Compile error on MacOS and Pystan

Interfaces PyStan
1

Getting a compilation error with pystan on MacOS, doesn’t appear to be the same as others already described.

  • OSX 10.15.15
  • pystan 2.19.1.1
  • python 3.7
  • using (or attempting to use) the anaconda compiler
  • already installed xcode with “xcode-select install”

Following the instructions here

What I believe is the relevant compiler output, in particular the “ld: unknown option: -platform_version”:

x86_64-apple-darwin13.4.0-clang++ -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/pdt2/o
pt/anaconda3/envs/phenom/lib -L/Users/pdt2/opt/anaconda3/envs/phenom/lib -flto -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_
dylibs -Wl,-rpath,/Users/pdt2/opt/anaconda3/envs/phenom/lib -L/Users/pdt2/opt/anaconda3/envs/phenom/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_s
trip_dylibs -Wl,-rpath,/Users/pdt2/opt/anaconda3/envs/phenom/lib -L/Users/pdt2/opt/anaconda3/envs/phenom/lib -march=core2 -mtune=haswell -mssse3 -ftree-vecto
rize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/pdt2/opt/anaconda3/envs/phenom/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isy
stem /Users/pdt2/opt/anaconda3/envs/phenom/include -arch x86_64 /var/folders/cz/7j2rv40n30z87t2fq2c51vrh001wdz/T/pystan_amcoits0/var/folders/cz/7j2rv40n30z87
t2fq2c51vrh001wdz/T/pystan_amcoits0/stanfit4anon_model_5944b02c79788fa0db5b3a93728ca2bf_5600958195541983510.o -o /var/folders/cz/7j2rv40n30z87t2fq2c51vrh001w
dz/T/pystan_amcoits0/stanfit4anon_model_5944b02c79788fa0db5b3a93728ca2bf_5600958195541983510.cpython-37m-darwin.so
ld: unknown option: -platform_version
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
Traceback (most recent call last):
File “/Users/pdt2/opt/anaconda3/envs/phenom/lib/python3.7/distutils/unixccompiler.py”, line 205, in link
self.spawn(linker + ld_args)
File “/Users/pdt2/opt/anaconda3/envs/phenom/lib/python3.7/distutils/ccompiler.py”, line 910, in spawn
spawn(cmd, dry_run=self.dry_run)
File “/Users/pdt2/opt/anaconda3/envs/phenom/lib/python3.7/distutils/spawn.py”, line 36, in spawn
_spawn_posix(cmd, search_path, dry_run=dry_run)
File “/Users/pdt2/opt/anaconda3/envs/phenom/lib/python3.7/distutils/spawn.py”, line 159, in _spawn_posix
% (cmd, exit_status))
distutils.errors.DistutilsExecError: command ‘x86_64-apple-darwin13.4.0-clang++’ failed with exit status 1

2

This answer indicated that a compiler flag can help, but I’m not sure how to accomplish that with stan compilation

3

Do you have both xcode compiler and anaconda compiler?

Maybe this is something similar as in libc++ vs libstdc++.

What happens if you try to compile with xcode?

4

And,

currently, there probably isn’t a way to add extra_link_args (but it goes to same location as does extra_compile_args).

5

Thanks for the fast reply! Solution was to update Xcode - duh!