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

Interfaces RStan
1

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)

Screen Shot 2020-09-04 at 9.22.11 AM
Screen Shot 2020-09-04 at 9.22.11 AM2560×1600 1.22 MB

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

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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 (Issues · stan-dev/rstan · GitHub) instead of the forums.

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

Looking forward to your topic!

2

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

3

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.

4

So all is ok now?

5

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

6

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… :)

7

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?

8

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 :)

9

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