Error in Installing rstan Package

[Shyue-Ming Loh]

Hi, I get this error when I tried to install the rstan R package:

> install.packages("rstan", dependencies=TRUE)

Installing package into ‘/usr/local/google/home/shyuemingloh/R/x86_64-pc-linux-gnu-library/3.1’

(as ‘lib’ is unspecified)

Warning in install.packages :

  dependency ‘loo’ is not available

trying URL 'http://cran.rstudio.com/src/contrib/rstan_2.7.0-1.tar.gz'

Content type 'application/x-gzip' length 1093296 bytes (1.0 Mb)

opened URL

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

downloaded 1.0 Mb

* installing *source* package ‘rstan’ ...

** package ‘rstan’ successfully unpacked and MD5 sums checked

** libs

[some output]

In file included from [usr/local/ folder]/home/shyuemingloh/R/x86_64-pc-linux-gnu-library/3.1/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:4:0,

                 from chains.cpp:19:

[usr/local/ folder]/home/shyuemingloh/R/x86_64-pc-linux-gnu-library/3.1/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:23: fatal error: Eigen/Dense: No such file or directory

 #include <Eigen/Dense>

                       ^

compilation terminated.

make: *** [chains.o] Error 1

ERROR: compilation failed for package ‘rstan’

* removing ‘[usr/local/ folder]/home/shyuemingloh/R/x86_64-pc-linux-gnu-library/3.1/rstan’

I've omitted the usr/local/ folder in the paths above, for confidentiality's sake.

I am not sure whether the error is due to the fact that the loo package is not installed. Here's my session info:

> sessionInfo()

R version 3.1.1 (2014-07-10)

Platform: x86_64-pc-linux-gnu (64-bit)

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       

 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):

[1] tools_3.1.1

The loo package is only available for R 3.1.2 and above.

[Shyue-Ming Loh]

[Ben Goodrich]

On Tuesday, July 28, 2015 at 4:22:50 PM UTC-4, Shyue-Ming Loh wrote:

In file included from [usr/local/ folder]/home/shyuemingloh/R/x86_64-pc-linux-gnu-library/3.1/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:4:0,

                 from chains.cpp:19:

[usr/local/ folder]/home/shyuemingloh/R/x86_64-pc-linux-gnu-library/3.1/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:23: fatal error: Eigen/Dense: No such file or directory

 #include <Eigen/Dense>

                       ^

compilation terminated.

make: *** [chains.o] Error 1

ERROR: compilation failed for package ‘rstan’

* removing ‘[usr/local/ folder]/home/shyuemingloh/R/x86_64-pc-linux-gnu-library/3.1/rstan’

Do you have RcppEigen installed? The loo thing is not really a problem because no rstan code utilizes it.

Ben

[Shyue-Ming Loh]

Apparently, I do. I executed installed.packages() and found the following the output:

Rcpp               NA                    NA      NA     "yes"            "3.1.1"

RcppEigen          NA                    NA      NA     "yes"            "3.1.1"

[Ben Goodrich]

On Tuesday, July 28, 2015 at 5:21:38 PM UTC-4, Shyue-Ming Loh wrote:

Apparently, I do. I executed installed.packages() and found the following the output:

I would try reinstalling RcppEigen. The rstan error says that it cannot find the Eigen headers, even though RcppEigen is in the LinkingTo line in rstan's DESCRIPTION file.

Ben

[Shyue-Ming Loh]

Thanks, Ben. I had an older version of RcppEigen. I updated to the latest version, and I can now install without any problems.