[R-sig-Geo] Rgdal on Centos 5.6

Roger Bivand Roger.Bivand at nhh.no
Sun Sep 9 23:36:08 CEST 2012 

On Sun, 9 Sep 2012, Guillermo Ponce-Campos wrote:

> Hello:
>
> Does anyone has an idea how to overcome this error after trying to install
> rgdal - gdal on Centos 5.6:
>
> *This is the Linux box I have installed:*
>
>> uname -a
> Linux  2.6.18-238.19.1.el5xen #1 SMP x86_64 x86_64 x86_64 GNU/Linux
>
> And R version:
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> *When I run the gdal installation I got an error*
>
> *# yum install gdal*
> Loaded plugins: dellsysid, fastestmirror, list-data, refresh-updatesd,
> verify
> Loading mirror speeds from cached hostfile
> * base: mirrors.cicku.me
> * dell-community: linux.dell.com
> * epel: ftp.osuosl.org
> * extras: mirror.5ninesolutions.com
> * rpmforge: mirror.hmc.edu
> * updates: mirrors.sonic.net
> Setting up Install Process
> Resolving Dependencies
> --> Running transaction check
> ---> Package gdal.i386 0:1.8.0-4.el5.elgis set to be updated
> --> Processing Dependency: libodbcinst.so.1 for package: gdal
> --> Processing Dependency: libdapserver.so.3 for package: gdal
> --> Processing Dependency: libgeotiff.so.1.2 for package: gdal
> --> Processing Dependency: libgif.so.4 for package: gdal
> --> Processing Dependency: libogdi.so.3 for package: gdal
> --> Processing Dependency: libhdf5.so.0 for package: gdal
> --> Processing Dependency: libxerces-c.so.27 for package: gdal
> --> Processing Dependency: libjasper.so.1 for package: gdal
> --> Processing Dependency: libnetcdf.so.4 for package: gdal
> --> Processing Dependency: libgeos_c.so.1 for package: gdal
> --> Processing Dependency: librx.so.0 for package: gdal
> --> Processing Dependency: libspatialite.so.2 for package: gdal
> --> Processing Dependency: libcfitsio.so.0 for package: gdal
> --> Processing Dependency: libdapclient.so.1 for package: gdal
> --> Processing Dependency: libdap.so.6 for package: gdal
> --> Processing Dependency: libodbc.so.1 for package: gdal
> ---> Package gdal.x86_64 0:1.8.0-4.el5.elgis set to be updated
> --> Processing Dependency: libogdi.so.3()(64bit) for package: gdal
> --> Processing Dependency: libhdf5.so.0()(64bit) for package: gdal
> --> Processing Dependency: libspatialite.so.2()(64bit) for package: gdal
> --> Processing Dependency: libdapclient.so.1()(64bit) for package: gdal
> --> Processing Dependency: libodbcinst.so.1()(64bit) for package: gdal
> --> Processing Dependency: libnetcdf.so.4()(64bit) for package: gdal
> --> Processing Dependency: libdap.so.6()(64bit) for package: gdal
> --> Processing Dependency: librx.so.0()(64bit) for package: gdal
> --> Processing Dependency: libgeos_c.so.1()(64bit) for package: gdal
> --> Processing Dependency: libjasper.so.1()(64bit) for package: gdal
> --> Processing Dependency: libdapserver.so.3()(64bit) for package: gdal
> --> Processing Dependency: libgeotiff.so.1.2()(64bit) for package: gdal
> --> Processing Dependency: libodbc.so.1()(64bit) for package: gdal
> --> Processing Dependency: libcfitsio.so.0()(64bit) for package: gdal
> --> Running transaction check
> ---> Package cfitsio.i386 0:3.030-2.el5 set to be updated
> ---> Package cfitsio.x86_64 0:3.030-2.el5 set to be updated
> ---> Package gdal.x86_64 0:1.8.0-4.el5.elgis set to be updated
> --> Processing Dependency: libhdf5.so.0()(64bit) for package: gdal
> ---> Package geos.i386 0:3.2.2-2.el5.elgis set to be updated
> ---> Package geos.x86_64 0:3.2.2-2.el5.elgis set to be updated
> ---> Package giflib.i386 0:4.1.3-7.3.3.el5 set to be updated
> ---> Package hdf5.i386 0:1.6.10-1.el5 set to be updated
> ---> Package jasper-libs.i386 0:1.900.1-14.el5 set to be updated
> ---> Package jasper-libs.x86_64 0:1.900.1-14.el5 set to be updated
> ---> Package libdap.i386 0:3.7.8-1.el5.1 set to be updated
> ---> Package libdap.x86_64 0:3.7.8-1.el5.1 set to be updated
> ---> Package libgeotiff.i386 0:1.2.4-3.el5 set to be updated
> ---> Package libgeotiff.x86_64 0:1.2.4-3.el5 set to be updated
> ---> Package librx.i386 0:1.5-8.el5 set to be updated
> ---> Package librx.x86_64 0:1.5-8.el5 set to be updated
> ---> Package libspatialite.i386 0:2.4.0-0.6_0.RC4.el5.elgis set to be
> updated
> ---> Package libspatialite.x86_64 0:2.4.0-0.6_0.RC4.el5.elgis set to be
> updated
> ---> Package netcdf.i386 0:3.6.2-7.el5 set to be updated
> ---> Package netcdf.x86_64 0:3.6.3-1.el5.rf set to be updated
> ---> Package ogdi.i386 0:3.2.0-0.12.beta2.el5 set to be updated
> ---> Package ogdi.x86_64 0:3.2.0-0.12.beta2.el5 set to be updated
> ---> Package unixODBC-libs.i386 0:2.2.11-10.el5 set to be updated
> ---> Package unixODBC-libs.x86_64 0:2.2.11-10.el5 set to be updated
> ---> Package xerces-c.i386 0:2.7.0-8.el5 set to be updated
> --> Finished Dependency Resolution
> gdal-1.8.0-4.el5.elgis.x86_64 from elgis has depsolving problems
>  --> Missing Dependency: libhdf5.so.0()(64bit) is needed by package
> gdal-1.8.0-4.el5.elgis.x86_64 (elgis)
> Error: Missing Dependency: libhdf5.so.0()(64bit) is needed by package
> gdal-1.8.0-4.el5.elgis.x86_64 (elgis)
> You could try using --skip-broken to work around the problem
> You could try running: package-cleanup --problems
>                        package-cleanup --dupes
>                        rpm -Va --nofiles --nodigest
>
> *I thought that installing rgdal with dependencies would try to install the
> gdal, but it seems that doesn't work like that... *


