Greetings:
When using R within GRASS6, and loading the rgdal library, I encounter
an error
loading a specific version of the HDF5 library that does not occur when
I perform
the same operation in R 'outside' of GRASS6:
Here is a record of the error on my ubuntu system:
---------- Start ---------
reeves at wallace:~$ grass2
Cleaning up temporary files.....
Starting GRASS ...
Welcome to GRASS 6.2.1 (2006)
GRASS homepage: http://grass.itc.it/
This version running thru: Bash Shell (/bin/bash)
Help is available with the command: g.manual -i
See the licence terms with: g.version -c
If required, restart the graphical user interface with: gis.m &
When ready to quit enter: exit
To run a command as administrator (user "root"), use "sudo
<command>".
See "man sudo_root" for details.
To run a command as administrator (user "root"), use "sudo
<command>".
See "man sudo_root" for details.
GRASS 6.2.1 (spearfish60):~ > R
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for dGRASS 6.2.1 (spearfish60):~
> R
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> library("rgdal")
Loading required package: sp
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/usr/local/lib/R/site-library/rgdal/libs/rgdal.so':
libhdf5-1.6.4.so.0: cannot open shared object file: No such file or
directory
Error: package/namespace load failed for 'rgdal'
>
istribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> library("rgdal")
Loading required package: sp
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/usr/local/lib/R/site-library/rgdal/libs/rgdal.so':
libhdf5-1.6.4.so.0: cannot open shared object file: No such file or
directory
Error: package/namespace load failed for 'rgdal'
>
------------------------- Trying the same thing Outside of GRASS
------------------------------
reeves at wallace:/usr$ R
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("rgdal")
Loading required package: sp
Geospatial Data Abstraction Library extensions to R successfully loaded
>
---------- End ---------
Would anyone have any suggestions?
I tried to find the 'missing' hdf5 library: libhdf5-1.6.4.so.0: in the
archives, to no avail.
Thanks, Rick Reeves
--
Rick Reeves
Scientific Programmer / Analyst
National Center for Ecological Analysis and Synthesis
UC Santa Barbara
reeves at nceas.ucsb.edu
www.nceas.ucsb.edu
805 892 2533
