OK. This is a pre-Stan problem (although there will be Stan problems once you get past this). Maybe @coatless recognizes this error with helloworld.cpp ?
Well thatās good to know (I guess) ā¦ I had RStan working 2 days ago until Catalina appeared. So the question is did the update do break that component or once something further down the track broke, did I break something upstream.
Catalina triggered the unknown exceptions problem, but that wouldnāt be relevant to that helloworld.cpp thing.
So I had some progress.
I applied this fix to Makevars
sudo touch ~/.R/Makevars && sudo echo 'CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"' >> ~/.R/Makevars
and this now runs:
example(stan_model, run.dontrun = TRUE)
which is great ā¦
but when I run something in brms
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] " c++ exception (unknown reason)"
back where we were!
Itās a game of inches I guess.
and helloworld.cpp works now crucially
OK. Weāll post on the Dealing with Catalina thread once we figure out how to deal with the āc++ exception (unknown reason)ā.
Quick note:
This is required on R 3.6.0. R version 3.6.1 and higher does not need this statement.
That said, better flag instructions probably would be:
sudo mkdir -p ~/.R
# Fill with appropriate flag statements
sudo cat <<- EOF > ~/.R/Makevars
# clang: start
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
# clang: end
EOF
Note the addition of CPPFLAGS.
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@bgoodri and @coatless, Iāve sent some more info in the other thread, but I tested something else now. I removed .R/Makevars completely. Then I ran foo.R (1.5 KB).
If I remove Makevars it samples nicely. If I put it back it gives me:
c++ exception (unknown reason)
and if I remove Makevars again, it samples nicely againā¦
My Makevars looks like this:
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
And if I put " around the ā-isysroot ā¦ sdkā it doesnāt work, and since itās a directory I even tried putting / at the end.
But now I tried another example and it gave me the same errorā¦
I use
system(āclang++ --versionā)
clang version 7.0.0 (tags/RELEASE_700/final)
Target: x86_64-apple-darwin19.0.0
Thread model: posix
InstalledDir: /usr/local/clang7/bin
1 Like
thanks @coatless, Iāve updated my flag instructions.
Thanks!!! This solved a similar problem on Mac M1 Monterey
For folks stumbling upon this issue, please note weāve discontinued the macOS installer package that set up the toolchain in favor of an R package called {macrtools}. You can obtain it from:
Code:
# install.packages("remotes")
remotes::install_github("coatless-mac/macrtools")
macrtools::macos_rtools_install()
Walkthrough video:
For more details, please see: