RGDAL installation fail after yum upgrade

On Fri, 21 Sep 2018, David.GIOVANNINI at ext.ec.europa.eu wrote:

 I have checked all the packages (GDAL v1.11.4, PROJ4 v4.9.1) and seems
 that the minimun required version has been satisfied. But on the system I
 have two version of PROJ4, the version v4.8.0 ( /usr/bin/proj ) and the
 version v4.9.1 ( /usr/local/bin/proj ).
David,

 This is the cause of many problems: two different versions of software on
the same host.

 So can I force the use of the new version of PROJ with some parameters
 during the installation of RGDAL?
 Take a look at your $PATH; it's likely that /usr/local/bin/ is checked
before usr/bin/. And different applications using, e.g., proj4, may look for
it in either place. This means that one application finds the 4.9.1 version
while another application finds the 4.8.0 version.
Rich: thanks - having multiple versions is indeed a challenge on platforms 
where R uses dynamically loaded libraries. On Windows and MacOS, most CRAN 
packages with external dependencies are built with static linking (the 
*old* way). However, executables are on the PATH, but dynamically loaded 
libraries - shared objects - are on LD_LIBRARY_PATH. Try:

echo $LD_LIBRARY_PATH

at the shell prompt, then inside R:

Sys.getenv("LD_LIBRARY_PATH")

and you'll see that R may have made modifications on startup. A typical 
trap is also forgetting to run /sbin/ldconfig -v as root after installing 
software in /usr/local/lib (and adding /usr/local/lib to a file in 
/etc/ld.so.conf.d) so that the shared objects are visible.

The easier route is to have just one version of external software 
installed where R can see it; it is harder but possibly on a cluster 
necessary to modify LD_LIBRARY_PATH locally and consistently. Also look at 
closed sf issues on github; there we stepped back from messing with 
LD_LIBRARY_PATH on a general basis.

Hope this helps,

Roger
 I recommend that you put all core binaries in /usr/bin (which means moving
4.9.1 from /usr/local/bin/ to /usr/bin/ and keeping in the latter only
software developed locally.

 My network runs Slackware so I don't know how difficult it might be for
you to re-organize your CentOS installations, but making the time to do this
will make life easier for you.

Best regards,

Rich

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Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
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RGDAL installation fail after yum upgrade

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