The LD_LIBRARY_PATH worked like a charm! Thanks again!
Sincerely, Erin ________________________________________ From: Roger Bivand [roger.biv...@nhh.no] Sent: Thursday, April 14, 2016 1:47 PM To: Hodgess, Erin Cc: r-sig-geo@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: hodge...@uhd.edu<mailto:hodge...@uhd.edu> > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > -- 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 _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo