I am trying to install the runjags package on a remote computer cluster. I am running R 3.4.0. I have JAGS 4.0.0 loaded, and can confirm that the rjags package will install and load. When I go to install the runjags package install.packages('runjags'), I get the following error:
configure: error: "Cannot load JAGS library in /share/pkg/jags/4.0.0/install/lib64"
I think part of the problem is that the directory /share/pkg/jags/4.0.0/install/lib64 does not exist in jags/4.0.0, but the directory /share/pkg/jags/4.0.0/install/lib, without the 64 does.
Any ideas how I can get runjags up and running?
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Thanks for your report. The runjags package is still using the same configure script as rjags 3.x, which assumes that the JAGS installation follows the same format as the R installation. However, there is a workaround for non-standard installs detailed in the README file within the runjags package:
The configure script will try to guess the location of the JAGS
library installation. It will look in /<prefix>/<lib>, where
- <prefix> is the determined from the location of the jags
script that launches the command line interface.
For example, if this is "/usr/local/bin/jags", then prefix will
be "/usr/local"
- <lib> is derived from the value of "LIBnn", returned by
"R CMD config LIBnn".
This is particularly important on 64-bit unix, where R is
installed by default in /usr/local/lib64 and LIBnn is "lib64"
The configure script will also look for JAGS headers in
/<prefix>/include/JAGS
If the configure script fails to find the JAGS headers or library,
you can set the environment variables JAGS_INCLUDE and JAGS_LIB
to point to the correct directory.
The header files for the module itself should be able to detect the
version of JAGS installed on your system, but a JAGS_MAJOR_VERSION
environmental variable can be set in case of problems which may be
encountered with some versions of JAGS - e.g. JAGS 4-beta requires:
export JAGS_MAJOR_VERSION=4
R CMD install runjags...
You have correctly observed that rjags version 4.x is more forgiving about installation paths as it tries to use pkg-config - I will update the configure script in the next version of runjags to do the same.
Hope that helps,
Matt
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Hello,
I am trying to install the
runjagspackage on a remote computer cluster. I am running R 3.4.0. I have JAGS 4.0.0 loaded, and can confirm that the rjags package will install and load. When I go to install the runjags packageinstall.packages('runjags'), I get the following error:configure: error: "Cannot load JAGS library in /share/pkg/jags/4.0.0/install/lib64"I think part of the problem is that the directory
/share/pkg/jags/4.0.0/install/lib64does not exist injags/4.0.0, but the directory/share/pkg/jags/4.0.0/install/lib, without the 64 does.Any ideas how I can get
runjagsup and running?Hi Colin
Thanks for your report. The runjags package is still using the same configure script as rjags 3.x, which assumes that the JAGS installation follows the same format as the R installation. However, there is a workaround for non-standard installs detailed in the README file within the runjags package:
You have correctly observed that rjags version 4.x is more forgiving about installation paths as it tries to use pkg-config - I will update the configure script in the next version of runjags to do the same.
Hope that helps,
Matt
This helps, thanks so much Matt. I should have digged deeper in the runjags documentation. I was able to get runjags to install using the following:
install.packages("runjags",configure.args = c("--with-jags-lib=/share/pkg/jags/4.0.0/install/lib"))