[R-sig-Geo] still having trouble with rgdal, please

[Hodgess, Erin]

The LD_LIBRARY_PATH worked like a charm!

Thanks again!

Sincerely,
Erin

________________________________________
From: Roger Bivand [Roger.Bivand at nhh.no]
Sent: Thursday, April 14, 2016 1:47 PM
To: Hodgess, Erin
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] still having trouble with rgdal, please

On Thu, 14 Apr 2016, Hodgess, Erin wrote:

> First of all, thanks to Roger Bivand for his great suggestions!  I am
> making gradual progress.
>
> However, not all is well yet.  One of my files from the gdal still seems
> to be missing:

Please read:

http://tldp.org/HOWTO/Program-Library-HOWTO/shared-libraries.html

and note that while you as non-super-user cannot use ldconfig to tell the
system to look in the right place for libgdal.so (it was found during
compilation and linking), you can set the environment
variable LD_LIBRARY_PATH despite the weaknesses that this has compared to
using ldconfig as super user. Running Sys.getenv("LD_LIBRARY_PATH") in R
shows you that R sets it up for its own purposes anyway (mostly for the
Java runtime engine).

Hope this helps,

Roger

>
>
>> install.packages("rgdal",lib="/work/01260/ehodgess/Rlibs",configure.args=c('--with-gdal-config=/work/01260/ehodgess/gdal/bin/gdal-config --with-proj-include=/work/01260/ehodgess/proj4/include --with-proj-lib=/work/01260/ehodgess/proj4/lib'),depen=TRUE)
> trying URL 'http://cran.revolutionanalytics.com/src/contrib/rgdal_1.1-8.tar.gz'
> Content type 'application/octet-stream' length 1649879 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package 'rgdal' ...
> ** package 'rgdal' successfully unpacked and MD5 sums checked
> configure: CC: gcc -std=gnu99
> configure: CXX: g++
> configure: rgdal: 1.1-8
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 616
> configure: gdal-config set to /work/01260/ehodgess/gdal/bin/gdal-config
> checking gdal-config exists... yes
> checking gdal-config executable... yes
> checking gdal-config usability... yes
> configure: GDAL: 2.0.2
> checking GDAL version >= 1.6.3... yes
> configure: experimental conditional use of GDAL2
>
>
> a bunch of good stuff....
>
>
> g++ -shared -L/usr/local/lib64 -o rgdal.so OGR_write.o gdal-bindings.o init.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/work/01260/ehodgess/gdal/lib -lgdal -L/work/01260/ehodgess/proj4/lib -lproj
> installing to /work/01260/ehodgess/Rlibs/rgdal/libs
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object '/work/01260/ehodgess/Rlibs/rgdal/libs/rgdal.so':
>  libgdal.so.20: cannot open shared object file: No such file or directory
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/work/01260/ehodgess/Rlibs/rgdal'
>
> The downloaded source packages are in
>        '/tmp/RtmpXX2VTF/downloaded_packages'
> Warning message:
> In install.packages("rgdal", lib = "/work/01260/ehodgess/Rlibs",  :
>  installation of package 'rgdal' had non-zero exit status
>> system("echo $PATH")
> /work/01260/ehodgess/custom-R-3.2.2/R-3.2.2/bin:/opt/apps/xalt/0.6/bin:/opt/apps/intel15/mvapich2/2.1/bin:/opt/apps/intel/15/composer_xe_2015.2.164/bin/intel64:
> /usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/opt/apps/xsede/gsi-openssh-5.7/bin:/usr/X11R6/bin:/opt/ofed/bin:/opt/ofed/sbin:.:/work/01260/ehodgess/gdal/bin:
> /work/01260/ehodgess/gdal/lib
>>
>
> So it's saying that libgdal.so.20 is not found.  However, it is in gdal/lib, which is in the path.   (See last line).
>
> Is there something else that I should be putting into the install.packages function, please?  I've tried all kinds of things (putting a copy of libgdal.so.20 into Rlibs, etc.), but no good.
>
>
> Thanks,
> Erin
>
>
>
> Erin M. Hodgess, Ph.D.
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: hodgesse at uhd.edu<mailto:hodgesse at uhd.edu>
>
>
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>
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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; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412