Error with RStan 2.26 and RTools 42

When i run the test in rstan
based on the shools_dat file I get a long series of errors. It is the same for other tests.

schools_dat <- list(J = 8, 
+                     y = c(28,  8, -3,  7, -1,  1, 18, 12),
+                     sigma = c(15, 10, 16, 11,  9, 11, 10, 18))
> fit <- stan(file = 'schools.stan', data = schools_dat)
make cmd is
  make -f "C:/PROGRA~1/R/R-42~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-42~1.0/share/make/winshlib.mk" -f "C:/Users/christiana/Documents/.R/Makevars.win" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file31a07a683d0e.dll" WIN=64 TCLBIN= OBJECTS="file31a07a683d0e.o"

make would use
Warning message:
In system(paste(cmd, "-n")) :
  'CreateProcess' failed to run 'C:\rtools42\usr\bin\make.exe -f "C:/PROGRA~1/R/R-42~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-42~1.0/share/make/winshlib.mk" -f "C:/Users/christiana/Documents/.R/Makevars.win" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file31a07a683d0e.dll" WIN=64 TCLBIN= OBJECTS="file31a07a683d0e.o" -n'
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Warning message:In system(cmd) :  'CreateProcess' failed to run 'C:\rtools42\usr\bin\make.exe -f "C:/PROGRA~1/R/R-42~1.0/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-42~1.0/share/make/winshlib.mk" -f "C:/Users/christiana/Documents/.R/Makevars.win" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file31a07a683d0e.dll" WIN=64 TCLBIN= OBJECTS="file31a07a683d0e.o"'
Error in sink(type = "output") : invalid connection

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

  • Operating System: Windows 10
  • RStan Version: rstan version 2.26.11 (Stan version 2.26.1)
  • 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 ‘C:/Users/christiana/Documents/.R/Makevars’: No such file or directory
  • Output of devtools::session_info("rstan")
  • Session info ------------------------------------------------------------------------------------------------------------------------------
    setting value
    version R version 4.2.0 (2022-04-22 ucrt)
    os Windows 10 x64 (build 19042)
    system x86_64, mingw32
    ui RStudio
    language (EN)
    collate C
    ctype C
    tz Europe/Berlin
    date 2022-05-03
    rstudio 2022.02.2+485 Prairie Trillium (desktop)
    pandoc NA

  • 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 3.7.0 2021-04-20 [1] CRAN (R 4.2.0)
    checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.0)
    cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0)
    colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
    crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0)
    curl 4.3.2 2021-06-23 [1] CRAN (R 4.2.0)
    desc 1.4.1 2022-03-06 [1] CRAN (R 4.2.0)
    digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0)
    ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
    fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
    farver 2.1.0 2021-02-28 [1] CRAN (R 4.2.0)
    ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.2.0)
    glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
    gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.0)
    gtable 0.3.0 2019-03-25 [1] CRAN (R 4.2.0)
    inline 0.3.19 2021-05-31 [1] CRAN (R 4.2.0)
    isoband 0.2.5 2021-07-13 [1] CRAN (R 4.2.0)
    jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0)
    labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
    lattice 0.20-45 2021-09-22 [2] CRAN (R 4.2.0)
    lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0)
    loo 2.5.1 2022-03-24 [1] CRAN (R 4.2.0)
    magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
    MASS 7.3-56 2022-03-23 [2] CRAN (R 4.2.0)
    Matrix 1.4-1 2022-03-23 [2] CRAN (R 4.2.0)
    matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.0)
    mgcv 1.8-40 2022-03-29 [2] CRAN (R 4.2.0)
    munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
    nlme 3.1-157 2022-03-25 [2] CRAN (R 4.2.0)
    pillar 1.7.0 2022-02-01 [1] CRAN (R 4.2.0)
    pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.0)
    pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
    prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
    processx 3.5.3 2022-03-25 [1] CRAN (R 4.2.0)
    ps 1.7.0 2022-04-23 [1] CRAN (R 4.2.0)
    R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
    RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
    Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.2.0)
    RcppEigen 0.3.3.9.2 2022-04-08 [1] CRAN (R 4.2.0)
    D RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.2.0)
    rlang 1.0.2 2022-03-04 [1] CRAN (R 4.2.0)
    rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
    rstan * 2.26.11 2022-04-23 [1] local
    scales 1.2.0 2022-04-13 [1] CRAN (R 4.2.0)
    StanHeaders * 2.26.11 2022-04-23 [1] local
    tibble 3.1.6 2021-11-07 [1] CRAN (R 4.2.0)
    utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
    V8 4.1.0 2022-02-06 [1] CRAN (R 4.2.0)
    vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0)
    viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.2.0)
    withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)

[1] C:/Users/christiana/AppData/Local/R/win-library/4.2
[2] C:/Program Files/R/R-4.2.0/library

D – DLL MD5 mismatch, broken installation.

