After an upgrade to MacOS Catalina, I find that I can no longer install packages from source in the RStudio IDE (v1.2.5001, current stable release).
Example:
> install.packages("processx", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/processx_3.4.1.tar.gz'
Content type 'application/x-gzip' length 123430 bytes (120 KB)
==================================================
downloaded 120 KB
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** libs
/usr/local/clang4/bin/clang -Wall -g -O2 -Wall tools/px.c -o tools/px
make: *** [tools/px] Killed: 9
ERROR: compilation failed for package ‘processx’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/processx’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/processx’
Warning in install.packages :
installation of package ‘processx’ had non-zero exit status
In the process I get a popup with this message:
“clang-4.0” cannot be opened because the developer cannot be verified.
It seems that RStudio is pointed at clang from XCode 11.1, rather than the clang 8 I got from CRAN https://cran.r-project.org/bin/macosx/tools/.
Straight from R (e.g. sudo -i R in my terminal) a source install works fine, so it seems to be a matter of getting RStudio to look in the right place for the clang binary.
Any ideas?
I changed my ~/.R/Makevars file to point to a newer version of clang (R recommends 8+), e.g. CC=/usr/local/opt/llvm/bin/clang. I commented out the clang4 lines and created a new set pointing to the updated clang. Worked like a charm, now able to install R packages as usual.
Note: I had previously used brew to update llvm, which installed clang9.
Hope that helps!