unable to install R package "marmap"

I am trying to install the R package marmap on my workstation at the uni. I am running Xubuntu LTS 14.04.5, kernel version 4.4.0-45, with RStudio Version 0.99.903 and R version 3.3.1. When installing the marmap package, there is a a lot (!) of information buzzing by, ending with

** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (igraph)
* installing *source* package ‘gdistance’ ...
** package ‘gdistance’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gdistance)
ERROR: dependency ‘ncdf4’ is not available for package ‘marmap’
* removing ‘/home/francesc/R/x86_64-pc-linux-gnu-library/3.3/marmap’
Warning in install.packages : installation of package ‘marmap’ had non-zero exit status

Here, I figured that "non-zero exit status" means, that it didn't install correctly. So, I'd install the package ncdf4 first, only to be confronted with the following:

install.packages("ncdf4") Installing package into ‘/home/francesc/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL '
Content type 'unknown' length 119570 bytes (116 KB)
==================================================
downloaded 116 KB
* installing *source* package ‘ncdf4’ ...
** package ‘ncdf4’ successfully unpacked and MD5 sums checked
configure.ac: starting
checking for nc-config... no
-----------------------------------------------------------------------------------
Error, nc-config not found or not executable. This is a script that comes with the
netcdf library, version 4.1-beta2 or later, and must be present for configuration
to succeed.
If you installed the netcdf library (and nc-config) in a standard location, nc-config
should be found automatically. Otherwise, you can specify the full path and name of
the nc-config script by passing the --with-nc-config=/full/path/nc-config argument
flag to the configure script. For example:
./configure --with-nc-config=/sw/dist/netcdf4/bin/nc-config
Special note for R users:
-------------------------
To pass the configure flag to R, use something like this:
R CMD INSTALL --configure-args="--with-nc-config=/home/joe/bin/nc-config" ncdf4
where you should replace /home/joe/bin etc. with the location where you have
installed the nc-config script that came with the netcdf 4 distribution.
-----------------------------------------------------------------------------------
ERROR: configuration failed for package ‘ncdf4’
* removing ‘/home/francesc/R/x86_64-pc-linux-gnu-library/3.3/ncdf4’
Warning in install.packages : installation of package ‘ncdf4’ had non-zero exit status
The downloaded source packages are in ‘/tmp/RtmpC5Luhz/downloaded_packages

When I tried to run the suggested command in a terminal:

R CMD INSTALL --configure-args="--with-nc-config=/home/francesc/bin/nc-config" ncdf4

The response was the following:

~$ sudo R CMD INSTALL --configure-args="--with-nc-config=/home/francesc/bin/nc-config" ncdf4
[sudo] password for :
Warning: invalid package ‘ncdf4’
Error: ERROR: no packages specified

Now I am a bit at a loss, can anyone point me in the right direction ? Much appreciated !

PS Earlier this month, I found and applied a super-simple command in the command line, to install an R package, but I can't seem to find anymore. Literally a five-word string, which faultlessly installed an R package from the terminal. Is there an easy way to install R packages from the command line ?

Francesc

1 Answer

ncdf4 require system libraries be installed, so you have a couple of options:

1. Install the pre-built ncdf4 package from the repositories:

   sudo apt-get install r-cran-ncdf4

   This will automatically pull in the required system dependencies.

2. Or, you can install the system dependencies explicitly:

   sudo apt-get install netcdf-bin

   Then, install the R package:

   > install.packages('ncdf4')