Trouble with installing cmdstan on Mac OS X - Big Sur

Interfaces
1

I’ve seen that others have been having this problem, but I can’t find anything that helps. I have a Mac Book Pro with the new M1 chip. I actually was able to install cmdstan just fine a few weeks ago on this machine and was using cmdstanr to estimate models. Things were working very well - and the performance was superb - more than a 5-fold increase in speed.

But then I (dumbly) upgraded to the latest version of Big Sur (11.3). I am also using development versions of R and Rstudio (again, it was all working well before). I can install the cmdstanr package, but cannot install cmdstan without errors. I was wondering if anyone might have some insight - I have literally spent 2 days trying to figure this out, so this is my last ditch effort to if others have figured out a solution.

Here’s my session info:

R version 4.1.0 alpha (2021-04-26 r80229)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/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] ps_1.5.0          crayon_1.4.1      digest_0.6.27     R6_2.5.0          jsonlite_1.7.2   
 [6] backports_1.2.1   magrittr_2.0.1    evaluate_0.14     rlang_0.4.10      stringi_1.5.3    
[11] checkmate_2.0.0   rmarkdown_2.7     tools_4.1.0       stringr_1.4.0     processx_3.4.5   
[16] xfun_0.22         yaml_2.2.1        parallel_4.1.0    compiler_4.1.0    htmltools_0.5.1.1
[21] cmdstanr_0.4.0    knitr_1.33

I’ve installed the latest version of gcc using homebrew, and I am using this Makevars file (and I’ve tried this without the Makevars file as well):

VER=-10.2.0_4
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10

The Apple installation of gcc version 4.2.1 is in the \usr\bin directory, and I am trying to avoid using that.

And finally - here are the first set of errors that I get when trying to run install_cmdstan(). It continues like this for a while:

The C++ toolchain required for CmdStan is setup properly!
* Latest CmdStan release is v2.26.1
* Installing CmdStan v2.26.1 in /Users/keith/.cmdstanr/cmdstan-2.26.1
* Downloading cmdstan-2.26.1.tar.gz from GitHub...
* Download complete
* Unpacking archive...
* Building CmdStan binaries...
cp bin/mac-stanc bin/stanc
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I 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_1.72.0 -I stan/lib/stan_math/lib/sundials_5.6.1/include    -DBOOST_DISABLE_ASSERTS         -c -fvisibility=hidden -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp
chmod +x bin/stanc
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I 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_1.72.0 -I stan/lib/stan_math/lib/sundials_5.6.1/include    -DBOOST_DISABLE_ASSERTS         -c -fvisibility=hidden -o bin/cmdstan/print.o src/cmdstan/print.cpp
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace
using ::isfinite;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
2

is there a reason you’re using g++ and not clang?

3

I’ve tried everything - just recently this Makevars, with the same result:

LLVM_LOC = /opt/homebrew/opt/llvm
CC=$(LLVM_LOC)/bin/clang 
CXX=$(LLVM_LOC)/bin/clang++
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
# CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
# CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
4

I’ve got an old MacBook (13-inch, early 2015) that’s at latest version of Big Sur and Xcode,
and I just did a fresh install of CmdStan - no problem. see: 1 CmdStan Installation | CmdStan User’s Guide

I think you need to use XCode, and the xcode-select CLI, unless there’s some M1 Xcode issue - is there? I don’t know about Makevars and LLVM_LOC - (not an R fan) - but with XCode, llvm and clang++ are all under /Library/Developer/CommandLineTools/usr/bin

the problems you’re seeing sound similar to what happened a while back here: Upgrade to Catalina incurred problems building math lib dynamic archives (sundials) - #2 by mitzimorris

5

Big Sur and M1 work very well with cmdstan. I cannot attest for R side, as I use python.

1 Like
6

and another “like” for using Python ;-)

1 Like
7

I totally believe you guys, as I had it working before on this same M1 machine with Big Sur, and it was great. And I didn’t have to mess with the Makevars or anything to get it working.

