[R-SIG-Mac] failed compilation "ld: library not found for -lquadmath"
David Winsemius
dwinsemius at comcast.net
Thu Feb 11 09:06:25 CET 2016
> On May 25, 2015, at 3:16 AM, Baptiste Auguie <baptiste.auguie at 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.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
>>
>
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David Winsemius
Alameda, CA, USA
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