[Bioc-devel] dyn.load() problem with RHDF5 package.

Mark.Oberfield at noaa.gov Mark.Oberfield at noaa.gov
Mon Mar 31 02:09:11 CEST 2008


I am hoping to use R to analyze climatological datasets packaged in
HDF5 format.  After consulting the R FAQ and various documentation
provided, I downloaded the HDF5 package and successfully
installed it. Unfortunately, I get an error after downloading the
file from this web site:

Error in
hdf5load("http://www.mdl.nws.noaa.gov/~avnfps/data/hdf5/KGUY.hd5") :
  can't handle hdf class 10

Okay. Turn to Plan B

R-project web page also makes references to RHDF5 package on the
Bioconductor web site.  After much searching and googling, I find
ver. 1.6.0, which is the latest I can find.  Compilation fails on
hdf_dataset.c and hdf_subassign.c due to missing prototype information
for the vectorSubscript() routine.  I get that fixed and install rhdf5
package into R. Now when I attempt to load it, I get the following

> library(rhdf5)
Error in dyn.load(file, ...) :
  unable to load shared library
  /some/directory/R-2.6.2/library/rhdf5/libs/rhdf5.so: undefined symbol:
Error in library(rhdf5) : .First.lib failed for 'rhdf5'

Well, for some reason, libR.so isn't built which contains the routine
subscript.c which has the desired function. So I get that created and
placed into $R_HOME/lib so that LD_LIBRARY_PATH technique will work.

$ nm -AP libR.so | grep Rf_mat2indsub
libR.so: Rf_mat2indsub t 001b12d8 00000241

Unfortunately, even with the new library, libR.so, I get the same
result as before.

This as far as I got with RHDF5 package -- can't get the libR.so
library (which I had to build manually) to load.

Why is this so difficult?  If RHDF5 package is obsolete (or not
maintained), why doesn't the Bioconductor and R pages state that
somewhere or stop making references to it at least.  I web searched
for RHDF5 and examined the various "hits" (and the R and Bioconductor
mailing lists) and did not come across anything to suggest this in
writing. It would a matter of courtesy for the former RHDF5 
maintainers to say that it (or any package) is depreciated for the
record, so others do not waste their time trying to get it to work.

However, if RHDF5 package *not* obsolete and is being maintained, then
can someone tell me how these library functions can get resolved? Or
point me to a more up-to-date version that is compatible with R 2.6.2?



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