I have an Intel-based macOS machine and have yet to resolve a path forward with cmdstan/cmdstanr after upgrading to Ventura (13.0). I’ve managed to replicate this issue on two different computers (both Intel macOS Ventura).
When I run cmdstanr::install_cmdstan() I get a an error at xattr -d com.apple.quarantine bin/stanc. From what I’ve been able to gather, the xattr -d com.apple.quarantine bin/stanc is attempting to change the attributes/metadata of the Stan compiler, so something is different about the way things get unpacked from GitHub by cmdstanr::install_cmdstan() that is unique to Intel-based macOS. Multiple people (@torkar, @Ara_Winter) have reported no issues with Apple chips.
I’m savvy enough to follow instructions for tweaking/adapting build instructions via Terminal, but not the person to invent novel work-arounds for these kinds of issues. Grateful for any help from the community!
- Operating System: macOS Ventura (13.0)
- CmdStan Version: 2.30.1
- Compiler/Toolkit: GitHub via CmdStanR
1 Like
Can you post the error you get from that command?
Sure, @andrjohns . The error I get from that command in particular is xattr: bin/stanc: No such xattr: com.apple.quarantine. I’ll go ahead and include my full R console output for reference:
> cmdstanr::install_cmdstan()
The C++ toolchain required for CmdStan is setup properly!
* Latest CmdStan release is v2.30.1
* Installing CmdStan v2.30.1 in /Users/pokey54/.cmdstan/cmdstan-2.30.1
* Downloading cmdstan-2.30.1.tar.gz from GitHub...
* Download complete
* Unpacking archive...
* Building CmdStan binaries...
cp bin/mac-stanc bin/stanc
clang++ -pipe -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.1.1/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.1.1/src/nvector/serial/nvector_serial.c -o stan/lib/stan_math/lib/sundials_6.1.1/src/nvector/serial/nvector_serial.o
chmod +x bin/stanc
xattr -d com.apple.quarantine bin/stanc
xattr: bin/stanc: No such xattr: com.apple.quarantine
make: *** [bin/stanc] Error 1
make: *** Waiting for unfinished jobs....
Warning message:
There was a problem during installation. See the error message(s) above.
And here’s the details for my R session, although the error above manifests with slight modifications of packages loaded, etc.
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.0
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.1 cli_3.4.1 tools_4.2.1
1 Like
Hi,
I am just echoing the question because I am having the exact same issue.
Is there some incompatibility between CmdStan and the OS Ventura?
cp bin/mac-stanc bin/stanc
arch -arch arm64e clang++ -pipe -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.1.1/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.1.1/src/nvector/serial/nvector_serial.c -o stan/lib/stan_math/lib/sundials_6.1.1/src/nvector/serial/nvector_serial.o
arch -arch arm64e clang++ -pipe -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.1.1/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.1.1/src/sundials/sundials_math.c -o stan/lib/stan_math/lib/sundials_6.1.1/src/sundials/sundials_math.o
arch -arch arm64e clang++ -pipe -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -O3 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DNO_FPRINTF_OUTPUT -O3 -c -x c -include stan/lib/stan_math/lib/sundials_6.1.1/include/stan_sundials_printf_override.hpp stan/lib/stan_math/lib/sundials_6.1.1/src/cvodes/cvodea.c -o stan/lib/stan_math/lib/sundials_6.1.1/src/cvodes/cvodea.o
chmod +x bin/stanc
xattr -d com.apple.quarantine bin/stanc
xattr: bin/stanc: No such xattr: com.apple.quarantine
make: *** [bin/stanc] Error 1
make: *** Waiting for unfinished jobs....
Warning message:
There was a problem during installation. See the error message(s) above.
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.0
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0
The issue seems to be related to Rstudio. I managed to run with no errors by using R directly.
This particular issues seems to be a bit more pervasive than my description of the problem. This thread seems to bump into the same issue, however, it seems like cmdstan/cmdstanrwill run (with some warning that can be safely ignored). It seems like this issue will go away with the next release.
Good to know that install via R directly will work without warnings or errors!