search for: hdf5load

...f file. i have downloaded the package 'hdf5' as it was advised on R seek. But when i try to load the file, the R console sends me an eror message: setwd("C:/Documents and Settings/Karine/Bureau/data/") #install.packages('hdf5') library("hdf5") sea_ice <- hdf5load("asi-s6250-20090704-v5i.hdf", load = TRUE, verbosity = 3, tidy = FALSE) Grid_ice <- hdf5load("LongitudeLatitudeGrid-s6250-Antarctic.hdf", load = TRUE, verbosity = 3, tidy = FALSE) > sea_ice <- hdf5load("asi-s6250-20090704-v5i.hdf", load = TRUE, verbosity...

...s one to load data into R from files in the HDF5 format. The bug appeared during a period in which R changed but the package did not. I include below both the R and C code, stripped of everything except what is needed to show the bug. What is supposed to happen is (*) the user calls R function hdf5load() (*) hdf5load() calls C function do_hdf5load() (*) do_hdf5load() opens the HDF5 file recording its HDF5 file id (fid) (*) do_hdf5load() calls C function setup_onexit, passing fid to it (*) setup_onexit sets up the on.exit call to be R function hdf5cleanup with fid as its argument (*) C function...

Dear R-users, I'm experiencing a segmentation fault when using hdf5load(file,load=FALSE). Library(hdf5) loads without problems but when loading a file, R crashes. I compiled R under Unix (Solaris for Sun). There is nothing wrong with the files, as I can run the same script at another place where R runs under Linux. Is it possible it has something to do with the hdf5 l...

...e 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...

...new subscriber, so I hope I'm posting in the right way. I need to load a hdf5 file, so I installed the hdf5 libraries ad the hdf5 R package; in downloaded a small sample file from the hdf5 website and I could correctly load it. But when I try to load my file: * require(hdf5) rm(list=ls()) ls() hdf5load("my_file.h5", verbosity=3) *I get this error message: * Errore in hdf5load("my_file.h5", verbosity = 1) : unable to open HDF file: my_file.h5 > HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: /Builds/unix/hdf5-1.8.4-patch1/src/H5F.c line 1514 in H5Fopen(...

The package works fine, but it seems not to provide access to fields, but only to the whole data in a certain file (function hdf5load(file, load = TRUE, verbosity = 0, tidy = FALSE)) Since hdf5 organizes the data and metadata in a hierarchical structure, we must explore in our problem (file>7GB), but it seems not possible with the functions in the package. Any suggestions? Please, let me know about such capabilities or inten...

...e objects. At the end, it uses rm() to remove objects. This is the same way we do it interactively, from the R prompt: testLoadSeveralHDF <- function(numFiles) { for (i in 0:(numFiles-1)) { filename <- paste("trial",i,".hdf",sep="") print(filename) hdf5load(filename) rm(list = ls(pat="g*")) } } However, after that program runs, the g* objects are not erased, but typing "rm(list=ls(pat="g*")) from the command line does erase them. I realized there's something about the environment that I need to tell the function...

Hello: Has anyone successfully installed the package hdf5-1.4.7 in R version 1.7.1? I get a fatal error with a core dump (see below) whenever I try to use hdf5load. Since I'm in the process of moving to a new machine, I'm not sure whether this is due to (my installations of) the HDF5 libs or the hdf5 package for R. Just for the record, the HDF5 data files were correctly generated in the new machine (therefore, I assume the HDF5 libs are good at least...

Dear All, I have data in HDF file format and would like to read it into R. I have tried the package hdf5 without success. Any ideas and suggestions?? Kind regards, Katrin -- Katrin Fleischer Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Subdepartment Hydrolgy and Geo-Environmental Sciences Room E-360 De Boelelaan 1085 1081 HV AMSTERDAM Tel: +31 20 59 87391

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

I've used the HDF5 library to bring some data into R. THe verbose output looks like this: > hdf5load("hdfGraphWed_Mar_16_13_33_37_2005.hdf",load=T,verbosity=1,tidy=T) Processing object: cprSeats ...... which is a Group Processing object: Seats 0 ...... its a dataset......Finished dataset Processing object: Seats 1 ...... its a dataset......Finished dataset Processing object: Seats 2 .......

I'm an R newbie, so please forgive if this question has been asked and answered many times before on this mailing list. I can't find anything in the manual (Notes or R), the FAQ or on CRAN, so... Has anyone implemented an interface so R can read NCSA's HDF? -- Terry J. Westley, Principal Engineer Veridian Engineering, Calspan Operations P.O. Box 400, Buffalo, NY 14225 twestley at

..._LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/westley/HDF/lib ./configure \ --prefix=/home/westley/R \ --with-g77=/usr/calspan/gnu/bin/g77 \ --x-lib=/usr/openwin/lib \ --with-hdf5-libs=/home/westley/HDF/lib 2) But, when I attempt to load an HDF file, I get this message: Error in hdf5load(file, load) : HDF5 support unavailable -- Terry J. Westley, Principal Engineer Veridian Engineering, Calspan Operations twestley at buffalo.veridian.com http://www.veridian.com/ ------------------------------------------------------- Author of TASH, an Ada binding to Tcl/Tk. Visit the TASH web s...

Hi, I am just beginning to use R for Windows and have two (perhaps naive) questions: 1. I am wanting to produce maps of the New Zealand coastline using R. I am aware of the map function in S-plus and was wondering if anyone had ported it to R yet. I could use the 'world' database for the data source but since it is very large I was also wondering if anyone had fine scale long and lat

Hi, I've been playing with R for only a few days, so I'm not terribly familiar with it yet. Has anyone ever done any work using HDF or NetCDF files with R? Both file formats have libraries which can be linked to a program to read and write data to these formats. Is this sort of thing possible with R? We are planning to use the HDF format to store experimental data collected by some

...+472,7 @@ #endif {"parse", do_parse, 0, 11, 4, PP_FUNCALL}, {"save", do_save, 0, 111, 3, PP_FUNCALL}, -{"load", do_load, 0, 111, 1, PP_FUNCALL}, +{"load", do_load, 0, 111, 2, PP_FUNCALL}, {"hdf5save", do_hdf5save, 0, 0, -1, PP_FUNCALL}, {"hdf5load", do_hdf5load, 0, 11, 2, PP_FUNCALL}, {"deparse", do_deparse, 0, 11, 2, PP_FUNCALL}, diff -r --unified R-0.63.2.orig/src/main/saveload.c R-0.63.2/src/main/saveload.c --- R-0.63.2.orig/src/main/saveload.c Tue Nov 10 19:23:54 1998 +++ R-0.63.2/src/main/saveload.c Tue Jan 26 16:14:57...

.../main/names.c 2000/01/29 00:23:18 *************** *** 515,522 **** {"parse", do_parse, 0, 11, 4, PP_FUNCALL}, {"save", do_save, 0, 111, 4, PP_FUNCALL}, {"load", do_load, 0, 111, 2, PP_FUNCALL}, - {"hdf5save", do_hdf5save, 0, 0, -1, PP_FUNCALL}, - {"hdf5load", do_hdf5load, 0, 11, 2, PP_FUNCALL}, {"deparse", do_deparse, 0, 11, 2, PP_FUNCALL}, {"dput", do_dput, 0, 111, 2, PP_FUNCALL}, {"dump", do_dump, 0, 111, 2, PP_FUNCALL}, --- 515,520 ---- Index: src/main/names.h ===============================================...