RStan 2.19.3 sampling error

Interfaces RStan
1

@bgoodri we’re running into a different problem on Catalina than the typical install problems. Models compile OK, but don’t run with sampling (the models do, however, run with vb). The user gets the following error message:

ErrorLog
ErrorLog1523×1014 136 KB

Have you seen this before? Details on versioning and packages below.

OS: Mac Catalina 10.15.3
Stan Version: 2.19.3
1:25
> writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
CXX14FLAGS=-O3 -march=native -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256
CXX14FLAGS=-O3 -march=native -mtune=native
CXX14FLAGS += -arch x86_64 -ftemplate-depth-256
1:27
> devtools::session_info("rstan")
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 3.6.3 (2020-02-29)
 os       macOS Catalina 10.15.3
 system   x86_64, darwin15.6.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2020-04-23
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────
 ! package      * version   date       lib source
   assertthat     0.2.1     2019-03-21 [1] CRAN (R 3.6.0)
   backports      1.1.5     2019-10-02 [1] CRAN (R 3.6.0)
   BH             1.72.0-3  2020-01-08 [1] CRAN (R 3.6.0)
 V callr          3.4.2     2020-03-28 [1] CRAN (R 3.6.2)
   checkmate      2.0.0     2020-02-06 [1] CRAN (R 3.6.0)
   cli            2.0.2     2020-02-28 [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         0.6.25    2020-02-23 [1] CRAN (R 3.6.0)
   ellipsis       0.3.0     2019-09-20 [1] CRAN (R 3.6.0)
   evaluate       0.14      2019-05-28 [1] CRAN (R 3.6.0)
   fansi          0.4.1     2020-01-08 [1] CRAN (R 3.6.0)
   farver         2.0.3     2020-01-16 [1] CRAN (R 3.6.0)
   ggplot2        3.3.0     2020-03-05 [1] CRAN (R 3.6.0)
 V glue           1.3.2     2020-04-03 [1] CRAN (R 3.6.2)
   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)
   isoband        0.2.0     2019-04-06 [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 3.6.3)
   lifecycle      0.2.0     2020-03-06 [1] CRAN (R 3.6.0)
   loo            2.2.0     2019-12-19 [1] CRAN (R 3.6.0)
   magrittr       1.5       2014-11-22 [1] CRAN (R 3.6.0)
   MASS           7.3-51.5  2019-12-20 [1] CRAN (R 3.6.3)
   Matrix         1.2-18    2019-11-27 [1] CRAN (R 3.6.3)
   matrixStats    0.56.0    2020-03-13 [1] CRAN (R 3.6.0)
   mgcv           1.8-31    2019-11-09 [1] CRAN (R 3.6.3)
   munsell        0.5.0     2018-06-12 [1] CRAN (R 3.6.0)
   nlme           3.1-144   2020-02-06 [1] CRAN (R 3.6.3)
   pillar         1.4.3     2019-12-20 [1] CRAN (R 3.6.0)
   pkgbuild       1.0.6     2019-10-09 [1] CRAN (R 3.6.0)
   pkgconfig      2.0.3     2019-09-22 [1] CRAN (R 3.6.0)
   pkgload        1.0.2     2018-10-29 [1] CRAN (R 3.6.0)
   praise         1.0.0     2015-08-11 [1] CRAN (R 3.6.0)
   prettyunits    1.1.1     2020-01-24 [1] CRAN (R 3.6.0)
   processx       3.4.2     2020-02-09 [1] CRAN (R 3.6.0)
   ps             1.3.2     2020-02-13 [1] CRAN (R 3.6.0)
   R6             2.4.1     2019-11-12 [1] CRAN (R 3.6.0)
   RColorBrewer   1.1-2     2014-12-07 [1] CRAN (R 3.6.0)
   Rcpp           1.0.4     2020-03-17 [1] CRAN (R 3.6.3)
   RcppEigen      0.3.3.7.0 2019-11-16 [1] CRAN (R 3.6.0)
   rlang          0.4.5     2020-03-01 [1] CRAN (R 3.6.0)
   rprojroot      1.3-2     2018-01-03 [1] CRAN (R 3.6.0)
   rstan          2.19.3    2020-02-11 [1] CRAN (R 3.6.0)
   rstudioapi     0.11      2020-02-07 [1] CRAN (R 3.6.0)
   scales         1.1.0     2019-11-18 [1] CRAN (R 3.6.0)
   StanHeaders    2.21.0-1  2020-01-19 [1] CRAN (R 3.6.0)
   testthat       2.3.2     2020-03-02 [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          0.2.4     2020-03-10 [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)
[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
 V ── Loaded and on-disk version mismatch.
2

Yeah, you have to install rstan from source, sometimes with some extra flags. With R 4.0 released tomorrow, they are using the Xcode toolchain to build everything on CRAN, so that shouldn’t be necessary anymore.

3

Thanks @bgoodri we’ll try this and hopefully it solves the problem.