Error in if()

General
21

For me that page goes to a Google login that is hosted by RStudio. Unfortunately, Stan is not going to work on your computer until the thing with the paths is resolved so that it can find the configuration files correctly.

22

Possibly (re)installing R to a typical directory such as C:\R will help rather than the network share drive that it appears to be installed on.

23

I have tried to fix this on GitHub. Can you try

devtools::install_github("stan-dev/rstan", ref = "develop", subdir = "rstan/rstan")
library(rstan)

to see if it gets past that error.

24

Thanks for the follow-up

It says
Error in loadNamespace(name) : there is no package called ‘devtools’

25

Okay, I have downloaded the devtools, and ran the
devtools::install_github(“stan-dev/rstan”, ref = “develop”, subdir = “rstan/rstan”)

It says
These packages have more recent versions available.
Which would you like to update?

1: rlang (0.2.2 -> 0.3.0) [CRAN]
2: stringi (1.1.7 -> 1.2.4) [CRAN]
3: CRAN packages only
4: All
5: None

Enter one or more numbers separated by spaces, or an empty line to cancel

should i update all of them?

26

yeah

27

Okay! I ran the following code after installing the packages.

library(rstan)
rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores())

cat(
’
//saved as 8schools.stan
data {
int<lower=0> J; //number of schools
real y[J]; // estimated treatment effects
real<lower=0> sigma[J]; // s.e. of effect estimates
}
parameters {
real mu;
real<lower=0> tau;
real eta[J];
}
transformed parameters {
real theta[J];
for (j in 1:J)
theta[j] = mu + tau * eta[j];
}
model {
target += normal_lpdf(eta | 0, 1);
target += normal_lpdf(y | theta, sigma);
}
',
file = “8school.stan”, sep="", fill=T)
#------------------------------------------------------------
#Prepare the data in R
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 the model to data
fit <- stan(file = ‘8school.stan’, data = schools_dat,
iter = 1000, chains = 4)

And got the error :
Error in if (grepl(pattern, makefile_txt[i])) { : argument is of length zero

which is the same error I got initially.

What’s happening?
After my last conversation, yesterday I installed R, RStudio and Rtools into C:\ drive (not to program file).

Thanks

28

I am not understanding this. In

out <- system2(file.path(Sys.getenv("R_HOME"), "bin", "R"),
                 args = "CMD SHLIB --dry-run", stdout = TRUE)
out <- grep("SHLIB", out, value = TRUE)
out

is " make -f “C:/PROGRA~1/R/R-35~1.1/etc/x64/Makeconf” -f “C:/PROGRA~1/R/R-35~1.1/share/make/winshlib.mk” -f “//…/documents/StaffHome/StaffGroups$/…/Documents/.R/Makevars” SHLIB="" WIN=64 TCLBIN=64 OBJECTS=""" right?

29

the out put for the “out” is:
" make -f "C:/R-35~1.1/etc/x64/Makeconf" -f "C:/R-35~1.1/share/make/winshlib.mk" -f "//…/documents/StaffHome/StaffGroups$/…/Documents/.R/Makevars" SHLIB="" WIN=64 TCLBIN=64 OBJECTS="""

30

@bgoodri

Apparently, the code worked from OneDrive and C drive.
Wondering what caused the error when I used my PC’s local Document drive ?

Thanks

31

The rstan 2.18.1 on CRAN can’t deal when that system2 line comes back with “UNC paths are not supported. Defaulting to Windows directory.” The rstan on GitHub ostensibly can.

32

I installed rstan using
install.packages(“rstan”, repos = “https://cloud.r-project.org/”, dependencies = TRUE)

as mentioned on https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Windows

Would you like to specify the alternative GitHub url which I can download rstan?
Thanks

33

devtools::install_github(“stan-dev/rstan”, ref = “develop”, subdir = “rstan/rstan”) is the only one

34

Thanks @bgoodi. Appreciate your help very much.

I did try previously installing rstan from GitHub, as seen on this thread, but it did not work for me when i use my PC’s Document drive.

35

You mean you still get the Error in if (grepl(pattern, makefile_txt[i])) { : argument is of length zero when rstan is installed from GitHub?

36

yes! i got the same error

37

This is mind-boggling to me. With the rstan installed from GitHub, what is

rstan:::get_makefile_txt()

Is it NULL or a bunch of strings?

38

Oh! I forgot the library(rstan) part.
The code works now, after installing rstan from GitHub

Many thanks for all your help.

39

That is after doing a library(rstan) ?

40

It works. Thanks for your help