Problems with loading Rstan in R

Question

I have installed RStan for R. The installation seems to be successful, but when I load the package and use it, I keep getting the error message indicating Rstan isn't installed:

> source("http://mc-stan.org/rstan/stan.R")
    > fit <- stan("7b Class.stan", data=list(N=1187, J=J, y=earn, height=height, male=male, edu=ed, cluster=cluster), iter=1000, chains=4)
    Fejl i packageDescription("rstan")$Date : 
      $ operator is invalid for atomic vectors
    In addition: Advarselsbesked:
    In packageDescription("rstan") : no package 'rstan' was found

I have a Mac OS.X 10.7.5. I have recently upgraded my R to 3.1.3 and I use R-studio as an interface. For the installation of Rstan I have followed the description from here: https://github.com/stan-dev/rstan/wiki/RStan-Mac-OS-X-Prerequisite-Installation-Instructions

I have installed X-code and the Command Line Tools (Mac OS.X Lion) through Apple Developer and when I check in R whether is correctly installed, I get this message:

> system('clang++ -v')
Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin11.4.2
Thread model: posix  

When I install Stan in R, I get following message:

> #Install STAN - https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
> ###Step 1 - Set numbers of processes to uge
> Sys.setenv(MAKEFLAGS = "-j4")
> ###Step 2 - Run the script
> source('http://mc-stan.org/rstan/install.R', echo = TRUE, max.deparse.length = 2000)

> 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", "BH", "RcppEigen"))
+   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')
+   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/contrib/3.1/inline_0.3.13.tgz'
Content type 'application/x-gzip' length 78503 bytes (76 KB)
opened URL
==================================================
downloaded 76 KB

trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.1/BH_1.55.0-3.tgz'
Content type 'application/x-gzip' length 7455235 bytes (7.1 MB)
opened URL
==================================================
downloaded 7.1 MB

trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.1/RcppEigen_0.3.2.4.0.tgz'
Content type 'application/x-gzip' length 3335332 bytes (3.2 MB)
opened URL
==================================================
downloaded 3.2 MB


The downloaded binary packages are in
    /var/folders/0x/zkhg5kyd7j3199jkj76v9p340000gn/T//Rtmpk2CfrS/downloaded_packages
Error in install.packages : Updating loaded packages

Attaching package: ‘inline’

The following object is masked from ‘package:Rcpp’:

    registerPlugin

trying URL 'http://rstan.org/repo/src/contrib/rstan_2.6.0.tar.gz'
Content type 'application/x-gzip' length 1423850 bytes (1.4 MB)
opened URL
==================================================
downloaded 1.4 MB

ERROR: failed to lock directory ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’ for modifying
Try removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-rstan’
Warning in install.packages :
  installation of package ‘rstan’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/0x/zkhg5kyd7j3199jkj76v9p340000gn/T/Rtmpk2CfrS/downloaded_packages’
Fejl i library(rstan) : there is no package called ‘rstan’
Called from: top level 

Restarting R session...

> install.packages("Rcpp", type = "source")
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.5.tar.gz'
Content type 'application/x-gzip' length 2353791 bytes (2.2 MB)
opened URL
==================================================
downloaded 2.2 MB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c Date.cpp -o Date.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c Module.cpp -o Module.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c Rcpp_init.cpp -o Rcpp_init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c api.cpp -o api.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c attributes.cpp -o attributes.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c barrier.cpp -o barrier.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)

The downloaded source packages are in
    ‘/private/var/folders/0x/zkhg5kyd7j3199jkj76v9p340000gn/T/RtmpZSUb93/downloaded_packages’

Then I read in rstan: library(rstan) and I get the message that there is no package called Rstan.

I hope someone can see why Rstan will not run for me.

Answer 1

Load the package by

require("rstan")

or

library("rstan")

Using require(rstan) fails because it tries to load from an object named rstan in the environment and fails to find such object. Hence you need to use the inverted quotes.

Answer 2

You never loaded the package. Use

library(rstan)

to load the package into your current R session.