I had already installed Xcode and everything is in /Library/Developer/CommandLineTools/usr/bin. And PATH is set to /Library/Developer/CommandLineTools/usr/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin:/Applications/RStudio.app/Contents/MacOS/postback, (and there is no longer a Makevars file) but I am still getting the same error messages:

The C++ toolchain required for CmdStan is setup properly!
* Latest CmdStan release is v2.26.1
* Installing CmdStan v2.26.1 in /Users/keith/.cmdstanr/cmdstan-2.26.1
* Downloading cmdstan-2.26.1.tar.gz from GitHub...
* Download complete
* Unpacking archive...
* Building CmdStan binaries...
cp bin/mac-stanc bin/stanc
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I 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_1.72.0 -I stan/lib/stan_math/lib/sundials_5.6.1/include    -DBOOST_DISABLE_ASSERTS         -c -fvisibility=hidden -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp
chmod +x bin/stanc
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I 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_1.72.0 -I stan/lib/stan_math/lib/sundials_5.6.1/include    -DBOOST_DISABLE_ASSERTS         -c -fvisibility=hidden -o bin/cmdstan/print.o src/cmdstan/print.cpp
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace
using ::isfinite;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace
using ::isfinite;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:329:7: error: no member named 'isless' in the global namespace; did you mean 'boost::is_less'?
using ::isless;
      ^~
stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/compare.hpp:191:22: note: 'boost::is_less' declared here
    using algorithm::is_less;
                     ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:330:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:331:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:332:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:329:7: error: no member named 'isless' in the global namespace; did you mean 'boost::is_less'?
using ::isless;
      ^~
stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/compare.hpp:191:22: note: 'boost::is_less' declared here
    using algorithm::is_less;
                     ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:333:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:330:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:331:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:332:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:333:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/err/invalid_argument.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/meta.hpp:175:
In file included from stan/lib/stan_math/stan/math/prim/meta/append_return_type.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:374:
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:722:16: error: no member named 'isfinite' in namespace 'std'
    using std::isfinite;
          ~~~~~^
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:737:16: error: no member named 'isinf' in namespace 'std'
    using std::isinf;
          ~~~~~^
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:752:16: error: no member named 'isnan' in namespace 'std'
    using std::isnan;
          ~~~~~^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/err/invalid_argument.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/meta.hpp:175:
In file included from stan/lib/stan_math/stan/math/prim/meta/append_return_type.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:374:
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:722:16: error: no member named 'isfinite' in namespace 'std'
    using std::isfinite;
          ~~~~~^
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:737:16: error: no member named 'isinf' in namespace 'std'
    using std::isinf;
          ~~~~~^
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:752:16: error: no member named 'isnan' in namespace 'std'
    using std::isnan;
          ~~~~~^
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast.hpp:32:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:63:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/inf_nan.hpp:34:
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/sign.hpp:30:17: error: no member named 'signbit' in namespace 'std'; did you mean simply 'signbit'?
        return (std::signbit)(x) ? 1 : 0;
                ^~~~~~~~~~~~
                signbit
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:891:8: note: 'signbit' declared here
   int signbit BOOST_NO_MACRO_EXPAND(T x);
       ^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast.hpp:32:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:63:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/inf_nan.hpp:34:
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/sign.hpp:30:17: error: no member named 'signbit' in namespace 'std'; did you mean simply 'signbit'?
        return (std::signbit)(x) ? 1 : 0;
                ^~~~~~~~~~~~
                signbit
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:891:8: note: 'signbit' declared here
   int signbit BOOST_NO_MACRO_EXPAND(T x);
       ^
In file included from src/cmdstan/stansummary.cpp:1:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast.hpp:32:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:63:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/inf_nan.hpp:35:
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/fpclassify.hpp:155:12: error: no member named 'fpclassify' in namespace 'std'; did you mean simply 'fpclassify'?
   return (std::fpclassify)(t);
           ^~~~~~~~~~~~~~~
           fpclassify
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:876:8: note: 'fpclassify' declared here
   int fpclassify BOOST_NO_MACRO_EXPAND(T t);
       ^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast.hpp:32:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:63:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/inf_nan.hpp:35:
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/fpclassify.hpp:155:12: error: no member named 'fpclassify' in namespace 'std'; did you mean simply 'fpclassify'?
   return (std::fpclassify)(t);
           ^~~~~~~~~~~~~~~
           fpclassify
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:876:8: note: 'fpclassify' declared here
   int fpclassify BOOST_NO_MACRO_EXPAND(T t);
       ^

        return (std::isfinite)(x);
                ^~~~~~~~~~~~~
                isfinite
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:879:9: note: 'isfinite' declared here
   bool isfinite BOOST_NO_MACRO_EXPAND(T z);
        ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [bin/cmdstan/print.o] Error 1
make: *** Waiting for unfinished jobs....
20 errors generated.
make: *** [bin/cmdstan/stansummary.o] Error 1

Warning message:
There was a problem during installation. See the error message(s) above.
8

Sorry just for clarification, on big sur are you able to do a fresh build of cmdstan? Those errors look like they are include errors when its trying to get definitions from xcode for things in the standard library headers

9

I am not able to do a fresh build of cmdstan. These are the errors I get when I run cmdstanr::install_cmdstan().

