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