I’m new to Stan. I’m using rstan 2.18.2 with R 3.5.2 in Windows 8.1.
When I try running the Eight Schools example from RStan Getting Started, the output (truncated) is:
> fit <- stan(file = "c:/work/Stan/Stan0001_8schools.stan",
+ data = schools_dat)
recompiling to avoid crashing R session
Warning message:
In system(paste(cmd, "-n")) : 'make' not found
SAMPLING FOR MODEL 'Stan0001_8schools' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup)
If I run print(fit, pars = c("mu", "tau")), there is no obvious problem:
Inference for Stan model: Stan0001_8schools.
4 chains, each with iter=2000; warmup=1000; thin=1;
post-warmup draws per chain=1000, total post-warmup draws=4000.
mean se_mean sd 2.5% 25% 50% 75% 97.5% n_eff Rhat
mu 8.15 0.13 5.09 -1.44 4.86 8.14 11.27 18.75 1428 1.01
tau 6.69 0.24 6.30 0.24 2.50 5.21 9.19 20.39 703 1.00
Samples were drawn using NUTS(diag_e) at Fri Mar 29 06:50:11 2019.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
My questions are:
- Does the
'make' not foundwarning indicate a major problem? That is, does it indicate that the results shouldn’t be trusted? - Even if the warning is harmless, how can I prevent it from appearing?
I have the model code in Stan0001_8schools.stan.The code I ran was:
library(rstan)
rstan_options(auto_write = TRUE)
dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, ifelse(.Platform$OS.type == "windows", "Makevars.win", "Makevars"))
if (!file.exists(M)) file.create(M)
cat("\nCXX14FLAGS=-O3 -march=native -mtune=native",
if( grepl("^darwin", R.version$os)) "CXX14FLAGS += -arch x86_64 -ftemplate-depth-256" else
if (.Platform$OS.type == "windows") "CXX11FLAGS=-O3 -march=native -mtune=native" else
"CXX14FLAGS += -fPIC",
file = M, sep = "\n", append = TRUE)
Sys.setenv(LOCAL_CPPFLAGS = '-march=native')
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 = "c:/work/Stan/Stan0001_8schools.stan",
data = schools_dat)
I have:
> pkgbuild::has_build_tools(debug = TRUE)
Scanning R CMD config CC...
cc_path:
'.exe' does not exist
Scanning path...
Scanning registry...
Found C:/Rtools for 3.5
VERSION.txt
Rtools version 3.5.0.4
[1] TRUE
> 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\seetom/.R/Makevars': No such file or directory
> devtools::session_info("rstan")
- Session info ---------------------------------------------------------
setting value
version R version 3.5.2 (2018-12-20)
os Windows 8.1 x64
system x86_64, mingw32
ui RTerm
language (EN)
collate English_Australia.1252
ctype English_Australia.1252
tz Australia/Sydney
date 2019-03-29
- Packages -------------------------------------------------------------
! package * version date lib source
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.2)
backports 1.1.3 2018-12-14 [1] CRAN (R 3.5.2)
BH 1.69.0-1 2019-01-07 [1] CRAN (R 3.5.2)
callr 3.1.1 2018-12-21 [1] CRAN (R 3.5.2)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.2)
colorspace 1.4-0 2019-01-13 [1] CRAN (R 3.5.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.2)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.2)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.5.2)
ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.5.2)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.5.2)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.2)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.5.2)
labeling 0.3 2014-08-23 [1] CRAN (R 3.5.2)
D lattice 0.20-38 2018-11-04 [1] CRAN (R 3.5.2)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.2)
loo 2.0.0 2018-04-11 [1] CRAN (R 3.5.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.2)
D MASS 7.3-51.1 2018-11-01 [1] CRAN (R 3.5.2)
D Matrix 1.2-15 2018-11-01 [1] CRAN (R 3.5.2)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.5.2)
mgcv 1.8-27 2019-02-06 [1] CRAN (R 3.5.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.2)
nlme 3.1-137 2018-04-07 [1] CRAN (R 3.5.2)
pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.2)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.2)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.2)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.2)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.2)
processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.2)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.2)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.5.2)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.5.2)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.2)
RcppEigen 0.3.3.5.0 2018-11-24 [1] CRAN (R 3.5.2)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.2)
rlang 0.3.1 2019-01-08 [1] CRAN (R 3.5.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.2)
rstan * 2.18.2 2018-11-07 [1] CRAN (R 3.5.2)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.2)
StanHeaders * 2.18.1 2019-01-28 [1] CRAN (R 3.5.2)
stringi 1.3.1 2019-02-13 [1] CRAN (R 3.5.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.5.2)
tibble 2.0.1 2019-01-12 [1] CRAN (R 3.5.2)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.5.2)
viridisLite 0.3.0 2018-02-01 [1] CRAN (R 3.5.2)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.2)
[1] c:/Program Files/R/R-3.5.2/library
D -- DLL MD5 mismatch, broken installation.
Clearly this suggests that there’s a problem, but I don’t understand what the problem is or how to fix it.
Thank you.