Error with RStan 2.26 and RTools 42

Signorelli · May 3, 2022, 5:57pm

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!

rok_cesnovar · May 4, 2022, 8:37pm

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

Signorelli · May 5, 2022, 3:17pm

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.

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Error with RStan 2.26 and RTools 42

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