I think we need both 4.0 and a 3.x instructions but 4.0 is recommended.
Stephen, I followed you html manual and still can’t run stan in R4.0.
I have the error message whte trying your test code:
sm <- stan_model(model_code = stan_code)
Error in file(con, “r”) : cannot open the connection
In addition: Warning messages:
1: In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-40~1.1/bin/x64/R CMD SHLIB file1bc42dc1b37.cpp 2> file1bc42dc1b37.cpp.err.txt’ had status 1
2: In file(con, “r”) :
cannot open file ‘file1bc42dc1b37.cpp.err.txt’: No such file or directory
Error in sink(type = “output”) : invalid connection
Do you know what is the problem?
Need more info here.
I think the R 4.0 instructions have worked for people so far, so I assume there’s something unique to your setup.
Questions:
- What is in your ~/.Renviron, ~/.Rprofile, and ~/.R/Makevars ?
- Where is your model file located? Is it in a networked directory (e.g., Box, dropbox, NFS, Windows/Samba share)?
About the files:
~/.Renviron
PATH=“${RTOOLS40_HOME}\usr\bin;${PATH}”
~/.Rprofile (this file is empty)
~/.R/Makevars (this folder/file file does not exist).
My model is located inside the current R script, just as your Test code:
# Load rstan
library(rstan)
# Set seed
set.seed(13)
# Make data
stan_data <- list(y = rnorm(500, 0, 1),
N = 500)
# Define model
stan_code <- "
/*
This model is just for testing.
*/
functions {
real times_two(real x) { // Custom function test.
return(x*2);
}
}
data {
int N; // Data length
vector[N] y; // Data
}
transformed data {
real a = 2.0; // Constant Test
}
parameters {
real<lower = 0> sigma; // Constraint test; residual SD
real mu; // Mean
}
transformed parameters {
real mu_over_sigma = mu / sigma; // Transformed param test.
}
model {
mu ~ normal(0, 1); // ~ syntax test.
target += student_t_lpdf(sigma | 5, 0, 1); // Increment test.
y ~ normal(mu, sigma); // Likelihood
}
generated quantities {
real b = normal_rng(0, 1); // RNG test
real c = times_two(a*b); // Custom Function test.
}
"
# Compile model
sm <- stan_model(model_code = stan_code)
At this stage, I have the error:
sm <- stan_model(model_code = stan_code)
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(cmd, intern = !verbose) :
running command 'C:/PROGRA~1/R/R-40~1.1/bin/x64/R CMD SHLIB file4374548ee21.cpp 2> file4374548ee21.cpp.err.txt' had status 1
2: In file(con, "r") :
cannot open file 'file4374548ee21.cpp.err.txt': No such file or directory
Error in sink(type = "output") : invalid connection
Some possible useful information:
-
It is my first time trying to install stan, I had never used it neither had older stan versions installed in my computer.
-
My OS is Windows 10.
-
I use the most recent versions of R (4.0.1) and RStudio (1.3.959).
