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

[Baptiste Auguie]

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]]