Today I run a STAN model from R and I have no problems as usual; after some hours I run again the same model but it doesen’t work (all chains remain stopped at first iteration) so I run the school.stan example code and I have that problem that I’ve never seen.
This is my simple code:
> library(rstan)
Carico il pacchetto richiesto: StanHeaders
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
Attaching package: ‘rstan’
The following object is masked from ‘package:tidyr’:
extract
>
> options(mc.cores = parallel::detectCores())
> rstan_options(auto_write = TRUE)
>
> 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 = 'STAN/schools.stan', data = schools_dat,
+ chains = 3)
Errore: cannot allocate vector of size 17075.9 Gb
Inoltre: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
'C:/rtools40/usr/mingw_/bin/g++' not found
Please, has someone any help or any ideas to solve the problem?
Can you post the output from:
Sys.getenv("BINPREF")
Sys.getenv("PATH")
readLines("~/.Rprofile")
readLines("~/.Renviron")
readLines("~/.R/Makevars.win")
Also, are you using R3.x or R4.x?
This is the output of these lines of code:
> Sys.getenv("BINPREF")
[1] ""
> Sys.getenv("PATH")
[1] "C:\\rtools40\\usr\\bin;C:\\Program Files\\R\\R-4.0.3\\bin\\x64;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:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;C:\\Program Files\\Git\\cmd;C:\\Users\\basil\\AppData\\Local\\Microsoft\\WindowsApps"
> readLines("~/.Rprofile")
Error in file(con, "r") : non posso aprire questa connessione
Inoltre: Warning message:
In file(con, "r") :
cannot open file 'C:/Users/basil/Documents/.Rprofile': No such file or directory
> readLines("~/.Renviron")
[1] "PATH=\"${RTOOLS40_HOME}\\usr\\bin;${PATH}\""
> readLines("~/.R/Makevars.win")
[1] ""
[2] " CXX14FLAGS += -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2"
i tried to reinstall Rcpp and Rstan but nothing change
This is my R version:
> version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 4
minor 0.3
year 2020
month 10
day 10
svn rev 79318
language R
version.string R version 4.0.3 (2020-10-10)
nickname Bunny-Wunnies Freak Out
Have you recently updated from R3.x?
What output do you get from:
devtools::session_info("rstan")
No, the first version of R I intalled on this pc was the 4.0.3 because I switch on this machine the first time 2 month ago.
This is the output of devtools::session_info(“rstan”)
> devtools::session_info("rstan")
- Session info -------------------------------------------------------------------------------------------------------
setting value
version R version 4.0.3 (2020-10-10)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate Italian_Italy.1252
ctype Italian_Italy.1252
tz Europe/Berlin
date 2021-03-07
- Packages -----------------------------------------------------------------------------------------------------------
! package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.3)
backports 1.2.0 2020-11-02 [1] CRAN (R 4.0.3)
BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.3)
brio 1.1.0 2020-08-31 [1] CRAN (R 4.0.3)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.3)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.3)
cli 2.1.0 2020-10-12 [1] CRAN (R 4.0.3)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.3)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.3)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.3)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.3)
diffobj 0.3.2 2020-10-05 [1] CRAN (R 4.0.3)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.3)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.3)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.3)
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.3)
ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.3)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.3)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.3)
inline 0.3.16 2020-09-06 [1] CRAN (R 4.0.3)
isoband 0.2.2 2020-06-20 [1] CRAN (R 4.0.3)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.3)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.3)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.3)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.3)
loo 2.3.1 2020-07-14 [1] CRAN (R 4.0.3)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.3)
MASS 7.3-53 2020-09-09 [2] CRAN (R 4.0.3)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.0.3)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.3)
mgcv 1.8-33 2020-08-27 [2] CRAN (R 4.0.3)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.3)
nlme 3.1-149 2020-08-23 [2] CRAN (R 4.0.3)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.3)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.3)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.3)
praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.3)
processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.3)
ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.3)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.3)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.4)
RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 4.0.3)
D RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.3)
rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.0.3)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.4)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.3)
rstan 2.21.2 2020-07-27 [1] CRAN (R 4.0.4)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.3)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.3)
StanHeaders 2.21.0-7 2020-12-17 [1] CRAN (R 4.0.3)
testthat 3.0.0 2020-10-31 [1] CRAN (R 4.0.3)
tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.3)
utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.3)
V8 3.4.0 2020-11-04 [1] CRAN (R 4.0.3)
vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.3)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.3)
waldo 0.2.3 2020-11-09 [1] CRAN (R 4.0.3)
withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.3)
[1] C:/Users/basil/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.3/library
D -- DLL MD5 mismatch, broken installation.