I am not sure this is relevant, but when I run clang++ --version this is what I get:

Apple clang version 12.0.5 (clang-1205.0.22.9)
Target: arm64-apple-darwin20.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

And when I run make --version, this is what I get

GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

This program built for i386-apple-darwin11.3.0

This seems a bit odd since it does not indicate it was built from arm64, but maybe that doesn’t matter?

10

Just an update - I did update the make file so now we have

make --version

GNU Make 4.3
Built for arm-apple-darwin20.2.0
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Unfortunately, the results is the same.

11

Just an update - I did update the make file so now we have

commands to run, from CmdStan top-level directory are - i.e. ~/.cmdstanr/cmdstan-2.26.1 if you’re using CmdStanR’s install_cmdstan function:

> make clean-all
> make build

(fwiw, I was kinda hoping we could get to common install dir for all CmdStanX interfaces - coordinate with CmdStanPy - single `.cmdstan` dir for install of CmdStan · Issue #454 · stan-dev/cmdstanr · GitHub)

12

Sorry it’s not clear to me, are you calling this from cmdstanr or did you try cloning cmdstan and running make build from there?

13

My worry is that something from a previous cmdstanr build or Rs makevars could be causing the issue

1 Like
14

looks like CmdStanR has function rebuild_cmdstan - Install CmdStan or clean and rebuild an existing installation — install_cmdstan • cmdstanr

15

I am calling cmdstanr::install_cmdstan() within Rstudio (though I’ve also tried in R). To be clear, at this stage I’m just trying to build Cmdstan.

16

I’m unclear if I should be trying something else, or if you guys are still thinking.

17

I’d like to know what when wrong, so if you’ll bear with us and help with diagnosing/debugging - back to your first message:

upgraded to the latest version of Big Sur (11.3). I am also using development versions of R and Rstudio (again, it was all working well before). I can install the cmdstanr package, but cannot install cmdstan without errors

could you try working in a terminal window and install CmdStan in a new directory - e.g. ~/scratch -
and could you try installing the latest release, 2.26.1 from the CmdStan releases page here:

you want to get this file: https://github.com/stan-dev/cmdstan/releases/download/v2.26.1/cmdstan-2.26.1.tar.gz

unpack the file, cd to directory cmdstan-2.26.1 then do make build - unless you’ve got environment variables set, this should work

1 Like
18

Didn’t work.

Here’s my PATH :

/opt/homebrew/bin:/opt/homebrew/sbin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin

And here is the output:

