R help - Nov 2009 - R and HDF5 Question

Hello All,

I just signed up to this list, so I apologize if this question has been
asked before.

I am trying to load an hdf5 file into R and running into some problems. Here
are the steps I took to configure my environment:

    * R 2.10.0 (x64) on Mac OS X 10.6
    * hdf5 1.8.3 installed via macports
    * hdf5_1.6.9.tar.gz from CRAN

I suspect the problem I am having relates to incompatibilities in my version
of HDF5 and the one the R module expects. For completeness here is how I
installed the R module:

    R CMD INSTALL --configure-vars='CPPFLAGS=-I/opt/local/include'
--configure-args='--with-hdf5=/opt/local' hdf5_1.6.9.tar.gz

This builds fine. The library seems to load without issue, but no data is
returned when I try to load a file:

    > library(hdf5)
    > hdf5load("test.h5")
    > NULL

Yet,

    osx:data scott$ h5dump test.h5 HDF5 "test.h5" { GROUP
"/" { DATASET
"dset" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 31 ) / ( 31 ) }
DATA {
(0): 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096, 8192, (14):
16384, 32768, 65536, 131072, 262144, 524288, 1048576, 2097152, (22):
4194304, 8388608, 16777216, 33554432, 67108864, 134217728, (28): 268435456,
536870912, 1073741824 } } } }

Any thoughts?

Thanks in advance.
Scott

	[[alternative HTML version deleted]]

G'day Scott,

On Fri, 13 Nov 2009 09:52:43 -0700
Scott MacDonald <scott.p.macdonald at gmail.com> wrote:
> I am trying to load an hdf5 file into R and running into some
> problems. 
It's a while that I used hdf5 files and that package in R, but:
> This builds fine. The library seems to load without issue, but no
> data is returned when I try to load a file:
> 
>     > library(hdf5)
>     > hdf5load("test.h5")
>     > NULL
Is NULL the return of the hdf5load command or are you typing it on the
command line?

Anyway, .hdf5 files can contain several objects, just as R's .rda
file.  load() will load an .rda file and put all objects in that file
into the workspace.  Likewise, hdf5load() loads an hdf5 file and puts
all objects in that file into the workspace. 
> Yet,
> 
>     osx:data scott$ h5dump test.h5 HDF5 "test.h5" { GROUP
> "/" { DATASET "dset" { DATATYPE H5T_STD_I32LE DATASPACE
SIMPLE
> { ( 31 ) / ( 31 ) } DATA { (0): 1, 2, 4, 8, 16, 32, 64, 128, 256,
> 512, 1024, 2048, 4096, 8192, (14): 16384, 32768, 65536, 131072,
> 262144, 524288, 1048576, 2097152, (22): 4194304, 8388608, 16777216,
> 33554432, 67108864, 134217728, (28): 268435456, 536870912,
> 1073741824 } } } }
> 
> Any thoughts?
Did you try an ls() after the hdf5load() command?  If the hdf5load()
command was successfull, an ls() should show you that an object with
name "dset" is now in your workspace; if I read the output above
correctly.

HTH.

Cheers,
	
	Berwin