Rstan not working on my machine

Stan was not working on my computer so I tried the 8 schools example from the Getting Started page and it didn’t work; see below. I don’t know what to do!

fit <- stan(file = ‘8schools.stan’, data = schools_dat)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! clang: warning: no such sysroot directory: ‘/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk’ [-Wmissing-sysroot]
In file included from file3a15598c2ae2.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/i
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file3a15598c2ae2.cpp 2> file3a15598c2ae2.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection

Mac 10.14.6
R version 3.6.1

writeLines(readLines(file.path(Sys.getenv(“HOME”), “.R/Makevars”)))

CXX14FLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-unknown-pragmas

CC=clang
CXX14=clang++ -arch x86_64 -ftemplate-depth-256

devtools::session_info(“rstan”)
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.6.1 (2019-07-05)
os macOS Mojave 10.14.6
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Paris
date 2019-08-13

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
BH 1.69.0-1 2019-01-07 [1] CRAN (R 3.6.0)
callr 3.3.1 2019-07-18 [1] CRAN (R 3.6.0)
checkmate 1.9.4 2019-07-04 [1] CRAN (R 3.6.0)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0)
ellipsis 0.2.0.1 2019-07-02 [1] CRAN (R 3.6.0)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.0)
ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.6.0)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.6.0)
labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
loo 2.1.0 2019-03-13 [1] CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
MASS 7.3-51.4 2019-03-31 [1] CRAN (R 3.6.1)
Matrix 1.2-17 2019-03-22 [1] CRAN (R 3.6.1)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.6.0)
mgcv 1.8-28 2019-03-21 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
nlme 3.1-141 2019-08-01 [1] CRAN (R 3.6.0)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
pkgbuild 1.0.4 2019-08-05 [1] CRAN (R 3.6.0)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.0)
RcppEigen 0.3.3.5.0 2018-11-24 [1] CRAN (R 3.6.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0)
rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
rstan * 2.19.2 2019-07-09 [1] CRAN (R 3.6.0)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.0)
StanHeaders * 2.18.1-10 2019-06-14 [1] CRAN (R 3.6.0)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.0)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.0)

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

What is in the directory /Library/Developer/CommandLineTools/SDKs/?

I don’t think I have such a directory!

Well, that would certainly explain the warning.

Also, I noticed that it looks like a copy-and-paste from one of the error messages was cut off:

Was there something after StanHeaders/i that didn’t get copied?

Below is the entire error message I got. It just seems weird because Stan used to work on my machine. Maybe I need to re-install R?

fit <- stan(file = ‘8schools.stan’, data = schools_dat)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! clang: warning: no such sysroot directory: ‘/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk’ [-Wmissing-sysroot]
In file included from file3a15598c2ae2.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/i
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file3a15598c2ae2.cpp 2> file3a15598c2ae2.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection

You need to call stan with verbose = TRUE to see the actual error message, but my guess is that it is fixable by one of

I tried verbose=TRUE but then the error message was so long that it rolled off the screen. It was larger than Rstudio’s buffer so I can’t even share the output here.

I went to the link and tried Step 1 (“Make sure you have opened Xcode once via Spotlight to accept its license”). This took a few minutes. When that was done, I closed Rstudio, uninstalled rstan and reinstalled it, and tried again and got the same error message.

I couldn’t understand Steps 2, 3, and 4, so I jumped to Step 5 (“Try xcode-select --install from the Terminal app or the Terminal tab of the RStudio console”) and that worked for me.

Thanks!