Problem to run a test stan function in rstan on mac catalina

Short summary of the problem

After running a test Stan function in Rstan on mac Catalina, the R 4.0.2 go to hang for longtime without any result.

code_to_run_your_model(if_applicable)

If possible, add also code to simulate data or attach a (subset of) the dataset you work with.

Don’t forget to add relevant tags to your topic (top right of this form) especially for application area. Delete this text before posting your question :-) Thx!

If your question relates to installation please provide the following information:

  • Operating System macOS Catalina 10.15.6
  • RStan Version 4.0.2
  • Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))

Error in file(con, “r”) : cannot open the connection
In addition: Warning message:
In file(con, “r”) :
*** cannot open file ‘/Users/arman-artin/.R/Makevars’: No such file or directory***

I remove this file before this the error is the same now.
This is backup file: Makevars.bck as:
CXX14FLAGS=-O3 -march=native -mtune=native -arch x86_64 -ftemplate-depth-256

  • Output of devtools::session_info("rstan")

devtools::session_info(“rstan”)
─ Session info ────────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS Catalina 10.15.6
system x86_64, darwin17.0
ui AQUA
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Asia/Tehran
date 2020-09-07

─ Packages ────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
backports 1.1.9 2020-08-24 [1] CRAN (R 4.0.2)
BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.2)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.2)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2)
ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
inline 0.3.15 2020-09-04 [1] Github (bgoodri/inline@21105c7)
isoband 0.2.2 2020-06-20 [1] CRAN (R 4.0.2)
jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.2)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
loo 2.3.1 2020-07-14 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
MASS 7.3-51.6 2020-04-26 [1] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2)
mgcv 1.8-31 2019-11-09 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
nlme 3.1-148 2020-05-24 [1] CRAN (R 4.0.2)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2)
ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.2)
Rcpp 1.0.5.2 2020-09-03 [1] local
RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.2)
RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.2)
rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
rstan 2.21.2 2020-07-27 [1] CRAN (R 4.0.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
StanHeaders 2.21.0-6 2020-08-16 [1] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2)
V8 3.2.0 2020-06-19 [1] CRAN (R 4.0.2)
vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.2)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

If you are reporting a bug (thank you!) please use the issue tracker (github.com/stan-dev/rstan/issues) instead of the forums.

When I install rstan packages , I see some warning but it is done.

Looking forward to your topic!

Please add code and data to this post so that we can reproduce this if possible :)

That is the codes to test RStan,
remotes::install_github(“bgoodri/inline”)
example(stan_model, package = “rstan”, run.dontrun = TRUE)

My R (4.0.2) go to hang when I load RStan as library(rstan).
When I have installed rstan , I saw many warning but it is done.

So all is ok now?

No, My R (4.0.2) go to hang when I use library(rstan).

Perhaps @bgoodri can help you out here. You say that you have OS X but you have an error msg saying that

*** cannot open file ‘/Users/arman-artin/.R/Makevars’: No such file or directory***

which is very strange, to say the least… :)

Thanks for your attention,
I have Makevars file, and it was as follows:

CXX14FLAGS=-O3 -march=native -mtune=native -arch x86_64 -ftemplate-depth-256

I remove this file, the problem is the same with this file.

can you guide me about the Makevar file? I must define it before installing RStan package?

Aah, ok then you can leave that file. Let’s see what @bgoodri has to say about this. I can’t wrap my brain around this :)

Possibly remove the -march=native -mtune=native from the Makevars file.