I’m trying to use rethinking::ulam(), cmdstan_model(), stan(), and I get the same error “mingw32-make: *** INTERNAL: readdir: Invalid argument”
I followed the useful “Getting started with CmdStanR” page.
Rtools42 is installed at c:\rtools42
check_cmdstan_toolchain() returns “The C++ toolchain required for CmdStan is setup properly!”
cmdstan_version() returns “2.32.2”
cmdstan_path() returns “C:/Users/first-last/OneDrive - MMC/Documents/.cmdstan/cmdstan-2.32.2”
I’m using the RGui because I’ve had trouble with corporate installing RStudio on my machine. Here’s my R version:
sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] digest_0.6.31 rethinking_2.31 rstan_2.21.8 StanHeaders_2.26.27 cmdstanr_0.5.3 bayesplot_1.10.0 gridExtra_2.3 PerformanceAnalytics_2.0.4 xts_0.13.1 zoo_1.8-12 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[14] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] shape_1.4.6 gtable_0.3.3 tensorA_0.36.2 xfun_0.39 processx_3.8.1 inline_0.3.19 lattice_0.21-8 callr_3.7.3 tzdb_0.4.0 quadprog_1.5-8 vctrs_0.6.3 tools_4.3.1 ps_1.7.5 generics_0.1.3 stats4_4.3.1 fansi_1.0.4 pkgconfig_2.0.3
[18] checkmate_2.2.0 distributional_0.3.2 RcppParallel_5.1.7 lifecycle_1.0.3 compiler_4.3.1 farver_2.1.1 munsell_0.5.0 codetools_0.2-19 pillar_1.9.0 crayon_1.5.2 MASS_7.3-60 abind_1.4-5 posterior_1.4.1 tidyselect_1.2.0 mvtnorm_1.2-2 stringi_1.7.12 labeling_0.4.2
[35] grid_4.3.1 colorspace_2.1-0 cli_3.6.1 magrittr_2.0.3 loo_2.6.0 pkgbuild_1.4.2 utf8_1.2.3 withr_2.5.0 prettyunits_1.1.1 scales_1.2.1 backports_1.4.1 bit64_4.0.5 timechange_0.2.0 matrixStats_1.0.0 bit_4.0.5 hms_1.1.3 coda_0.19-4
[52] knitr_1.43 rlang_1.1.1 Rcpp_1.0.10 glue_1.6.2 vroom_1.6.3 jsonlite_1.8.5 R6_2.5.1
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Reading these forums, I’ve seen that the Windows environment “PATH” variable sometimes needs updating.
I’ve used Sys.setenv("PATH" = ...) to try differnt recommended locations, like including rtools42 instead of rtools43. When I restart R, this is what I get:
> Sys.getenv("PATH")
[1] "c:/rtools43/x86_64-w64-mingw32.static.posix/bin;c:/rtools43/usr/bin;\\usr\\bin;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath;C:\\windows\\system32;C:\\windows;C:\\windows\\System32\\Wbem;C:\\windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\windows\\System32\\OpenSSH\\;C:\\Users\\Administrator\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Program Files (x86)\\Adaptiva\\AdaptivaClient\\bin\\x32;C:\\Program Files (x86)\\Adaptiva\\AdaptivaClient\\bin\\x64;C:\\Program Files\\dotnet\\;C:\\Program Files\\WinZip\\;C:\\Program Files\\SASHome\\x86\\Secure\\ccme4;C:\\Program Files\\SASHome\\Secure\\ccme4;C:\\Users\\first-last\\AppData\\Local\\Microsoft\\WindowsApps;"
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I’ve also tried running pacman -Syu mingw-w64-x86_64-make from Rtools Bash. I’m not sure what this is supposed to do, but again, I’ve been trying anything I can find, and I’m still stuck.
The part that’s confusing to me is that I can run, successfully, rstanarm::stan_glm() So I thought the other Stan-based tools would work too.
What are the chances the Stan experts can help me? Thanks!