at 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]]