Why would you think that, when the README file in the package, also 
available in:

https://r-forge.r-project.org/scm/viewvc.php/pkg/inst/README?view=markup&root=rgdal

says nothing of the sort? It, and the package description on CRAN, say 
that GDAL and PROJ.4 must be installed first with their dependencies, 
especially dependencies for the drivers you need.

It is often the case that GDAL binaries are bundled with many dependencies 
that are irrelevant for users - most common drivers are provided when 
installing from source. You also seem to have an unhealthy mix of 32 and 
64 bit dependencies. I strongly advise first establishing which drivers 
you need, then running ./configure in a source install of GDAL, and seeing 
which dependencies are missing for the drivers you need. You need to 
address these, and of course install PROJ.4, which may be less of a 
problem. Once you have a working GDAL, rgdal installs without further 
difficulty.

Hope this clarifies,

Roger

PS. Current stable GDAL is 1.9.1, not 1.8.0, which came out in January 
2011; building from source gives you more recent software too.

> *
> *
>> install.packages("rgdal",dependencies=TRUE)
> *Installing package(s) into /usr/lib64/R/library*
> *trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/rgdal_0.7-18.tar.gz'*
> *Content type 'application/x-gzip' length 1433864 bytes (1.4 Mb)*
> *opened URL*
> *==================================================*
> *downloaded 1.4 Mb*
> *
> *
> ** installing *source* package rgdal ...*
> *** package rgdal successfully unpacked and MD5 sums checked*
> *configure: gdal-config: gdal-config*
> *checking gdal-config usability... ./configure: line 2058: gdal-config:
> command not found*
> *no*
> *Error: gdal-config not found*
> *The gdal-config script distributed with GDAL could not be found.*
> *If you have not installed the GDAL libraries, you can*
> *download the source from  http://www.gdal.org/*
> *If you have installed the GDAL libraries, then make sure that*
> *gdal-config is in your path. Try typing gdal-config at a*
> *shell prompt and see if it runs. If not, use:*
> * --configure-args='--with-gdal-config=/usr/local/bin/gdal-config'*
> *with appropriate values for your installation.*
> *
> *
> *ERROR: configuration failed for package rgdal*
> ** removing /usr/lib64/R/library/rgdal*
> *
> *
> *The downloaded source packages are in*
> *        /tmp/Rtmpseez2s/downloaded_packages*
> *Updating HTML index of packages in '.Library'*
> *Making packages.html  ... done*
> *Warning message:*
> *In install.packages("rgdal", dependencies = TRUE) :*
> *  installation of package rgdal had non-zero exit status*
>
>
> Thanks
> Guillermo
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> 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

More information about the R-sig-Geo mailing list