Hello Cmdstan community! I upgraded to MacOS Ventura recently, and (as usual) it screwed up my whole conda data science setup.
I am hoping to use Cmdstan with conda (miniforge, specfically); and I cannot compile the Bernoulli example.
My setup is the following:
- Operating System: MacOS Ventura 13.3.1
- CmdStan Version: 2.31 (conda-forge)
- Compiler/Toolkit: Xcode 14.3
After getting stuck in a spagetti of installations I uninstalled as much as possible and did as fresh as possible of full installation. Here is my step-by-step procedure. I hope someone can help.
My procedure
- Deleted XCode Command Line Tools, Xcode, and entire conda installation (miniconda3)
- Restarted computer
- Made sure
clang --versionfails - Installed Xcode 14.3 from App Store
- Opened Xcode
- Check
clang --version:
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
Target: x86_64-apple-darwin22.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
Looks good!
7. Restarted computer
8. Installed miniforge
9. Created env: conda create -n Stan232 cmdstan (success)
Conda packages:
## Package Plan ##
environment location: /Users/thomaskeefe/miniforge3/envs/Stan233
added / updated specs:
- cmdstan
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/osx-64::ca-certificates-2022.12.7-h033912b_0
cctools_osx-64 conda-forge/osx-64::cctools_osx-64-973.0.1-hcc6d90d_13
clang conda-forge/osx-64::clang-14.0.6-h694c41f_0
clang-14 conda-forge/osx-64::clang-14-14.0.6-default_h55ffa42_0
clang_osx-64 conda-forge/osx-64::clang_osx-64-14.0.6-h3113cd8_6
clangxx conda-forge/osx-64::clangxx-14.0.6-default_h55ffa42_0
clangxx_osx-64 conda-forge/osx-64::clangxx_osx-64-14.0.6-h6f97653_6
cmdstan conda-forge/osx-64::cmdstan-2.31.0-h21365d3_0
compiler-rt conda-forge/osx-64::compiler-rt-14.0.6-h613da45_0
compiler-rt_osx-64 conda-forge/noarch::compiler-rt_osx-64-14.0.6-hab78ec2_0
ld64_osx-64 conda-forge/osx-64::ld64_osx-64-609-hfd63004_13
libclang-cpp14 conda-forge/osx-64::libclang-cpp14-14.0.6-default_h55ffa42_0
libcxx conda-forge/osx-64::libcxx-16.0.1-h71dddab_0
libllvm14 conda-forge/osx-64::libllvm14-14.0.6-h5b596cc_1
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
llvm-tools conda-forge/osx-64::llvm-tools-14.0.6-h5b596cc_1
make conda-forge/osx-64::make-4.3-h22f3db7_1
openssl conda-forge/osx-64::openssl-3.1.0-hfd90126_0
sigtool conda-forge/osx-64::sigtool-0.1.3-h88f4db0_0
tapi conda-forge/osx-64::tapi-1100.0.11-h9ce4665_0
tbb conda-forge/osx-64::tbb-2021.9.0-hb8565cd_0
tbb-devel conda-forge/osx-64::tbb-devel-2021.9.0-hb8565cd_0
Env looks good, now we activate it and try to compile Bernoulli:
conda activate Stan232- Navigate to cmdstan dir:
cd $CMDSTAN -
export CXXFLAGS="$CXXFLAGS -Wno-deprecated-declarations"(to hide some warnings) make examples/bernoulli/bernoulli
I have to post the output in 2 parts to fit the 32,000 char limit.
--- Compiling, linking C++ code ---
x86_64-apple-darwin13.4.0-clang++ -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/thomaskeefe/miniforge3/envs/Stan232/include -Wno-deprecated-declarations -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes -I /Users/thomaskeefe/miniforge3/envs/Stan232/include/ -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.9 -I stan/lib/stan_math/lib/boost_1.78.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -D_FORTIFY_SOURCE=2 -isystem /Users/thomaskeefe/miniforge3/envs/Stan232/include -DBOOST_DISABLE_ASSERTS -DTBB_INTERFACE_NEW -DTBB_INTERFACE_NEW -c -x c++ -o examples/bernoulli/bernoulli.o examples/bernoulli/bernoulli.hpp
In file included from examples/bernoulli/bernoulli.hpp:3:
In file included from stan/src/stan/model/model_header.hpp:4:
In file included from stan/lib/stan_math/stan/math.hpp:19:
In file included from stan/lib/stan_math/stan/math/rev.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Core:96:
In file included from /Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/complex:236:
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/cmath:607:12: error: no matching function for call to 'isinf'
return std::isinf(__lcpp_x);
^~~~~~~~~~
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/complex:598:29: note: in instantiation of function template specialization 'std::__constexpr_isinf<stan::math::var_value<double>>' requested here
bool __z_inf = std::__constexpr_isinf(__a) || std::__constexpr_isinf(__b);
^
stan/lib/stan_math/stan/math/prim/fun/asinh.hpp:64:31: note: in instantiation of function template specialization 'std::operator*<stan::math::var_value<double>>' requested here
auto y = log(z + sqrt(1 + z * z));
^
stan/lib/stan_math/stan/math/rev/fun/asinh.hpp:89:32: note: in instantiation of function template specialization 'stan::math::internal::complex_asinh<stan::math::var_value<double>>' requested here
return stan::math::internal::complex_asinh(z);
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:429:87: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'float' for 1st argument
_LIBCPP_NODISCARD_EXT inline _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isinf(float __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:433:114: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'double' for 1st argument
_LIBCPP_NODISCARD_EXT inline _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI _LIBCPP_PREFERRED_OVERLOAD bool isinf(double __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:437:87: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'long double' for 1st argument
