Fwd: Problems with RSTAN install

[Bob Carpenter]

I'm forwarding this message which came to our e-mail rather

than the mailing list (with the permission of the e-mail author,

of course).

This looks familiar, so It thought someone would know the

answer.

- Bob

Begin forwarded message:

From: Sam Weiss <samc...@gmail.com>

Subject: Problems with RSTAN

Date: May 3, 2014 at 12:19:19 PM GMT+2

To: d...@mc-stan.org

Hey I Installed RSTAN exactly https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started here and getting this error when i run school code: 

TRANSLATING MODEL 'schools_code' FROM Stan CODE TO C++ CODE NOW.

COMPILING THE C++ CODE FOR MODEL 'schools_code' NOW.

 *** caught segfault ***

address 0x20, cause 'memory not mapped'

Traceback:

 1: .Call(Module__functions_names, xp)

 2: Module(module, mustStart = TRUE)

 3: .getModulePointer(x)

 4: <S4 object of class "Module">$stan_fit4model6776b37d1c0_schools_code

 5: <S4 object of class "Module">$stan_fit4model6776b37d1c0_schools_code

 6: eval(expr, envir, enclos)

 7: eval(call("$", mod, paste("stan_fit4", model_cppname, sep = "")))

 8: .local(object, ...)

 9: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init,     check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file,     verbose = verbose, algorithm = match.arg(algorithm), control = control,     ...)

10: sampling(sm, data, pars, chains, iter, warmup, thin, seed, init,     check_data = TRUE, sample_file = sample_file, diagnostic_file = diagnostic_file,     verbose = verbose, algorithm = match.arg(algorithm), control = control,     ...)

11: stan(model_code = schools_code, data = schools_dat, iter = 1000,     chains = 4)

Possible actions:

1: abort (with core dump, if enabled)

2: normal R exit

3: exit R without saving workspace

4: exit R saving workspace

How can I fix this?

Sam

[Rob J. Goedman]

In nearly all cases I've seen this, it happens when versions don't match, e.g. picking up old library files/packages and/or installing libraries with non-matching tools/compilers.

Sam, it looks you've gotten a bit further over the weekend, is that correct? What did you do?

Rob J. Goedman

goe...@icloud.com

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[Fredrik Falkenström]

Dear list,

I am a newcomer to this list and to Stan. I have exactly the same problem with RStan as Sam Weiss described. I saw in another thread that someone solved it by installing an older version of R. I thought if there is another possibility I'd rather use that, so I thought I'd ask the list if anyone knows a solution (perhaps Sam has solved it)?

Best,

Fredrik Falkenström

[Ben Goodrich]

Downgrading R is never really the answer. It is just a matter of getting everything aligned. The first thing to try seems to be reinstalling Rcpp from source with

install.packages(c("Rcpp", "inline"), type = "source")

If that is insufficient to get rstan working, then should do a

remove.packages("rstan")

and then install rstan again. If you are using the latest version of the Mac operating system, then I think you have to install rstan with CXX=g++ in ~/.R/Makevars and then change it to CXX=clang++ when you want to run models.

Ben

[Fredrik Falkenström]

Thank you very much Ben, it was sufficient just to reinstall Rcpp.

Best,

Fredrik

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[Rob Trangucci]

Hey all,

I just wanted to alert the list that I just installed RStan on a new Mac (Mavericks, latest Xcode) and had a similar problem to Fredrik and Sam compiling the 8 schools code . I followed the instructions on the RStan Getting Started page and had R crash on me when I tried to run the 8 schools example. I followed Ben's instructions above to reinstall Rcpp and inline (copy/pasted Ben's above into the R console) from source, and the 8 schools code now runs fine. Given that a few other users have had similar problems, I wonder if there is a versioning issue with what R installs when install.packages(c('Rcpp','inline')) is called vs. install.packages(c('Rcpp', 'inline'), type = 'source').

Rob

[Michael Margolis]

I'm having a similar issue, and since I have the latest Mac OS I thought I should try following this advice:

If you are using the latest version of the Mac operating system, then I think you have to install rstan with CXX=g++ in ~/.R/Makevars and then change it to CXX=clang++ when you want to run models.

 I don't know how to that  -- the "install with" looks like it might be a parameter setting in install.packages(), but then how would I change it?

Thanks,
Michael

[Luc Coffeng]

Hi Michael,

You need to find the file "Makevars" that is in the folder ~/.R/ (where "~" is something like usr/[username]). ".R" starts with a period, so this indicates it is a hidden folder. You can't find it with finder, unless you do some tweaks. See here how to do that.

Btw, I recently got a new Macbook Pro, and I was able to successfully install rstan with CXX=clang++ in my Makevars file (and having installed inline and Rcpp from source).

Luc

[Michael Margolis]

Thanks, Luc. I added the line

CXX=clang++

to Makevars. The problem remains. I am off to start a new thread called "Vignette Failure".