Problem Installing RStan

[Jalaj Bhandari]

Hi friends,

I am having trouble installing RStan.

R - Version 3.1.2

OS X - Yosemite Version 10.10.3

XCode Version 6.3.2

R Studio - Version 0.98.1091

I have a 64-bit RStudio version so I execute:  Sys.setenv(R_ARCH = '/x86_64') and so R_ARCH is not empty. I upgraded my OS X to Yosemite to install the latest XCode version.

I set the number of cores to 4 - Sys.setenv(MAKEFLAGS = "-j4")

I then proceed to install RStan

source('http://mc-stan.org/rstan/install.R', echo = TRUE, max.deparse.length = 2000)
install_rstan()

This I what i see in the console:

> install_rstan <- function() {

+   on.exit(Sys.unsetenv("R_MAKEVARS_USER"))

+   on.exit(Sys.unsetenv("R_MAKEVARS_SITE"), add = TRUE)

+ 

+   try(remove.packages("rstan"), silent = TRUE)

+   Sys.setenv(R_MAKEVARS_USER = "foobar")

+   Sys.setenv(R_MAKEVARS_SITE = "foobar")

+   install.packages(c("inline", "RcppEigen"))

+   devtools::install_url("http://cran.r-project.org/src/contrib/Archive/BH/BH_1.55.0-3.tar.gz")

+   install.packages("Rcpp", type = "source")

+   library(inline) 

+   library(Rcpp)

+   src <- ' 

+     std::vector<std::string> s; 

+     s.push_back("hello");

+     s.push_back("world");

+     return Rcpp::wrap(s);

+   '

+   hellofun <- cxxfunction(body = src, includes = '', plugin = 'Rcpp', verbose = FALSE)

+   test <- try(hellofun())

+   if(inherits(test, "try-error")) stop("hello world failed; ask for help on Rcpp list")

+ 

+   options(repos = c(getOption("repos"), 

+           rstan = "http://rstan.org/repo/"))

+   install.packages("rstan", type = 'source', dependencies = FALSE)

+   library(rstan)

+   set_cppo("fast")

+   if (any(grepl("^darwin", R.version$os, ignore.case = TRUE))) {

+     cat('\nCC=clang', 'CXX=clang++ -arch x86_64 -ftemplate-depth-256', 

+         file = "~/.R/Makevars", sep = "\n", append = TRUE)

+   }

+   return(invisible(NULL))

+ }

> install_rstan()

Removing package from ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’

(as ‘lib’ is unspecified)

Error in remove.packages : there is no package called ‘rstan’

trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.1/inline_0.3.14.tgz'

Content type 'application/x-gzip' length 90593 bytes (88 Kb)

opened URL

==================================================

downloaded 88 Kb

trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.1/RcppEigen_0.3.2.4.0.tgz'

Content type 'application/x-gzip' length 3885638 bytes (3.7 Mb)

opened URL

==================================================

downloaded 3.7 Mb

The downloaded binary packages are in

/var/folders/x7/mdj6334j0sgbwzzm29x3dds80000gn/T//RtmpDAmpaV/downloaded_packages

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

Called from: eval(expr, envir, enclos)

Browse[1]> 

The error seems to be in the devtools part.

Please help.

Thanks

Jalaj

[Ben Goodrich]

First do

install.packages("devtools")

Then

install_rstan()

Ben

[Jalaj Bhandari]

Thanks Ben. I tried that and this is the new error i get:

> install_rstan()

Removing package from ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’

(as ‘lib’ is unspecified)

Error in remove.packages : there is no package called ‘rstan’

trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.1/inline_0.3.14.tgz'

Content type 'application/x-gzip' length 90593 bytes (88 Kb)

opened URL

==================================================

downloaded 88 Kb

trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.1/RcppEigen_0.3.2.4.0.tgz'

Content type 'application/x-gzip' length 3885638 bytes (3.7 Mb)

opened URL

==================================================

downloaded 3.7 Mb

The downloaded binary packages are in

/var/folders/x7/mdj6334j0sgbwzzm29x3dds80000gn/T//RtmpKeTxBK/downloaded_packages

Downloading package from url: http://cran.r-project.org/src/contrib/Archive/BH/BH_1.55.0-3.tar.gz

Installing BH

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore  \

  CMD INSTALL  \

  '/private/var/folders/x7/mdj6334j0sgbwzzm29x3dds80000gn/T/RtmpKeTxBK/devtools8d14751c3a1/BH'  \

  --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library' --install-tests 

/Library/Frameworks/R.framework/Resources/bin/R: line 140: /Library/Frameworks/R.framework/Resources/etc/x86_64/ldpaths: No such file or directory

Error: Command failed (1)

Called from: top level 

[Ben Goodrich]

Someone with Mavericks or at least OS X would have to help you figure out why it is looking for a non-existent

/Library/Frameworks/R.framework/Resources/etc/x86_64/ldpaths

Ben

[Bob Carpenter]

I have Yosemite and it doesn't have that file.

$ ls /Library/Frameworks/R.framework/Resources/etc/
Makeconf Renviron javaconf ldpaths repositories

So there's no x86_64 in the path. So there's an ldpaths,
but no x86_64 directory.

- Bob

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[Jiqiang Guo]

Try not to set environment variable R_ARCH and/or try to install it not in RStudio. 

Jiqiang 

On Jun 25, 2015, at 5:59 PM, Jalaj Bhandari <jalajb...@gmail.com> wrote:

 Sys.setenv(R_ARCH = '/x86_64')

[Jalaj Bhandari]

I set the environment variable R_ARCH to blank and it works. Thanks!