For me something weird happens, which I haven’t been able to figure out why. If I use library(rstan) I get a similar error to @rcpedroso. However, I do not get the error, and everything works fine, if I use rstan:: statements without first loading the library. For example:
stan_code <- structure("data {\n int<lower=0> J; // number of schools\n real y[J]; // estimated treatment effect (school j)\n real<lower=0> sigma[J]; // std err of effect estimate (school j)\n}\nparameters {\n real mu;\n real theta[J];\n real<lower=0> tau;\n}\nmodel {\n theta ~ normal(mu, tau); \n y ~ normal(theta,sigma);\n}",
model_name2 = "eight_schools")
sm <- rstan::stan_model(model_code = stan_code)
Works fine. However,
library(rstan)
stan_code <- structure("data {\n int<lower=0> J; // number of schools\n real y[J]; // estimated treatment effect (school j)\n real<lower=0> sigma[J]; // std err of effect estimate (school j)\n}\nparameters {\n real mu;\n real theta[J];\n real<lower=0> tau;\n}\nmodel {\n theta ~ normal(mu, tau); \n y ~ normal(theta,sigma);\n}",
model_name2 = "eight_schools")
sm <- rstan::stan_model(model_code = stan_code)
gives the following error:
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(cmd, intern = !verbose) :
running command 'C:/PROGRA~1/R/R-40~1.0/bin/x64/R CMD SHLIB file323c106d3c60.cpp 2> file323c106d3c60.cpp.err.txt' had status 1
2: In file(con, "r") :
cannot open file 'file323c106d3c60.cpp.err.txt': No such file or directory
Error in sink(type = "output") : invalid connection
The problem seems to be with the rstan package. For instance, brms does not give me any errors. The example:
library(brms)
bprior1 <- prior(student_t(5,0,10), class = b) +
prior(cauchy(0,2), class = sd)
fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient),
data = epilepsy, family = poisson(), prior = bprior1)
Works fine. But loading rstan first gives me an error.
Session Info:
> devtools::session_info()
- Session info ---------------------------------------------------------------------------------------------------------------
setting value
version R version 4.0.0 (2020-04-24)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Netherlands.1252
ctype English_Netherlands.1252
tz Europe/Berlin
date 2020-06-12
- Packages -------------------------------------------------------------------------------------------------------------------
! package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.7 2020-05-13 [1] CRAN (R 4.0.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0)
bayesplot 1.7.2 2020-05-28 [1] CRAN (R 4.0.0)
bridgesampling 1.0-0 2020-02-26 [1] CRAN (R 4.0.0)
brms * 2.13.0 2020-05-27 [1] CRAN (R 4.0.0)
Brobdingnag 1.2-6 2018-08-13 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
coda 0.19-3 2019-07-05 [1] CRAN (R 4.0.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
colourpicker 1.0 2017-09-27 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 4.0.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
dplyr 1.0.0 2020-05-29 [1] CRAN (R 4.0.0)
DT 0.13 2020-03-23 [1] CRAN (R 4.0.0)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
ggplot2 * 3.3.1 2020-05-28 [1] CRAN (R 4.0.0)
ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.0)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httpuv 1.5.3.1 2020-05-26 [1] CRAN (R 4.0.0)
igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.0)
inline 0.3.15 2018-05-18 [1] CRAN (R 4.0.0)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.0)
D lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
loo 2.2.0 2019-12-19 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
markdown 1.1 2019-08-07 [1] CRAN (R 4.0.0)
D Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 4.0.0)
D nlme 3.1-147 2020-04-13 [1] CRAN (R 4.0.0)
pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
promises 1.1.0 2019-10-04 [1] CRAN (R 4.0.0)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
Rcpp * 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.0)
rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rsconnect 0.8.16 2019-12-13 [1] CRAN (R 4.0.0)
rstan * 2.19.3 2020-02-11 [1] CRAN (R 4.0.0)
rstantools 2.1.0 2020-06-01 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
shiny 1.4.0.2 2020-03-13 [1] CRAN (R 4.0.0)
shinyjs 1.1 2020-01-13 [1] CRAN (R 4.0.0)
shinystan 3.0.0 2020-06-08 [1] local
shinythemes 1.1.2 2018-11-06 [1] CRAN (R 4.0.0)
StanHeaders * 2.21.0-3 2020-05-28 [1] CRAN (R 4.0.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
threejs 0.3.3 2020-01-21 [1] CRAN (R 4.0.0)
tibble 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
vctrs 0.3.0 2020-05-11 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
xts 0.12-0 2020-01-19 [1] CRAN (R 4.0.0)
zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.0)
[1] C:/Program Files/R/R-4.0.0/library
D -- DLL MD5 mismatch, broken installation.