Looking forward to your topic!

Hi, this is a known issue. Please see Stan & R 4.2 on Windows – The Stan Blog

1 Like

Hei,
Thank you for following up. I tried to downgrade to an earlier R version 4.1.2.

I still get error from running the testfile:

Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
Warning message:In system(cmd) : ‘CreateProcess’ failed to run ‘C:\rtools40\usr\bin\make.exe -f “C:/PROGRA~1/R/R-41~1.2/etc/x64/Makeconf” -f “C:/PROGRA~1/R/R-41~1.2/share/make/winshlib.mk” -f “C:/Users/christiana/Documents/.R/Makevars.win” CXX=’(CXX14) (CXX14STD)’ CXXFLAGS=’(CXX14FLAGS)' CXXPICFLAGS='(CXX14PICFLAGS)’ SHLIB_LDFLAGS=’(SHLIB_CXX14LDFLAGS)' SHLIB_LD='(SHLIB_CXX14LD)’ SHLIB=“file65842c45504a.dll” WIN=64 TCLBIN=64 OBJECTS=“file65842c45504a.o”’

Below I supply the session info.

Output from 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 ‘C:/Users/christiana/Documents/.R/Makevars’: No such file or directory
But in fact there is a file:
C:\Users\christiana\Documents.R

Ourput from devtools::session_info(“rstan”):

  • Session info --------------------------------------------------------------------------------
    setting value
    version R version 4.1.2 (2021-11-01)
    os Windows 10 x64 (build 19042)
    system x86_64, mingw32
    ui RStudio
    language (EN)
    collate Norwegian Bokmål_Norway.1252
    ctype Norwegian Bokmål_Norway.1252
    tz Europe/Berlin
    date 2022-05-05
    rstudio 2022.02.2+485 Prairie Trillium (desktop)
    pandoc NA

  • Packages ------------------------------------------------------------------------------------
    ! package * version date (UTC) lib source
    backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2)
    BH 1.78.0-0 2021-12-15 [1] CRAN (R 4.1.2)
    callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.3)
    checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.1.3)
    cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.3)
    colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.3)
    crayon 1.5.1 2022-03-26 [1] CRAN (R 4.1.3)
    desc 1.4.1 2022-03-06 [1] CRAN (R 4.1.3)
    digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.3)
    ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.3)
    fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.3)
    farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.3)
    ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.1.2)
    glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.3)
    gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.3)
    gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.3)
    inline 0.3.19 2021-05-31 [1] CRAN (R 4.1.3)
    isoband 0.2.5 2021-07-13 [1] CRAN (R 4.1.3)
    labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.1)
    lattice 0.20-45 2021-09-22 [2] CRAN (R 4.1.2)
    lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.3)
    loo 2.5.1 2022-03-24 [1] CRAN (R 4.1.3)
    magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
    MASS 7.3-54 2021-05-03 [2] CRAN (R 4.1.2)
    Matrix 1.3-4 2021-06-01 [2] CRAN (R 4.1.2)
    matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.1.3)
    mgcv 1.8-38 2021-10-06 [2] CRAN (R 4.1.2)
    munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.3)
    nlme 3.1-153 2021-09-07 [2] CRAN (R 4.1.2)
    pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.3)
    pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.3)
    pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.3)
    prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.3)
    processx 3.5.3 2022-03-25 [1] CRAN (R 4.1.3)
    ps 1.7.0 2022-04-23 [1] CRAN (R 4.1.3)
    R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.3)
    RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.1.3)
    Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.1.3)
    RcppEigen 0.3.3.9.2 2022-04-08 [1] CRAN (R 4.1.3)
    D RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.1.3)
    rlang 1.0.2 2022-03-04 [1] CRAN (R 4.1.3)
    rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.1.3)
    rstan * 2.21.5 2022-04-11 [1] CRAN (R 4.1.3)
    scales 1.2.0 2022-04-13 [1] CRAN (R 4.1.3)
    StanHeaders * 2.21.0-7 2020-12-17 [1] CRAN (R 4.1.3)
    tibble * 3.1.6 2021-11-07 [1] CRAN (R 4.1.3)
    utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.3)
    vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.3)
    viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.3)
    withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.3)

[1] C:/Users/christiana/Documents/R/win-library/4.1
[2] C:/Program Files/R/R-4.1.2/library

D – DLL MD5 mismatch, broken installation.