rgdal install problems in a module environment

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rgdal install problems in a module environment

Anderson, Richard O - (ric)

When various applications are split into modules (RHEL/CentOS environment-modules package), such that

  module load R proj gdal

is needed to make those applications and their pkg-config files available, the R

  install.packages(‘rgdal’)

fails because it assumes proj and gdal are in the same place, and omits the -L… link option for proj’s library path.

 

An easy workaround until this is fixed is

  export proj_lib_path=`pkg-config proj --libs | awk '{print $1}'`

before you start R, then “install.packages(‘rgdal’)” works as expected.

 

The author of the package is working on a real fix, so this workaround may not be needed for long.

 

Cheers,

Ric

-- 

Ric AndersonSystems Administrator Description: Description: Description: Description: Description: Description: Description: http://redbar.web.arizona.edu/logos/images/thumb_pawprints.gif

Research And Discovery Tech | HPC Large Systems Support

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Re: rgdal install problems in a module environment

Roger Bivand
Administrator
On Fri, 25 Oct 2019, Anderson, Richard O - (ric) wrote:

> When various applications are split into modules (RHEL/CentOS environment-modules package), such that
>  module load R proj gdal
> is needed to make those applications and their pkg-config files available, the R
>  install.packages(‘rgdal’)
> fails because it assumes proj and gdal are in the same place, and omits the -L… link option for proj’s library path.
>
> An easy workaround until this is fixed is
>  export proj_lib_path=`pkg-config proj --libs | awk '{print $1}'`
> before you start R, then “install.packages(‘rgdal’)” works as expected.
>
> The author of the package is working on a real fix, so this workaround
> may not be needed for long.
Thanks for the report, the fixed configure file is now on R-Forge and the
package (version > 1.4-6 on CRAN) should be installable using

install.packages("rgdal", repos="http://R-Forge.R-project.org")

(only affects source installs)

Roger

>
> Cheers,
> Ric
> --
> Ric Anderson| Systems Administrator [Description: Description: Description: Description: Description: Description: Description: http://redbar.web.arizona.edu/logos/images/thumb_pawprints.gif]
> Research And Discovery Tech | HPC Large Systems Support
> XSEDE Campus Champion
> [hidden email]<mailto:[hidden email]>         (V):  +1-520-626-1642
> [cid:image005.png@01D01593.CF7DFA60]
>
>
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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Roger Bivand
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