I have a similar error and behavior, and if I add the verbose flag to the compilation:
library(rstan)
stan_code <- structure("data {\n int<lower=0> J; // number of schools\n real y[J]; // estimated treatment effect (school j)\n real<lower=0> sigma[J]; // std err of effect estimate (school j)\n}\nparameters {\n real mu;\n real theta[J];\n real<lower=0> tau;\n}\nmodel {\n theta ~ normal(mu, tau); \n y ~ normal(theta,sigma);\n}",
model_name2 = "eight_schools")
sm <- rstan::stan_model(model_code = stan_code,verbose=TRUE)
I get the error:
g++.exe: error: Johnson/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
I believe you’ll get the different behaviour when not loading RStan first if you have spaces in the path to your home directory.
This is because the compilation arguments to include Eigen.hpp header slightly differ depending on whether RStan is loaded first.
If I load RStan, the compilation argument includes:
-include C:/Users/Andrew Johnson/Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp
Because there’s no quotations around the call, it interprets it as two separate commands (split at the space between ‘Andrew’ and ‘Johnson’).
If I don’t load RStan first, the compilation argument includes:
-include stan/math/prim/mat/fun/Eigen.hpp
Where the relative addressing bypasses the issues with the space
1 Like
Ugh, that’s not good, thanks for the heads up. @bgoodri is this something that needs fixing in RStan or is this really coming from attaching the StanHeaders package?
With the verbose flag added I get a similar problem:
g++.exe: error: Files/R/R-4.0.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
It seems to go wrong at the program files with the space in between.
@ducoveen, it worked for me with the rstan:: statement and without loading the library, as you did. As expected, I identify the same problem with verbose=T, that is,
g++.exe: error: Files/R/R-4.0.1/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
I don’t know if it will be useful, but these are my session informations:
> devtools::session_info()
- Session info -----------------------------------------------------------------------------------------
setting value
version R version 4.0.1 (2020-06-06)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language en
collate Portuguese_Brazil.1252
ctype Portuguese_Brazil.1252
tz America/Sao_Paulo
date 2020-06-13
- Packages ---------------------------------------------------------------------------------------------
! package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.7 2020-05-13 [1] CRAN (R 4.0.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0)
bayesplot 1.7.2 2020-05-28 [1] CRAN (R 4.0.0)
bridgesampling 1.0-0 2020-02-26 [1] CRAN (R 4.0.0)
brms * 2.13.0 2020-05-27 [1] CRAN (R 4.0.0)
Brobdingnag 1.2-6 2018-08-13 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
coda 0.19-3 2019-07-05 [1] CRAN (R 4.0.0)
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.1)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
colourpicker 1.0 2017-09-27 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 4.0.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
dplyr 1.0.0 2020-05-29 [1] CRAN (R 4.0.0)
DT 0.13 2020-03-23 [1] CRAN (R 4.0.0)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
ggplot2 * 3.3.1 2020-05-28 [1] CRAN (R 4.0.0)
ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.0)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.0)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.0)
igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.0)
inline 0.3.15 2018-05-18 [1] CRAN (R 4.0.0)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.1)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
loo 2.2.0 2019-12-19 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
markdown 1.1 2019-08-07 [1] CRAN (R 4.0.0)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.1)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
mvtnorm 1.1-1 2020-06-09 [1] CRAN (R 4.0.0)
nlme 3.1-148 2020-05-24 [1] CRAN (R 4.0.1)
pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.0)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
Rcpp * 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
D RcppParallel 5.0.1 2020-05-06 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.0)
rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rsconnect 0.8.16 2019-12-13 [1] CRAN (R 4.0.0)
rstan * 2.19.3 2020-02-11 [1] CRAN (R 4.0.1)
rstantools 2.0.0 2019-09-15 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
shiny 1.4.0.2 2020-03-13 [1] CRAN (R 4.0.0)
shinyjs 1.1 2020-01-13 [1] CRAN (R 4.0.0)
shinystan 2.5.0 2018-05-01 [1] CRAN (R 4.0.0)
shinythemes 1.1.2 2018-11-06 [1] CRAN (R 4.0.0)
StanHeaders * 2.21.0-5 2020-06-09 [1] CRAN (R 4.0.0)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
threejs 0.3.3 2020-01-21 [1] CRAN (R 4.0.0)
tibble 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
xts 0.12-0 2020-01-19 [1] CRAN (R 4.0.0)
zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.0)
[1] C:/Program Files/R/R-4.0.1/library
D -- DLL MD5 mismatch, broken installation.