keith@180MADPHMLT052 cmdstan-2.26.1 % make build
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I 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_1.72.0 -I stan/lib/stan_math/lib/sundials_5.6.1/include    -DBOOST_DISABLE_ASSERTS               -Wl,-L,"/Users/keith/scratch/cmdstan-2.26.1/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/Users/keith/scratch/cmdstan-2.26.1/stan/lib/stan_math/lib/tbb"      bin/cmdstan/stansummary.o         -o bin/stansummary
ld: warning: directory not found for option '-L/Users/keith/scratch/cmdstan-2.26.1/stan/lib/stan_math/lib/tbb'
clang++ -std=c++1y -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2019_U8/include   -O3 -I src -I stan/src -I 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_1.72.0 -I stan/lib/stan_math/lib/sundials_5.6.1/include    -DBOOST_DISABLE_ASSERTS         -c -fvisibility=hidden -o bin/cmdstan/print.o src/cmdstan/print.cpp
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace
using ::isfinite;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:329:7: error: no member named 'isless' in the global namespace; did you mean 'boost::is_less'?
using ::isless;
      ^~
stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/compare.hpp:191:22: note: 'boost::is_less' declared here
    using algorithm::is_less;
                     ^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:4:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string.hpp:23:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/split.hpp:16:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/iter_find.hpp:27:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/find_iterator.hpp:24:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/detail/find_iterator.hpp:18:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function.hpp:30:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/detail/prologue.hpp:17:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/function/function_base.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index.hpp:29:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/type_index/stl_type_index.hpp:47:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/hash.hpp:21:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/hash_float.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/container_hash/detail/float_functions.hpp:14:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/no_tr1/cmath.hpp:21:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:330:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:331:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:332:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:333:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/err/invalid_argument.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/meta.hpp:175:
In file included from stan/lib/stan_math/stan/math/prim/meta/append_return_type.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:374:
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:722:16: error: no member named 'isfinite' in namespace 'std'
    using std::isfinite;
          ~~~~~^
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:737:16: error: no member named 'isinf' in namespace 'std'
    using std::isinf;
          ~~~~~^
stan/lib/stan_math/lib/eigen_3.3.9/Eigen/src/Core/MathFunctions.h:752:16: error: no member named 'isnan' in namespace 'std'
    using std::isnan;
          ~~~~~^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast.hpp:32:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:63:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/inf_nan.hpp:34:
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/sign.hpp:30:17: error: no member named 'signbit' in namespace 'std'; did you mean simply 'signbit'?
        return (std::signbit)(x) ? 1 : 0;
                ^~~~~~~~~~~~
                signbit
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:891:8: note: 'signbit' declared here
   int signbit BOOST_NO_MACRO_EXPAND(T x);
       ^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast.hpp:32:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:63:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/inf_nan.hpp:35:
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/fpclassify.hpp:155:12: error: no member named 'fpclassify' in namespace 'std'; did you mean simply 'fpclassify'?
   return (std::fpclassify)(t);
           ^~~~~~~~~~~~~~~
           fpclassify
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:876:8: note: 'fpclassify' declared here
   int fpclassify BOOST_NO_MACRO_EXPAND(T t);
       ^
In file included from src/cmdstan/print.cpp:2:
In file included from src/cmdstan/stansummary_helper.hpp:4:
In file included from stan/src/stan/mcmc/chains.hpp:4:
In file included from stan/src/stan/io/stan_csv_reader.hpp:5:
In file included from stan/lib/stan_math/stan/math/prim.hpp:10:
In file included from stan/lib/stan_math/stan/math/prim/core.hpp:4:
In file included from stan/lib/stan_math/stan/math/prim/core/init_threadpool_tbb.hpp:6:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast.hpp:32:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical.hpp:54:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/converter_lexical_streams.hpp:63:
In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/lexical_cast/detail/inf_nan.hpp:35:
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/fpclassify.hpp:314:17: error: no member named 'isfinite' in namespace 'std'; did you mean simply 'isfinite'?
        return (std::isfinite)(x);
                ^~~~~~~~~~~~~
                isfinite
stan/lib/stan_math/lib/boost_1.72.0/boost/math/special_functions/math_fwd.hpp:879:9: note: 'isfinite' declared here
   bool isfinite BOOST_NO_MACRO_EXPAND(T z);
        ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [bin/cmdstan/print.o] Error 1
19

so you installed CmdStanR and then used it to install CmdStan and then you compiled and ran some of your models and everything was OK?

then you upgraded to Big Sur 11.3 and everything broke?

the problem looks like the compiler can’t find the standard libraries - this flag:

your path makes it look like you have installed a bunch of stuff using Homebrew. I’m not sure what the M1 situation is, but I think what you want to do is get a clean install of XCode and then install the Xcode command line tools and maybe fix your path. here’s some SO discussion that might be valid for M1/Big Sur: python - Big Sur clang "invalid version" error due to MACOSX_DEPLOYMENT_TARGET - Stack Overflow

20

To respond to your question - yes, I installed cmdstanr and cmdstan successfully with Big Sur 11.2 on my new M1 Mac, and I was able to run my models successfully (and with great performance). I “upgraded” to 11.3 and everything broke. I can still install cmdstanr but cannot build cmdstan. I tried to build cmdstan in Rstudio, but also version 2.26.1 using make build. I still got errors.

I uninstalled homebrew and xcode, and reinstalled xcode only (no homebrew), and ran xcode-select --intsall, and tried to build cmdstan again: still getting the same error messages.

This is my current $PATH:

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/R/arm64:/Library/TeX/texbin:/Library/Apple/usr/bin

This is my clang++ version:

Apple clang version 12.0.5 (clang-1205.0.22.9)
Target: arm64-apple-darwin20.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin