On Jul 8, 2019, at 04:21, a.chandhial--- via R-SIG-Mac <r-sig-mac at 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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