I am a begginer about R packages, but I don’t like this last sentence: D – DLL MD5 mismatch, broken installation. Is it a problem?
Thank you (and all others) for the help, I hope to contribute in the future with some solutions and not only questions!
Which version of StanHeaders?
Sumarised from my last post:
> devtools::session_info()
- Session info -----------------------------------------------------------------------------------------
setting value
version R version 4.0.1 (2020-06-06)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language en
collate Portuguese_Brazil.1252
ctype Portuguese_Brazil.1252
tz America/Sao_Paulo
date 2020-06-13
> devtools::session_info()
- Packages ---------------------------------------------------------------------------------------------
rstan * 2.19.3 2020-02-11 [1] CRAN (R 4.0.1)
StanHeaders * 2.21.0-5 2020-06-09 [1] CRAN (R 4.0.0)
The same information is available for @ducoveen session_info in his post above, that is:
> devtools::session_info()
- Session info ---------------------------------------------------------------------------------------------------------------
setting value
version R version 4.0.0 (2020-04-24)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Netherlands.1252
ctype English_Netherlands.1252
tz Europe/Berlin
date 2020-06-12
- Packages -------------------------------------------------------------------------------------------------------------------
rstan * 2.19.3 2020-02-11 [1] CRAN (R 4.0.0)
StanHeaders * 2.21.0-3 2020-05-28 [1] CRAN (R 4.0.0)
I wouldn’t try to use StanHeaders 2.21 with rstan 2.19 even though those are the current versions on CRAN. Try
install.packages(
"https://cran.r-project.org/src/contrib/Archive/StanHeaders/StanHeaders_2.19.2.tar.gz",
repos = NULL, type = "source")
I installed StanHeaders 2.19.2 as you suggested:
> packageVersion("rstan")
[1] ‘2.19.3’
> packageVersion("StanHeaders")
[1] ‘2.19.2’
The problem still happens, and now the strategy proposed by @ducoveen does not work anymore.
@ducoveen strategy: rstan:: statement and without loading the library:
> sm <- rstan::stan_model(model_code = stan_code)
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(cmd, intern = !verbose) :
running command 'C:/PROGRA~1/R/R-40~1.1/bin/x64/R CMD SHLIB file9cc42701a2f.cpp 2> file9cc42701a2f.cpp.err.txt' had status 1
2: In file(con, "r") :
cannot open file 'file9cc42701a2f.cpp.err.txt': No such file or directory
Error in sink(type = "output") : invalid connection
Normal procedure:
> library(rstan)
> sm <- stan_model(model_code = stan_code)
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(cmd, intern = !verbose) :
running command 'C:/PROGRA~1/R/R-40~1.1/bin/x64/R CMD SHLIB file9cc55da7b9d.cpp 2> file9cc55da7b9d.cpp.err.txt' had status 1
2: In file(con, "r") :
cannot open file 'file9cc55da7b9d.cpp.err.txt': No such file or directory
Error in sink(type = "output") : invalid connection
My session informations now:
> devtools::session_info()
- Session info -----------------------------------------------------------------------------------------
setting value
version R version 4.0.1 (2020-06-06)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language en
collate Portuguese_Brazil.1252
ctype Portuguese_Brazil.1252
tz America/Sao_Paulo
date 2020-06-13
- Packages ---------------------------------------------------------------------------------------------
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.7 2020-05-13 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
dplyr 1.0.0 2020-05-29 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
ggplot2 * 3.3.1 2020-05-28 [1] CRAN (R 4.0.0)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
inline 0.3.15 2018-05-18 [1] CRAN (R 4.0.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
loo 2.2.0 2019-12-19 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rstan * 2.19.3 2020-02-11 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
StanHeaders * 2.19.2 2020-02-11 [1] CRAN (R 4.0.1)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
tibble 3.0.1 2020-04-20 [1] CRAN (R 4.0.0)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
[1] C:/Program Files/R/R-4.0.1/library
I installed again StanHeaders and @ducoveen strategy now works:
packageVersion(“rstan”)
[1] ‘2.19.3’
packageVersion(“StanHeaders”)
[1] ‘2.21.0.5’
I’m also getting the error Error in file(con, "r") : cannot open the connection in R 4.0, Windows 10 64-bit, rstan 2.19.3. I’ve tried StanHeaders 2.21.0.5 and 2.19.2, and I get an error with both.
