Hello, i’ve working with Rstudio and rstan for university tasks and due to a problem with ggplot2, i ve been forced to uninstall r, rstudio and rtools to try fixing it. I ve testing R 4.0.0 and R 3.6.3 and i have got several problems with both versions that doesn´t allow me to run rstan in neither of those. Both problems happen in rstudio 1.2
- R 4.0.0
- rtools is not installed properly because i can’t install packages from source. This outcome is revealed when i follow the example posted in https://cran.r-project.org/bin/windows/Rtools/. The following code show the inputs.
-writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
-Sys.which("make")
## "C:\\rtools40\\usr\\bin\\make.exe"
Before this, all clear, no error.
-install.packages("jsonlite", type = "source")
- when rtools was installed properly, ggplot2 is not found due rlang. i paste the following ouput
- R/win-library/4.0’
(as ‘lib’ is unspecified)
probando la URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rlang_0.4.5.zip'
Content type 'application/zip' length 1110537 bytes (1.1 MB)
downloaded 1.1 MB
package ‘rlang’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Álvaro López\AppData\Local\Temp\Rtmps5SWLZ\downloaded_packages
> library(rlang)
Error: package or namespace load failed for ‘rlang’ in get(Info[i, 1], envir = env):
no fue posible abrir el archivo 'C:/Users/Ãlvaro López/Documents/R/win-library/4.0/rlang/R/rlang.rdb': No such file or directory
> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
Error: package or namespace load failed for ‘ggplot2’ in get(Info[i, 1], envir = env):
no fue posible abrir el archivo 'C:/Users/Ãlvaro López/Documents/R/win-library/4.0/rlang/R/rlang.rdb': No such file or directory
Error: package ‘ggplot2’ could not be loaded
> rstan_options(auto_write=TRUE)
Error in rstan_options(auto_write = TRUE) :
no se pudo encontrar la función "rstan_options"
-
R 3.6.3
-rtools doesn´t install, when i write library(“rstan”), the following output is
- Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.3, 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)
For improved execution time, we recommend calling
Sys.setenv(LOCAL_CPPFLAGS = '-march=corei7 -mtune=corei7')
although this causes Stan to throw an error on a few processors.
-rtools doesn´t end installing, when i introduce a stan code. RStudio asks me “Building R package from source requires installation of additional buy tools. Do you want to install the additional tools now?”
- i accept, introduce the code for the second time and RStudio asks me the same question. If i refuse, it appears the following output
- Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! make: "C:/Users/Ãlvaro López/Documents/.R/Makevars.win": No such file or directory
make: *** No rule to make target '"C:/Users/Ãlvaro López/Documents/.R/Makevars.win"'. Stop.
Además: Warning message:
In system(cmd, intern = !verbose) :
comando ejecutado 'C:/PROGRA~1/R/R-36~1.3/bin/x64/R CMD SHLIB file36f031e12d62.cpp 2> file36f031e12d62.cpp.err.txt' tiene estatus 1
Error in sink(type = "output") : conexión inválida
This is the stan code which i ve been testing
library(rstan)
y<-c(15,28,16,12,29,33,48,23,15,33,41,49,18,4,59,73,27,16,14,29)
x<-c(8,5,7,8,5,4,4,5,6,5,4,4,6,10,3,2,6,6,9,5)
n<-length(y)
datos<-list(n=n,y=y,x=x)
codigo <- "
data{
int n;
int x[n];
int y[n];
}
parameters {
real tau ;
real omega;
}
model {
real lambda;
tau ~ normal(0,4);
omega ~ normal(0,4);
for(i in 1:n){
lambda = exp(tau + omega*x[i]);
y[i] ~ poisson(lambda);
}
}
"
fit_stan <- stan(model_code = codigo, data=datos)
print(fit_stan)
- Operating System - I think it is below
- RStan Version 2.19.3
- Output of
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
Error in file(con, "r") : no se puede abrir la conexión
Además: Warning message:
In file(con, "r") :
cannot open file 'C:\Users\Álvaro López\Documents/.R/Makevars': No such file or directory
- Output of
devtools::session_info("rstan")
- Session info ----------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.6.3 (2020-02-29)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate Spanish_Spain.1252
ctype Spanish_Spain.1252
tz Europe/Paris
date 2020-05-01
- Packages --------------------------------------------------------------------------------------------------------------------------------------
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.3)
backports 1.1.6 2020-04-05 [1] CRAN (R 3.6.3)
BH 1.72.0-3 2020-01-08 [1] CRAN (R 3.6.2)
callr 3.4.3 2020-03-28 [1] CRAN (R 3.6.3)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 3.6.3)
cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.3)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.3)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.3)
digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.3)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.3)
evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.3)
fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.3)
farver 2.0.3 2020-01-16 [1] CRAN (R 3.6.3)
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 3.6.3)
glue 1.4.0 2020-04-03 [1] CRAN (R 3.6.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.3)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.3)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.6.3)
isoband 0.2.1 2020-04-12 [1] CRAN (R 3.6.3)
labeling 0.3 2014-08-23 [1] CRAN (R 3.6.0)
lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.3)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.3)
loo 2.2.0 2019-12-19 [1] CRAN (R 3.6.3)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.3)
MASS 7.3-51.5 2019-12-20 [2] CRAN (R 3.6.3)
Matrix 1.2-18 2019-11-27 [2] CRAN (R 3.6.3)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 3.6.3)
mgcv 1.8-31 2019-11-09 [2] CRAN (R 3.6.3)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.3)
nlme 3.1-144 2020-02-06 [2] CRAN (R 3.6.3)
pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.3)
pkgbuild 1.0.7 2020-04-25 [1] CRAN (R 3.6.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.3)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.3)
praise 1.0.0 2015-08-11 [1] CRAN (R 3.6.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.3)
processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.3)
ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.3)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.3)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 3.6.3)
RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 3.6.3)
rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.3)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.3)
rstan * 2.19.3 2020-02-11 [1] CRAN (R 3.6.3)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.3)
scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.3)
StanHeaders * 2.21.0-1 2020-01-19 [1] CRAN (R 3.6.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 3.6.3)
tibble 3.0.1 2020-04-20 [1] CRAN (R 3.6.3)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.3)
vctrs 0.2.4 2020-03-10 [1] CRAN (R 3.6.3)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.6.3)
withr 2.2.0 2020-04-20 [1] CRAN (R 3.6.3)
[1] C:/Users/Álvaro López/Documents/R/win-library/3.6
[2] C:/Program Files/R/R-3.6.3/library