I’m trying to install CmdStanR on my Mac and am running into trouble. Since I haven’t been able to solve this problem via Googling, I thought I’d try and get some help here because someone may have run into the same issue.
I started out by installing the CmdStanR packages:
> install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) Warning in install.packages : unable to access index for repository https://mc-stan.org/r-packages/bin/macosx/el-capitan/contrib/3.6: cannot open URL 'https://mc-stan.org/r-packages/bin/macosx/el-capitan/contrib/3.6/PACKAGES' installing the source package ‘cmdstanr’ trying URL 'https://mc-stan.org/r-packages/src/contrib/cmdstanr_0.1.3.tar.gz' Content type 'application/gzip' length 831895 bytes (812 KB) ================================================== downloaded 812 KB * installing *source* package ‘cmdstanr’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cmdstanr) The downloaded source packages are in ‘/private/var/folders/6j/mkww2sy511q8ypd70xhdfcl40000gp/T/Rtmp3brOxI/downloaded_packages’
So far, so good I think. Next I loaded the CmdStanR libary:
> library(cmdstanr) This is cmdstanr version 0.1.3 - Online documentation and vignettes at mc-stan.org/cmdstanr - CmdStan path set to: /Users/andrew/.cmdstanr/cmdstan-2.24.1 - Use set_cmdstan_path() to change the path
I next ran
install_cmdstan() as done in this vignette:
> install_cmdstan(cores = 2, overwrite = TRUE) * Latest CmdStan release is v2.24.1 * Installing CmdStan v2.24.1 in /Users/andrew/.cmdstanr/cmdstan-2.24.1 * Downloading cmdstan-2.24.1.tar.gz from GitHub... * Removing the existing installation of CmdStan... * 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 stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.3.7 -I stan/lib/stan_math/lib/boost_1.72.0 -I stan/lib/stan_math/lib/sundials_5.2.0/include -DBOOST_DISABLE_ASSERTS -c -fvisibility=hidden -o bin/cmdstan/stansummary.o src/cmdstan/stansummary.cpp chmod +x bin/stanc cd stan/lib/stan_math/lib/boost_1.72.0; ./bootstrap.sh Building Boost.Build engine with toolset clang... 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:18: In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/algorithm/string/std_containers_traits.hpp:18: In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config.hpp:57: In file included from stan/lib/stan_math/lib/boost_1.72.0/boost/config/platform/macos.hpp:28: stan/lib/stan_math/lib/boost_1.72.0/boost/config/detail/posix_features.hpp:18:15: fatal error: 'unistd.h' file not found # include <unistd.h> ^~~~~~~~~~ 1 error generated. make: *** [bin/cmdstan/stansummary.o] Error 1 make: *** Waiting for unfinished jobs.... Failed to build Boost.Build build engine Consult 'bootstrap.log' for more details make: *** [stan/lib/stan_math/lib/boost_1.72.0/stage/lib/libboost_program_options.a] Error 1 Warning message: There was a problem during installation. See the error message(s) above.
As you can see, this is where I started running into trouble. I’m not sure what is causing this error - I couldn’t find a similar issue when I was Googling.
I know that CmdStanR isn’t working right because I can’t run simple examples from the vignette:
> file <- file.path(cmdstan_path(), "examples", "bernoulli", "bernoulli.stan") > mod <- cmdstan_model(file) Compiling Stan program... stan/lib/stan_math/lib/sundials_5.2.0/src/nvector/serial/nvector_serial.c:19:10: fatal error: 'stdio.h' file not found #include <stdio.h> ^~~~~~~~~ 1 error generated. Error: An error occured during compilation! See the message above for more information.
I’d appreciate any help that can be provided. Here’s my session info in case it’s helpful:
> sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  cmdstanr_0.1.3 loaded via a namespace (and not attached):  processx_3.4.3 compiler_3.6.1 backports_1.1.8 R6_2.4.1 rsconnect_0.8.15 tools_3.6.1 rstudioapi_0.11 crayon_1.3.4 checkmate_2.0.0  jsonlite_1.7.1 ps_1.3.4 ```