I am trying to run an MCMC model on a cluster computing platform but cannot install rstan.
The error I get is this:
Installing package into ‘/home/lixx5010/.libraries/R/3.6/library’
(as ‘lib’ is unspecified)
also installing the dependency ‘V8’
trying URL 'https://cran.rstudio.com/src/contrib/V8_3.4.2.tar.gz'
Content type 'application/x-gzip' length 801493 bytes (782 KB)
==================================================
downloaded 782 KB
trying URL 'https://cran.rstudio.com/src/contrib/rstan_2.21.2.tar.gz'
Content type 'application/x-gzip' length 1152008 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
* installing *source* package ‘V8’ ...
** package ‘V8’ successfully unpacked and MD5 sums checked
** using staged installation
Not using CXX14
Using CXXCPP=g++ -std=gnu++11 -E
Using PKG_CFLAGS=-I/usr/include/v8 -I/usr/include/v8-3.14
Using PKG_LIBS=-lv8 -lv8_libplatform
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find the libv8 engine library. Try installing:
* deb: libv8-dev or libnode-dev (Debian / Ubuntu)
* rpm: v8-devel (Fedora, EPEL)
* brew: v8 (OSX)
* csw: libv8_dev (Solaris)
Alternatively, on Linux (x86_64) or MacOS you can set environment variable:
DOWNLOAD_STATIC_LIBV8=1
to automatically download a static version of libv8.
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
---------------------------[ ERROR MESSAGE ]----------------------------
<stdin>:1:16: fatal error: v8.h: No such file or directory
compilation terminated.
------------------------------------------------------------------------
ERROR: configuration failed for package ‘V8’
* removing ‘/home/lixx5010/.libraries/R/3.6/library/V8’
Warning in install.packages :
installation of package ‘V8’ had non-zero exit status
ERROR: dependency ‘V8’ is not available for package ‘rstan’
* removing ‘/home/lixx5010/.libraries/R/3.6/library/rstan’
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status
The downloaded source packages are in
‘/var/tmp/pbs.50604.compute.cla/RtmpWo0rb2/downloaded_packages’
Then I try to load the library but am told there is no such library installed. The whole error message is too confusing to me. Please help! Thanks!
2
Answers
I’m running R under Ubuntu 18.04 and the following command worked for me.
apt-get install libv8-dev
The answer from @CompToxDoc works for ubuntu, the more general solution that works on any Linux distribution is to run the following in the R terminal.
Sys.setenv("DOWNLOAD_STATIC_LIBV8"=1)
and then try again.