[GRASS-user] HDF5 library conflict between R 2.4 and GRASS 6.2:

[Hamish]

[starting R's rgral package from within GRASS fails, outside of GRASS
it's ok]

Rick Reeves wrote:
 > 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'
..
> I tried to find the 'missing' hdf5 library: libhdf5-1.6.4.so.0: in the
> archives, to no avail.



does ubuntu have an apt-file package? If it does, you can use that tool
to
find the missing package.


e.g. on Debian/Sarge:

$ apt-file search libhdf5- | grep so

libhdf5-doc: usr/share/doc/libhdf5-doc/html/Tutor/software.html
libhdf5-lam-1.6.2-0: usr/lib/libhdf5-1.6.2.so.0
libhdf5-lam-1.6.2-0: usr/lib/libhdf5-1.6.2.so.0.0.0
libhdf5-mpich-1.6.2-0: usr/lib/libhdf5-1.6.2.so.0
libhdf5-mpich-1.6.2-0: usr/lib/libhdf5-1.6.2.so.0.0.0
libhdf5-serial-1.6.2-0: usr/lib/libhdf5-1.6.2.so.0
libhdf5-serial-1.6.2-0: usr/lib/libhdf5-1.6.2.so.0.0.0

another way of searching: (requries more guessing)

$ apt-cache search libhdf5
libhdf5-doc - Hierarchical Data Format 5 (HDF5) - Documentation
libhdf5-lam-1.6.2-0 - Hierarchical Data Format 5 (HDF5) - runtime files - LAM version
libhdf5-lam-dev - Hierarchical Data Format 5 (HDF5) - development files - LAM version
libhdf5-mpich-1.6.2-0 - Hierarchical Data Format 5 (HDF5) - runtime files - MPICH version
libhdf5-mpich-dev - Hierarchical Data Format 5 (HDF5) - development files - MPICH version
libhdf5-serial-1.6.2-0 - Hierarchical Data Format 5 (HDF5) - runtime files - serial version
libhdf5-serial-dev - Hierarchical Data Format 5 (HDF5) - development files - serial version
mpb-mpi - MIT Photonic-Bands, parallel (mpich) version
libhdf5-serial-1.6.1-0 - Hierarchical Data Format 5 (HDF5) - runtime files - serial version


or is it already on your machine?
$ locate libhdf5- | grep so

if so, which package it came from:
$ dpkg -S /usr/lib/libhdf5-1.6.1.so.0.0.0
libhdf5-serial-1.6.1-0: /usr/lib/libhdf5-1.6.1.so.0.0.0


my (very rough) guess though is that CRAN (R) is providing a precompiled
binary, which was compiled on someone else's machine with libraries in
different places. perhaps you need to use the R package install method
with compiles the module locally after source download?


??,
Hamish