Hello all,
Since upgrading to R 4.2.2 and Rtools42 I haven’t been able to get brms (or Stan) to work. Ack. I’m definitely short a few hairs since starting. I’m hoping with your help I can find a way to resolve the problem without having to resort to the nuclear option of uninstalling/reinstalling R etc.
So far I’ve upgraded the C++ toolchain for 4.2 as described at :
Configuring C Toolchain for Windows · stan-dev/rstan Wiki · GitHub and
Stan & R 4.2 on Windows – The Stan Blog
But when I run example(stan_model,run.dontrun=T), I end up with the same error message at the end of a pile of code (omitted top 423 lines–please let me know if you’d like to see them!). Here is the gist of the errors:
ERROR(s) during compilation: source code errors or compiler configuration errors!
Program source:
1:
2: // includes from the plugin
3: // [[Rcpp::plugins(cpp14)]]
4:
5:
6: // user includes
7: #include <Rcpp.h>
8: using namespace Rcpp;
9: #ifndef MODELS_HPP
10: #define MODELS_HPP
11: #define STAN__SERVICES__COMMAND_HPP
12: #include <rstan/rstaninc.hpp>
13: #ifndef USE_STANC3
14: #define USE_STANC3
15: #endif
…and the final error:
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
g++.exe: error: x86_64: No such file or directoryg++.exe: error: unrecognized command-line option '-arch'make: *** [C:/PROGRA~1/R/R-42~1.2/etc/x64/Makeconf:260: file17dc17416ba0.o] Error 1
Here is some additional info:
> Sys.getenv("PATH")
[1] "C:\\rtools42\\usr\\bin;C:\\rtools42\\x86_64-w64-mingw32.static.posix\\bin;C:\\rtools42\\usr\\bin;C:\\rtools42\\usr\\bin;C:\\Program Files\\R\\R-4.2.2\\bin\\x64;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath_target_634954671;C:\\Windows\\System32;C:\\Windows;C:\\Windows\\System32\\wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Windows\\System32\\OpenSSH;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\Windows\\System32;C:\\Windows;C:\\Windows\\System32\\wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Windows\\System32\\OpenSSH;C:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;C:\\Windows\\System32;C:\\Windows;C:\\Windows\\System32\\wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Windows\\System32\\OpenSSH;C:\\Program Files\\dotnet;D:\\Git\\cmd;C:\\ProgramData\\chocolatey\\bin;;C:\\Program Files\\Docker\\Docker\\resources\\bin;C:\\Users\\shaun\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\shaun\\AppData\\Local\\GitHubDesktop\\bin;C:\\Users\\shaun\\AppData\\Local\\Pandoc;C:\\Users\\shaun\\AppData\\Local\\gitkraken\\bin;C:\\Users\\shaun\\AppData\\Roaming\\TinyTeX\\bin\\win32;;C:\\Program Files\\RStudio\\resources\\app\\bin\\quarto\\bin;C:\\Program Files\\RStudio\\resources\\app\\bin\\rpostback;C:\\Program Files\\RStudio\\resources\\app\\bin\\postback"
The path looks insanely messy imho–though I’m not sure how to remedy this or if it is even a problem.
>Sys.getenv("BINPREF")
[1] ""
>readLines("~/.Rprofile")
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
cannot open file 'D:/documents/.Rprofile': No such file or directory
^^ The .Rprofile file was deleted when trying to move back to Rtools 40 at one point (it’s been a journey!)
> writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
CXX14FLAGS += -O3 -mtune=native -arch x86_64 -ftemplate-depth-256
^^ the error message I get when compiling the test model mentions the -arch as an ‘unrecognized command-line option’. Maybe a problem with Makevars config?
> readLines("~/.Renviron")
[1] "PATH=\"${RTOOLS42_HOME}\\usr\\bin;${PATH}\""
devtools::session_info("rstan")
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.2 (2022-10-31 ucrt)
os Windows 10 x64 (build 19045)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Canada.utf8
ctype English_Canada.utf8
tz America/New_York
date 2022-12-20
rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
pandoc 2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
BH 1.78.0-0 2021-12-15 [1] CRAN (R 4.2.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.2)
checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.2)
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.2)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.2)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.2)
curl 4.3.3 2022-10-06 [1] CRAN (R 4.2.2)
desc 1.4.2 2022-09-08 [1] CRAN (R 4.2.2)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.2)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.2)
ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.2)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.2)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.2.2)
isoband 0.2.6 2022-10-06 [1] CRAN (R 4.2.2)
jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.2)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.2)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.2)
loo 2.5.1 2022-03-24 [1] CRAN (R 4.2.2)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.2)
MASS 7.3-58.1 2022-08-03 [1] CRAN (R 4.2.2)
Matrix * 1.5-3 2022-11-11 [1] CRAN (R 4.2.2)
matrixStats 0.63.0 2022-11-18 [1] CRAN (R 4.2.2)
mgcv * 1.8-41 2022-10-21 [1] CRAN (R 4.2.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.2)
nlme * 3.1-161 2022-12-15 [1] CRAN (R 4.2.2)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.2)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.2)
processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.2)
ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.2)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
Rcpp * 1.0.9 2022-07-08 [1] CRAN (R 4.2.2)
RcppEigen 0.3.3.9.3 2022-11-05 [1] CRAN (R 4.2.2)
RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.2.2)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.2)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.2)
rstan * 2.26.13 2022-06-25 [1] local
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.2)
StanHeaders * 2.26.13 2022-06-25 [1] local
tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.2)
V8 4.2.2 2022-11-03 [1] CRAN (R 4.2.2)
vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.2)
viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.2)
[1] D:/documents/ConspiracyProject/renv/library/R-4.2/x86_64-w64-mingw32
[2] C:/Users/shaun/AppData/Local/Temp/RtmpWaDRTQ/renv-system-library
I’m thinking this has to do with a communication problem between R and C? Maybe a problem with renv? Anyhow, I’ll leave it there for now. Btw, this is my first time requesting help so huge apologies if I missed something or formatted things incorrectly! Your help is SUPER appreciated :) Thank you!
Shauna