_LIBCPP_NODISCARD_EXT inline _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isinf(long double __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:417:80: note: candidate template ignored: requirement 'std::is_arithmetic<stan::math::var_value<double, void>>::value' was not satisfied [with _A1 = stan::math::var_value<double>]
_LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isinf(_A1 __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:424:5: note: candidate template ignored: requirement 'std::is_arithmetic<stan::math::var_value<double, void>>::value' was not satisfied [with _A1 = stan::math::var_value<double>]
isinf(_A1) _NOEXCEPT {
^
In file included from examples/bernoulli/bernoulli.hpp:3:
In file included from stan/src/stan/model/model_header.hpp:4:
In file included from stan/lib/stan_math/stan/math.hpp:19:
In file included from stan/lib/stan_math/stan/math/rev.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Core:96:
In file included from /Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/complex:236:
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/cmath:587:12: error: no matching function for call to 'isnan'
return std::isnan(__lcpp_x);
^~~~~~~~~~
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/complex:601:19: note: in instantiation of function template specialization 'std::__constexpr_isnan<stan::math::var_value<double>>' requested here
(std::__constexpr_isnan(__a) && std::__constexpr_isnan(__b))
^
stan/lib/stan_math/stan/math/prim/fun/asinh.hpp:64:31: note: in instantiation of function template specialization 'std::operator*<stan::math::var_value<double>>' requested here
auto y = log(z + sqrt(1 + z * z));
^
stan/lib/stan_math/stan/math/rev/fun/asinh.hpp:89:32: note: in instantiation of function template specialization 'stan::math::internal::complex_asinh<stan::math::var_value<double>>' requested here
return stan::math::internal::complex_asinh(z);
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:455:87: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'float' for 1st argument
_LIBCPP_NODISCARD_EXT inline _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isnan(float __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:459:114: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'double' for 1st argument
_LIBCPP_NODISCARD_EXT inline _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI _LIBCPP_PREFERRED_OVERLOAD bool isnan(double __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:463:87: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'long double' for 1st argument
_LIBCPP_NODISCARD_EXT inline _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isnan(long double __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:445:80: note: candidate template ignored: requirement 'std::is_floating_point<stan::math::var_value<double, void>>::value' was not satisfied [with _A1 = stan::math::var_value<double>]
_LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isnan(_A1 __x) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/math.h:450:80: note: candidate template ignored: requirement 'std::is_integral<stan::math::var_value<double, void>>::value' was not satisfied [with _A1 = stan::math::var_value<double>]
_LIBCPP_NODISCARD_EXT _LIBCPP_CONSTEXPR_SINCE_CXX23 _LIBCPP_HIDE_FROM_ABI bool isnan(_A1) _NOEXCEPT {
^
In file included from examples/bernoulli/bernoulli.hpp:3:
In file included from stan/src/stan/model/model_header.hpp:4:
In file included from stan/lib/stan_math/stan/math.hpp:19:
In file included from stan/lib/stan_math/stan/math/rev.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22:
In file included from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Dense:1:
In file included from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Core:96:
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/complex:637:19: error: no matching function for call to '__constexpr_copysign'
__a = std::__constexpr_copysign(std::__constexpr_isinf(__a) ? _Tp(1) : _Tp(0), __a);
^~~~~~~~~~~~~~~~~~~~~~~~~
stan/lib/stan_math/stan/math/prim/fun/asinh.hpp:64:31: note: in instantiation of function template specialization 'std::operator*<stan::math::var_value<double>>' requested here
auto y = log(z + sqrt(1 + z * z));
^
stan/lib/stan_math/stan/math/rev/fun/asinh.hpp:89:32: note: in instantiation of function template specialization 'stan::math::internal::complex_asinh<stan::math::var_value<double>>' requested here
return stan::math::internal::complex_asinh(z);
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/cmath:630:54: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'float' for 1st argument
_LIBCPP_CONSTEXPR inline _LIBCPP_HIDE_FROM_ABI float __constexpr_copysign(float __x, float __y) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/cmath:634:55: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'double' for 1st argument
_LIBCPP_CONSTEXPR inline _LIBCPP_HIDE_FROM_ABI double __constexpr_copysign(double __x, double __y) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/cmath:639:1: note: candidate function not viable: no known conversion from 'stan::math::var_value<double>' to 'long double' for 1st argument
__constexpr_copysign(long double __x, long double __y) _NOEXCEPT {
^
/Users/thomaskeefe/miniforge3/envs/Stan232/bin/../include/c++/v1/cmath:647:5: note: candidate template ignored: requirement 'std::is_arithmetic<stan::math::var_value<double, void>>::value' was not satisfied [with _A1 = stan::math::var_value<double>, _A2 = stan::math::var_value<double>]
__constexpr_copysign(_A1 __x, _A2 __y) _NOEXCEPT {
^
Grateful for any help. Thank you!