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List: r-sig-mac
Subject: Re: [R-SIG-Mac] In install.packages(), C compiler cannot create executables
From: Naresh Gurbuxani <naresh_gurbuxani () hotmail ! com>
Date: 2019-07-29 10:40:20
Message-ID: BN8PR18MB269025C88CD94EB76DA8EF07FADD0 () BN8PR18MB2690 ! namprd18 ! prod ! outlook ! com
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Thanks for your explanation. I ended up with a different solution.
After reading 'R for Mac OS X' on the cran website, I installed clang and gfortran \
packages provided at the website. These install into /usr/local/.
After these installations, I was able to successfully install R packages.
Naresh
From: Luis Puerto <luiss.puerto@gmail.com>
Sent: Monday, July 29, 2019 12:23 AM
To: Naresh Gurbuxani <naresh_gurbuxani@hotmail.com>
Cc: R-sig-mac ML R-Project <r-sig-mac@r-project.org>
Subject: Re: [R-SIG-Mac] In install.packages(), C compiler cannot create executables
Install R from cask, as James suggested will provide all the capabilities since it's \
downloaded from CRAN. The one that does't provide all the capabilities is Homebrew \
core.
Seth's one will provide all the capabilities too, but you are going to need to build \
it and then build all the packages you install.
Other think is you want to use OpenBLAS and OpenMP. You should be able to use those \
libraries with CRAN version —either directly or through brew cask— but I'm not sure \
since I use Seth's version.
Best Regards
Luis Puerto
luispuerto.net
> On 28 Jul, 2019, at 19:07, Naresh Gurbuxani <naresh_gurbuxani@hotmail.com> wrote:
>
> JJB,
>
> I installed R using instructions given here.
>
> https://github.com/sethrfore/homebrew-r-srf
>
> It seems that installing R using brew cask will not provide all capabilities. In \
> any case, I want to use R with Emacs.
>
> I will try to reinstall and see if the problem goes away.
>
> Thanks,
> Naresh
>
>
>
>
>
>
> From: R-SIG-Mac <r-sig-mac-bounces@r-project.org> on behalf of Balamuta, James \
> Joseph <balamut2@illinois.edu>
>
> Sent: Sunday, July 28, 2019 6:34 PM
>
> To: r-sig-mac@r-project.org <r-sig-mac@r-project.org>
>
> Subject: Re: [R-SIG-Mac] In install.packages(), C compiler cannot create \
> executables
>
>
>
>
> Greetings and Salutations Naresh Gurbuxani,
>
>
>
> Don't use homebrew to install R. If you must use homebrew, install R via the brew \
> cask project to obtain the CRAN binary vs. the homebrew compiled variant.
>
>
>
> Sincerely,
>
>
>
> JJB
>
>
>
> On 7/28/19, 5:28 PM, "R-SIG-Mac on behalf of Naresh Gurbuxani" \
> <r-sig-mac-bounces@r-project.org on behalf of naresh_gurbuxani@hotmail.com> wrote:
>
>
>
> Hello,
>
>
>
> 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?
>
>
>
> Naresh
>
>
>
> > 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
>
> ‘/private/var/folders/nv/778l86d50jx2_wlzdw6m16l40000gn/T/Rtmp3hnR8I/downloaded_packages’
>
>
> Warning message:
>
> In install.packages("stringi", repos = "https://cran.r-project.org") :
>
> installation of package ‘stringi’ had non-zero exit status
>
> > R.Version()
>
> $platform
>
> [1] "x86_64-apple-darwin17.7.0"
>
>
>
> $arch
>
> [1] "x86_64"
>
>
>
> $os
>
> [1] "darwin17.7.0"
>
>
>
> $system
>
> [1] "x86_64, darwin17.7.0"
>
>
>
> $status
>
> [1] ""
>
>
>
> $major
>
> [1] "3"
>
>
>
> $minor
>
> [1] "6.1"
>
>
>
> $year
>
> [1] "2019"
>
>
>
> $month
>
> [1] "07"
>
>
>
> $day
>
> [1] "05"
>
>
>
> $`svn rev`
>
> [1] "76782"
>
>
>
> $language
>
> [1] "R"
>
>
>
> $version.string
>
> [1] "R version 3.6.1 (2019-07-05)"
>
>
>
> $nickname
>
> [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')
>
> /usr/bin/gcc
>
> > system('brew doctor')
>
> Your system is ready to brew.
>
> >
>
>
>
>
>
>
>
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>
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>
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>
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>
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>
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>
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