Install ncdf4 package: Error, nc-config not found or not executable

Question

I have tried to install ncdf4 package. I have R version 3.1.1.

The problem seems to be finding the nc-config. If I Google for this specific problem, then I find people with the same problem, who solved it by installing the Debian package libnetcdf-dev before installing ncdf4.

I already installed that package but I keep having the same problem,

The error is as follows:

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.

What you can do is open a fresh terminal and do `which nc-config`. This will show you where the file is actually located in your system. If this file is indeed installed, the problem is probably that Linux installs it in a given location, and R expects it somewhere else (`/usr/local/bin` vs `/usr/bin` for example). You can try to fix the issue by adding the library containing `nc-config` to your `PATH` environment variable. Or the problem could be unrelated, e.g. 32 bit vs 64 bit.\ — Paul Hiemstra, Mar 19 '17 at 19:24

score 33 · Answer 1 · answered Jul 10 '18 at 19:30

33

I was having a similar problem and these answers didn't quite work for me (Ubuntu 16.04.4 LTS).

I had to install the developer version using:

sudo apt-get install libnetcdf-dev

answered Jul 10 '18 at 19:30

Oatman

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It works for me in the Ubuntu 18.04 and R version 3.4.4 (2018-03-15). – fvfaleiro Aug 21 '19 at 20:40
and 19.10, 3.6.1 – dez93_2000 Oct 29 '19 at 01:39
Contributor @Faith-Jones reports that this also works in Ubuntu 20.04. – Jeremy Caney Jun 18 '20 at 18:57
That works for me on Linux Mint 20.1 “Ulyssa”! Thanks! – Mohamed Ismaiel Ahmed Mar 16 '21 at 00:30

score 10 · Answer 2 · answered Jan 22 '18 at 14:06

10

On CentOS 7, using sudo yum install netcdf-devel.x86_64 in a terminal did the trick.

answered Jan 22 '18 at 14:06

F. Privé

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yum install netcdf-devel – Feng Tian Sep 08 '20 at 12:05

score 8 · Accepted Answer · edited Jan 10 '18 at 10:51

As @PaulHiemstra mentioned in the comments, find out where your nc-config is:

What you can do is open a fresh terminal and do which nc-config. This will show you where the file is actually located in your system. If this file is indeed installed, the problem is probably that Linux installs it in a given location, and R expects it somewhere else (/usr/local/bin vs /usr/bin for example). You can try to fix the issue by adding the library containing nc-config to your PATH environment variable. Or the problem could be unrelated, e.g. 32 bit vs 64 bit.\

For me, it is:

ubuntu@dark-horse:~$ which nc-config 
/home/ubuntu/miniconda3/bin/nc-config

I start with installing netcdf essentials using the below command

sudo apt-get install r-cran-ncdf4

The above command should have gotten nc-config installed, if not try:

sudo apt-get install netcdf-bin

Now, download the netcdf4 source

wget http://cirrus.ucsd.edu/~pierce/ncdf/ncdf4_1.13.tar.gz

Now, try to do the install

sudo R CMD INSTALL ncdf4_1.13.tar.gz --configure-args="--with-nc-config=/home/ubuntu/miniconda3/bin/nc-config"

score 0 · Answer 4 · answered Mar 07 '21 at 05:18

I also face the same issue, but you need to install

sudo apt install libgdal-dev libproj-dev libgeos-dev libudunits2-dev libnode-dev libcairo2-dev libnetcdf-dev

and

sudo apt install libglu1-mesa-dev freeglut3-dev mesa-common-dev

This will solve the issue

score 0 · Answer 5 · answered Aug 04 '22 at 06:21

0

Using conda may a good option conda install -c anaconda netcdf4

answered Aug 04 '22 at 06:21

upuil

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Install ncdf4 package: Error, nc-config not found or not executable

5 Answers5