On Mon, 13 Aug 2012, Andrew Harley wrote:
Hi All, I'm getting an error when compiling the latest version of rgdal. It's saying unable to find GDALAllRegister in libgdal. We are running gdal v1.8.0 from elgis repository. I noticed we had two versions of gdal-config (one for 64 bit), but the error remains the same not matter which one I use. Here are the ./configure options for our version of gdal (from http://wiki.osgeo.org/wiki/Enterprise_Linux_GIS <http://wiki.osgeo.org/wiki/Enterprise_Linux_GIS> ): ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --target=x86_64-redhat-linux-gnu --program-prefix= --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/usr/com --mandir=/usr/share/man --infodir=/usr/share/info --prefix=/usr --includedir=/usr/include/gdal/ --datadir=/usr/share/gdal/ --with-threads=yes --with-dods-root=/usr/lib64 --with-ogdi --with-cfitsio=/usr --with-geotiff=external --with-tiff=external --with-libtiff=external --with-libz --with-netcdf --with-hdf4 --with-hdf5 --with-geos --with-jasper --with-png --with-gif --with-jpeg --with-odbc --with-sqlite --with-mysql --with-curl --with-python --with-perl --with-pcraster --with-ruby --with-java --with-xerces --with-xerces-lib=-lxerces-c --with-xerces-inc=/usr/include --with-jpeg12=no --enable-shared --with-gdal-ver=1.8.0 --with-! spatialite=yes And here is the output of our install of rgdal. I've also tried pointing it to the gdalconfig by using --configure-args='--with-gdalconfig=/usr/bin/gdal-config', but the same error occurs. Any help you guys can provide would be great! # R CMD INSTALL rgdal_0.7-12.tar.gz * installing to library '/usr/lib64/R/library' * installing *source* package 'rgdal' ... ** package 'rgdal' successfully unpacked and MD5 sums checked configure: gdal-config: gdal-config checking gdal-config usability... yes configure: GDAL: 1.8.0 checking GDAL version > 1.5.4... yes checking for gcc... gcc -m64 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -m64 -std=gnu99 accepts -g... yes checking for gcc -m64 -std=gnu99 option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking gdal.h usability... yes checking gdal.h presence... yes checking for gdal.h... yes checking gdal: linking with --libs only... no checking gdal: linking with --libs and --dep-libs... no configure: error: GDALAllRegister not found in libgdal. ERROR: configuration failed for package 'rgdal' * removing '/usr/lib64/R/library/rgdal' gdal-config output: # gdal-config --libs -lgdal # gdal-config --dep-libs -L/usr/lib64 -lgeos_c -lodbc -lodbcinst -lexpat -lxerces-c -ljasper -lhdf5 -L/usr/lib64/hdf -L/usr/lib64/hdf -lmfhdf -ldf -logdi -lgif -ljpeg -lgeotiff -ltiff -lpng -lnetcdf -lcfitsio -L/usr/lib64 -lpq -lz -lpthread -lm -lrt -ldl -ldap -ldapclient -ldapserver -lpthread -lrx -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz -lxml2 -lz -lm -lspatialite -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz -rdynamic -L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -L/usr/lib64 -lssl -lcrypto
This is obviously a difficult case. I suggest unpacking the tarball, running R CMD INSTALL rgdal, and examining the contents of the rgdal directory, specifically the config.log, config.status and errors.txt files. The final file should record the compiler and linker error messages. It is likely that you have multiple installs of libgdal.so*, and/or that you have not run ldconfig after installing GDAL. Hope this helps, Roger
Thanks, Andrew Harley Linux Systems Administrator Climate and Water Division (ICT Operations) Bureau of Meteorology, Australia 03 9616 8441 http://www.bom.gov.au/water/
_______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand Department of Economics, NHH Norwegian School of Economics, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: Roger.Bivand at nhh.no