Hi all,
I was able to successfully install rstan using the binary file from CRAN. However, I have been unable to run the Eight Schools example following the instructions here (https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started).
schools.stan is saved in my working directory.
> 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)
The NEXT version of Stan will not be able to pre-process your Stan program.
Please open an issue at
https://github.com/stan-dev/stanc3/issues
if you can share or at least describe your Stan program. This will help ensure that Stan
continues to work on your Stan programs in the future. Thank you!
This message can be avoided by wrapping your function call inside suppressMessages().
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file18587ca30fc.o:file18587ca30fc.cpp:(.text+0x161c): undefined reference to `rstan::stan_fit::stan_fit(SEXPREC*, int)'
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file18587ca30fc.o:file18587ca30fc.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D1Ev[_ZN3tbb8internal26task_scheduler_observer_v3D1Ev]+0x14): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file18587ca30fc.o:file18587ca30fc.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1c): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'
C:/rtools40/mingw64/bin/../lib/gcc/x86_64
In addition: Warning message:
In file.remove(c(unprocessed, processed)) :
cannot remove file 'C:\Users\Karthik\AppData\Local\Temp\RtmpQBZTi2\file18582d9e2a83.stan', reason 'No such file or directory'
Error in sink(type = "output") : invalid connection
Here are details on the setup I am using:
- Operating System: Windows 7 SP 1
- R Version: 4.0.2
- RStudio Version: 1.3.959
- RStan Version: 2.21.1
- StanHeaders Version: 2.21.0-5
- Output of
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
> 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\Karthik\Documents/.R/Makevars': No such file or directory
- Output of
devtools::session_info("rstan")
- Session info ---------------------------------------------------------------------------------------
setting value
version R version 4.0.2 (2020-06-22)
os Windows 7 x64 SP 1
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/Chicago
date 2020-07-10
- Packages -------------------------------------------------------------------------------------------
! package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
backports 1.1.7 2020-05-13 [1] CRAN (R 4.0.0)
BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.2)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2)
ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
inline 0.3.15 2018-05-18 [1] CRAN (R 4.0.2)
isoband 0.2.2 2020-06-20 [1] CRAN (R 4.0.2)
jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.2)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
loo 2.3.0 2020-07-07 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
MASS 7.3-51.6 2020-04-26 [1] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.2)
mgcv 1.8-31 2019-11-09 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
nlme 3.1-148 2020-05-24 [1] CRAN (R 4.0.2)
pillar 1.4.5 2020-07-09 [1] CRAN (R 4.0.2)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.2)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.2)
D RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.2)
rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
rstan * 2.21.1 2020-07-08 [1] CRAN (R 4.0.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
StanHeaders * 2.21.0-5 2020-06-09 [1] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
tibble 3.0.2 2020-07-07 [1] CRAN (R 4.0.2)
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2)
V8 3.2.0 2020-06-19 [1] CRAN (R 4.0.2)
vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.2)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.2)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2)
[1] C:/R-4.0.2/library
D -- DLL MD5 mismatch, broken installation.
A few other things I’ve tried:
-
Installed both R and Rtools in a file path without spaces (directly in C:)
-
Test for Rtools
> pkgbuild::has_build_tools(debug = TRUE)
[1] TRUE
Clearly, the DLL MD5 mismatch also seems like a problem, but I’m not really sure what to do about it (persisted despite uninstalling and reinstalling RcppParallel from CRAN). Sorry if I am missing something basic here, I am very new to RStan. Any help would be greatly appreciated - thank you so much! Please let me know if there’s any other information I can provide.