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Microsoft R Open Installation on Mac OSX RRS feed

  • Question

  • Microsoft R Open Installation on Mac OSX - Attempt to install a package e.g.:

    install.packages('rgdal')

    Lead to an error about missing clang executable:

    > install.packages('rgdal')
    also installing the dependency ‘sp’
    
    trying URL 'https://mran.microsoft.com/snapshot/2018-06-01/src/contrib/sp_1.2-7.tar.gz'
    Content type 'application/octet-stream' length 1133397 bytes (1.1 MB)
    ==================================================
    downloaded 1.1 MB
    
    trying URL 'https://mran.microsoft.com/snapshot/2018-06-01/src/contrib/rgdal_1.2-20.tar.gz'
    Content type 'application/octet-stream' length 1650449 bytes (1.6 MB)
    ==================================================
    downloaded 1.6 MB
    
    * installing *source* package ‘sp’ ...
    ** package ‘sp’ successfully unpacked and MD5 sums checked
    ** libs
    /usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include  -c Rcentroid.c -o Rcentroid.o
    make: /usr/local/clang4/bin/clang: No such file or directory
    make: *** [Rcentroid.o] Error 1
    ERROR: compilation failed for package ‘sp’
    * removing ‘/Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/library/sp’
    ERROR: dependency ‘sp’ is not available for package ‘rgdal’
    * removing ‘/Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/library/rgdal’
    
    The downloaded source packages are in
    	‘/private/var/folders/9_/y9wx48cd4qv0rbp_9wrg70k00000gn/T/RtmpZ0GkbN/downloaded_packages’
    Warning messages:
    1: In install.packages("rgdal") :
      installation of package ‘sp’ had non-zero exit status
    2: In install.packages("rgdal") :
      installation of package ‘rgdal’ had non-zero exit status

    I'm not sure is the right approach but, for now, I fixed it by adding a symlink in the right directory:

    sudo mkdir /usr/local/clang4/bin/
    sudo ln -s /usr/bin/clang /usr/local/clang4/bin/
    sudo ln -s /usr/bin/clang++ /usr/local/clang4/bin/

    Wednesday, June 13, 2018 9:54 AM

All replies

  • Hi,

    I ran into the same issue.

    De-installed & re-installed MRO 3.5, then applied the fix suggested immediately above.

    The C compiler now's recognized during the package installation.

    No longer getting the 'non-zero exit status" errors when starting & packaging installs from the command line.

    *Microsoft*, would be advisable to get a confirmation this is the fix.

    Tuesday, July 3, 2018 8:24 PM
  • Apparently this is a known, re-occurring issue when new MRO OSX versions are released.

    https://community.rstudio.com/t/unable-to-install-libraries-on-microsoft-r-open-3-5-macos-high-sierra-r-studio-1-1-453/10097

    https://social.msdn.microsoft.com/Forums/en-US/f4ed5dd2-6c7f-427b-8130-306c230891d0/error-with-331-on-mac-os-x?forum=ropen

    I'm not quite there yet on giving up on MRO as the MPP gains are signif.

    Are there any more current recommendations or work around solutions to get MRO 3.5 to correctly recognize the C & Fortran compilers?

    Please advise.

    Tuesday, August 28, 2018 1:22 AM
  • Worked for me.

    Had problems installing a few packages on RStudio (Mac OSX) especially Shiny and Shinydashboard.

    Getting this error..

    make: /usr/local/clang4/bin/clang: No such file or directory
    make: *** [rawmatch.o] Error 1
    ERROR: compilation failed for package ‘mime’

    The commands above sorted it out a treat!

    Wednesday, April 17, 2019 9:26 PM