Hi all, I'm testing the use of the hdf5 R library under Windows XP. With some simple example (an R list with several subobjects as showed in the examples in the library) the library exports and imports .hdf files adequately. However, if I try to open the exported file with another program (HDFView 2.5) I receive the message that the file is an unsupported format. HDFView 2.5 does not seems to have any problem with another hdf5 files. Has anyone experienced a similar problem with R exporte hdf5 files and could indicate if it is likely originated by either the R interface or the hdf library in my computer? Thanks and best regards, Javier --
On Mon, 14 Dec 2009, jgarcia at ija.csic.es wrote:> Hi all, > I'm testing the use of the hdf5 R library under Windows XP. > > With some simple example (an R list with several subobjects as showed in > the examples in the library) the library exports and imports .hdf files > adequately. However, if I try to open the exported file with another > program (HDFView 2.5) I receive the message that the file is an > unsupported format. HDFView 2.5 does not seems to have any problem with > another hdf5 files. > > Has anyone experienced a similar problem with R exporte hdf5 files and > could indicate if it is likely originated by either the R interface or the > hdf library in my computer?Well, it is the hdf5 library that writes the file, so that must be the origin. Beyond that, please do read the posting guide, and send a small reproducible example to the package maintainer.> > Thanks and best regards, > Javier > -- > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
I am having the same issue with the HDF5 package. I installed the latest hdf5 DLLs from HDFGroup. I also installed the HDFView application from the same. This was all done on Windows. The example in ?hdf5load can be used to test. The example works fine for saving and loading the structure, but the ex1.hdf file file produced is not readable by HDFView. I have an hdf5 file written on Linux using visitconvert to write a 3D file format to hdf5 format. This file is readable by HDFView on Windows but cannot be loaded by hdf5load on Windows. When attempting to load the file, the process apparently goes into a loop producing multiple lines of Processing object: .. ...... which is a Group and finally ends with Error: C stack usage is too close to the limit This can be reproduced by using the data below to create a file named test.3D and converting the file to an HDF5 structure using (Linux) visitconvert test.3D test Silo and supplying 1 for HDF5 and 0 for Single File at the prompts. x y z theta 740322.174 181641.09 0.5 22.7385591768410 740332.174 181641.09 0.5 22.5965486314811 740342.174 181641.09 0.5 22.3900892567167 740352.174 181641.09 0.5 22.0708441524548 740362.174 181641.09 0.5 21.5597876586419 740372.174 181641.09 0.5 20.8148058389816 740382.174 181641.09 0.5 20.3085959981628 740392.174 181641.09 0.5 20.7148449544629 740402.174 181641.09 0.5 21.3456158108870 740412.174 181641.09 0.5 21.7777806643177 740422.174 181641.09 0.5 21.9911529065165 740382.174 181411.09 16.5 23.7646023452337 740392.174 181411.09 16.5 23.7251135887479 740402.174 181411.09 16.5 23.6082663058794 740412.174 181411.09 16.5 23.5401409105013 Mark