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: hodge...@uhd.edu<mailto:hodge...@uhd.edu>
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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.biv...@nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412
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