Can you run:
example(stan_model,run.dontrun = TRUE,verbose=TRUE)
And post the line that starts with error:?
Here are the lines with errors:
Compilation argument: C:/PROGRA~1/R/R-40~1.0/bin/x64/R CMD SHLIB file2b8039f440d1.cpp 2> file2b8039f440d1.cpp.err.txt "C:/rtools40/mingw64/bin/"g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG -I"C:/Program Files/R/Packages/Rcpp/include/" -I"C:/Program Files/R/Packages/RcppEigen/include/" -I"C:/Program Files/R/Packages/RcppEigen/include/unsupported" -I"C:/Program Files/R/Packages/BH/include" -I"C:/Program Files/R/Packages/StanHeaders/include/src/" -I"C:/Program Files/R/Packages/StanHeaders/include/" -I"C:/Program Files/R/Packages/rstan/include" -DEIGEN_NO_DEBUG -D_REENTRANT -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -include stan/math/prim/mat/fun/Eigen.hpp -std=c++1y -march=core2 -include C:/Program Files/R/Packages/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I "C:/Program Files/R/Packages/StanHeaders/include" -I "C:/Program Files/R/Packages/RcppEigen/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file2b8039f440d1.cpp -o file2b8039f440d1.o g++.exe: error: Files/R/Packages/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory make: *** [C:/PROGRA~1/R/R-40~1.0/etc/x64/Makeconf:229: file2b8039f440d1.o] Error 1
Error in file(con, "r") : cannot open the connection In addition: Warning messages: 1: In find.package(package, lib.loc, verbose = verbose) : package ‘base’ found more than once, using the first from “C:/PROGRA~1/R/R-40~1.0/library/base”, “C:/Program Files/R/R-4.0.0/library/base” 2: In file(con, "r") : cannot open file 'file2b8039f440d1.cpp.err.txt': No such file or directory
This is the issue mentioned above about using RStan 2.19 with StanHeaders 2.21, you can work around this by not loading the RStan package before sampling. So rather than:
library(rstan)
stan(model, data)
Use:
rstan::stan(model, data)
That’s very helpful. Using rstan::stan() worked for me. Thanks for the workaround until the issue is fixed. Much appreciated.
1 Like
Hi @andrjohns and @bgoodri,
I got the same error messages when I tried running " rstan::stan(file = “schools.stan”, data = school.dat)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! g++.exe: error: Files/R/R-3.6.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
make: *** [C:/PROGRA~1/R/R-36~1.0/etc/x64/Makeconf:215: file49a433f81349.o] Error 1
In addition: Warning messages:
1: In file.remove(c(unprocessed, processed)) :
cannot remove file ‘C:\Users\n1103343\AppData\Local\Temp\RtmpIl4ZnM\file49a467be37f3.stan’, reason ‘No such file or directory’
2: In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-36~1.0/bin/x64/R CMD SHLIB file49a433f81349.cpp 2> file49a433f81349.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection
My rstan version is 2.21.1
stanheaders version is 2.21.0-5
Rtools version is rtools35