[R-SIG-Mac] Source versions of packages not updating R version 3.6.1

[Simon Urbanek]

It looks like you're broken compilers. Instead of googling incorrect suggestions, please consider reading the documentation. If you use R from CRAN please do NOT use tools from homebrew, download clang7 from the CRAN website instead and prepend it to the PATH. Also do remove ~/.R/Makevars - it is not necessary unless you have custom needs and know what you're doing.

Cheers,
Simon


> On Jul 8, 2019, at 04:21, a.chandhial--- via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
> 
> 
> Hi,
> 
> I am having difficulties with updating source versions of packages in R. 
> I am on a MacBook Pro, MacOS Mojave 10.14.5.
> 
> I updated to gcc 9.1.0, via:
> brew update
> brew upgrade
> brew info gcc
> brew install gcc
> brew cleanup
> 
> brew info gcc gives the following:
> gcc: stable 9.1.0 (bottled), HEAD
> GNU compiler collection
> https://gcc.gnu.org/
> /usr/local/Cellar/gcc/9.1.0 (1,461 files, 287MB) *
>   Poured from bottle on 2019-05-31 at 20:31:20
> From: 
> https://github.com/Homebrew/homebrew-core/blob/master/Formula/gcc.rb
> ==> Dependencies
> Required: gmp ✔, isl ✔, libmpc ✔, mpfr ✔
> ==> Options
> --HEAD
> 	Install HEAD version
> ==> Analytics
> install: 59,839 (30 days), 273,269 (90 days), 874,830 (365 days)
> install_on_request: 26,639 (30 days), 126,289 (90 days), 419,789 (365 
> days)
> build_error: 0 (30 days)
> 
> 
> gcc --version gives the following:
> Apple clang version 11.0.0 (clang-1100.0.20.17)
> Target: x86_64-apple-darwin18.6.0
> Thread model: posix
> InstalledDir: /Library/Developer/CommandLineTools/usr/bin
> 
> 
> For R version 3.6.0, I did
> update.packages()
> after replying Y to install from sources, R was 'pointing' at 
> /usr/local/Cellar/gcc/8.2.0/bin/gcc-8, and the source versions were 
> failing to update.
> 
> I have recently updated to R version 3.6.1, and after Googling have 
> manually updated the ~/.R/MakeVars file (which had 8.2.0's and g++-8, in 
> the appropriate places) to:
> CC=/usr/local/Cellar/gcc/9.1.0/bin/gcc-9CXX=/usr/local/Cellar/gcc/9.1.0/bin/g++-9CXX11=/usr/local/Cellar/gcc/9.1.0/bin/g++-9CXX14=/usr/local/Cellar/gcc/9.1.0/bin/g++-9cxx17=/usr/local/cellar/gcc/9.1.0/bin/g++-9cxx1X=/usr/local/cellar/gcc/9.1.0/bin/g++-9LDFLAGS=-L/usr/local/Cellar/gcc/9.1.0/lib
> 
> 
> If now do
> update.packages()
> the source versions still don't update.
> 
> For example, for package vctrs I get:
> Do you want to install from sources the package which needs compilation? 
> (Yes/no/cancel) yinstalling the source package ‘vctrs’trying URL 
> 'https://cloud.r-project.org/src/contrib/vctrs_0.2.0.tar.gz'Content type 
> 'application/x-gzip' length 668258 bytes (652 
> KB)==================================================downloaded 652 KB* 
> installing *source* package ‘vctrs’ ...** package ‘vctrs’ successfully 
> unpacked and MD5 sums checked** using staged installation** 
> libs/usr/local/Cellar/gcc/9.1.0/bin/gcc-9 
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG 
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
> -I/usr/local/include  -fPIC  -Wall -g -O2  -c arg-counter.c -o 
> arg-counter.oIn file included from 
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdlib.h:61, 
> from /Library/Frameworks/R.framework/Resources/include/R.h:55, 
> from vctrs.h:2,                 from 
> arg-counter.c:1:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/Availability.h:257:22: 
> error: missing binary operator before token "("  257 |     #if 
> __has_builtin(__is_target_arch)      |                      ^make: *** 
> [arg-counter.o] Error 1ERROR: compilation failed for package ‘vctrs’* 
> removing 
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/vctrs’* 
> restoring previous 
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/vctrs’The 
> downloaded source packages are in	 
> ‘/private/var/folders/r3/40n9b5sd0s789hw9h_vgt6500000gn/T/Rtmp3P2lwy/downloaded_packages’Warning 
> message:In install.packages(update[instlib == l, "Package"], l, repos = 
> repos,  :  installation of package ‘vctrs’ had non-zero exit status
> 
> 
> 
> Please advise,
> Many thanks,
> Amarjit
> 
> 
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> 
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