[R-SIG-Mac] In install.packages(), C compiler cannot create executables

Naresh Gurbuxani n@re@h_gurbux@n| @end|ng |rom hotm@||@com
Mon Jul 29 00:27:41 CEST 2019


On my Mac, everything is installed using brew.  I am not able to install some R packages which look for C compiler.  Below is an example session on the terminal.  

I will be thankful for any suggestions.  If this question does not belong to this group, can you suggest where to look?


> install.packages('stringi', repos='https://cran.r-project.org')
Installing package into ‘/usr/local/lib/R/3.6/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/stringi_1.4.3.tar.gz'
Content type 'application/x-gzip' length 7290890 bytes (7.0 MB)
downloaded 7.0 MB

* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for R_HOME... /usr/local/Cellar/r/3.6.1/lib/R
checking for R... /usr/local/Cellar/r/3.6.1/lib/R/bin/R
checking for endianness... little
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... no
checking for cat... /bin/cat
checking for local ICUDT_DIR... icu61/data
checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
checking whether the C compiler works... no
configure: error: in `/private/var/folders/nv/778l86d50jx2_wlzdw6m16l40000gn/T/Rtmp3KDSQ5/R.INSTALL87262e900de6/stringi':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/usr/local/lib/R/3.6/site-library/stringi’

The downloaded source packages are in
Warning message:
In install.packages("stringi", repos = "https://cran.r-project.org") :
  installation of package ‘stringi’ had non-zero exit status
> R.Version()
[1] "x86_64-apple-darwin17.7.0"

[1] "x86_64"

[1] "darwin17.7.0"

[1] "x86_64, darwin17.7.0"

[1] ""

[1] "3"

[1] "6.1"

[1] "2019"

[1] "07"

[1] "05"

$`svn rev`
[1] "76782"

[1] "R"

[1] "R version 3.6.1 (2019-07-05)"

[1] "Action of the Toes"

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
> system('gcc --version')
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.10.44.4)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
> system('which gcc')
> system('brew doctor')
Your system is ready to brew.

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