There is a problem in RcppParallel, might be usefull to reinstall?
That RcppParallel is normal, safe to ignore. What happens when you run the rstan example model:
example(stan_model,package="rstan",run.dontrun=T)
It gives me a compilation error
> example(stan_model,package="rstan",run.dontrun=T)
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
stn_md> stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}'
stn_md> mod <- stan_model(model_code = stancode, verbose = TRUE)
TRANSLATING MODEL '73fc79f8b1915e8208c736914c86d1a1' FROM Stan CODE TO C++ CODE NOW.
successful in parsing the Stan model '73fc79f8b1915e8208c736914c86d1a1'.
COMPILING THE C++ CODE FOR MODEL '73fc79f8b1915e8208c736914c86d1a1' NOW.
OS: x86_64, mingw32; rstan: 2.21.2; Rcpp: 1.0.6; inline: 0.3.16
>> setting environment variables:
LOCAL_LIBS = "C:/Users/basil/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/basil/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb
PKG_CPPFLAGS = -I"C:/Users/basil/Documents/R/win-library/4.0/Rcpp/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/RcppEigen/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/RcppEigen/include/unsupported" -I"C:/Users/basil/Documents/R/win-library/4.0/BH/include" -I"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/include/src/" -I"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/RcppParallel/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include "C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp" -std=c++1y
>> Program source :
....
make cmd is
make -f "C:/PROGRA~1/R/R-40~1.3/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-40~1.3/share/make/winshlib.mk" -f "C:/Users/basil/Documents/.R/Makevars.win" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file3b987a8828c8.dll" WIN=64 TCLBIN=64 OBJECTS="file3b987a8828c8.o"
make would use
"C:/rtools40/mingw64/bin/"g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.3/include" -DNDEBUG -I"C:/Users/basil/Documents/R/win-library/4.0/Rcpp/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/RcppEigen/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/RcppEigen/include/unsupported" -I"C:/Users/basil/Documents/R/win-library/4.0/BH/include" -I"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/include/src/" -I"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/RcppParallel/include/" -I"C:/Users/basil/Documents/R/win-library/4.0/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include "C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp" -std=c++1y -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -c file3b987a8828c8.cpp -o file3b987a8828c8.o
if test "zfile3b987a8828c8.o" != "z"; then \
if test -e "file3b987a8828c8-win.def"; then \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file3b987a8828c8.dll file3b987a8828c8-win.def file3b987a8828c8.o "C:/Users/basil/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/basil/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file3b987a8828c8.dll file3b987a8828c8-win.def file3b987a8828c8.o "C:/Users/basil/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/basil/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
"C:/rtools40/mingw64/bin/"nm file3b987a8828c8.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file3b987a8828c8.dll tmp.def file3b987a8828c8.o "C:/Users/basil/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/basil/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file3b987a8828c8.dll tmp.def file3b987a8828c8.o "C:/Users/basil/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a" -L"C:/Users/basil/Documents/R/win-library/4.0/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/basil/Documents/R/win-library/4.0/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
ERROR(s) during compilation: source code errors or compiler configuration errors!
>> Program source :
...
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/basil/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file3b987a8828c8.o:file3b987a8828c8.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/basil/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::QC'; file3b987a8828c8.o:file3b987a88
Inoltre: Warning messages:
1: package ‘rstan’ was built under R version 4.0.4
2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
'C:/rtools40/usr/mingw_/bin/g++' not found
Alright, so there are two issues here. The Unable to allocate vector... error was (I’m guessing) caused by a .rds file leftover from a previous rstan install. If you look in the folder where the schools.stan file is stored, there should also be a file called schools.rds. Delete that .rds file.
For the compilation errors in the example model, you need to restart your R session (making sure that rstan is not loaded) and then reinstall rstan and StanHeaders from source:
# Compile packages using all cores
Sys.setenv(MAKEFLAGS = paste0("-j",parallel::detectCores()))
install.packages(c("StanHeaders","rstan"),type="source")
1 Like
Thanks! I finally solve the problem: I delete all *.rds file reinstall from source rstan and StanHeaders and now it works perfectly as before!
2 Likes