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@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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac