Displaying 20 results from an estimated 800 matches similar to: "Problem with package hdf5-1.4.7 in R-1.7.1"
2001 Mar 23
2
Memory problems, HDF5 library and R-1.2.2 garbage collection
Hello:
I've recently started using R to process data in HDF5 format. My files
come in 1.5MB chunks, but they can be as big as 50MB.
The problem I am facing with R-1.2.2 is that when I try to load 50 of
the 1.5MB HDF5 files (using the hdf5 library) in a loop, my Linux box
gets close to its memory limit around the file #15 (256MB RAM and
256MB swap). This happens even if I load file ->
2011 Mar 04
2
Fixing the HDF5 package: the on.exit mystery
Dear all,
I'm trying to fix a subtle bug in the hdf5 package. This package provides an
interfaces to the HDF5 library and hence allows 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
2013 Feb 04
1
Problem loading hdf5 file
*Hi everyone, I am a 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:
*
2009 Nov 13
1
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
2009 Mar 19
2
Package HDF5
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
1999 May 14
1
HDF5 support in R
Has anyone succeeded in using HDF5 in R?
Using Solaris R version 0.64.0:
1) R was configured in this way:
cd /home/westley/R/R-0.64.0
setenv LD_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
2010 Jan 26
2
hdf files
hello,
I have a problem to open an hdf 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 =
2005 Mar 16
1
working with pairlists imported from HDF5, converting to data frames?
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:
2009 Dec 14
2
hdf5 package
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
2005 May 04
1
segmentation fault using hdf5load() under Unix
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 libraries where
2000 Jan 29
1
HDF5 as a module
--=-=-=
Included below are:
1) Diffs to to remove HDF5 from R
2) Diffs to pass thru --with-* options to a module's configure
script during "R INSTALL". (To reiterate a plea for this
capability...) This applies only to Unix, the Windows (mingw32 in
my case) build approach of passing in make variables like
*-CFLAGS and *-LDFLAGS works fine. The only hitch
2002 Mar 01
1
Building hdf5 on Windows
Hi all,
I try to use the hdf5 package. I downloaded the Windows binary version, and
it claims it requires hdf5dll.dll library, so I download the whole hdf5
1.4.3 package from NCSA. Unfortunatelly, it crashes R. I suspect it is
because the package was probably compiled against version 1.2 of hdf5 (as
evoked in the help file?) or any other previous version, so I downloaded the
source of the package
2003 Mar 18
1
Building hdf5 for ms-windows
I am trying to build hdf5 for ms-windows. I downloaded the hdf5_1.4.7.tar.gz, gunzipped it and got a tar file. I extracted everything into a directory tree called hdf5. I also found a Makevars.win and libhdf5.def in the R help archives from March 2002. I put those two in hdf5 as well.
I issued the command Rcmd build --binary hdf5
but got this message complaining it can''t find
2011 Feb 18
1
hdf5 library install issue
Dear all
I'm trying to install the hdf5 library into R. The HDF5 package is
installed in a special directory, distributed accross my cluster:
/share/apps/HDF5
So i put the args option to the configure command as i read in previous
post in the list:
jerome]# R CMD INSTALL --configure-vars='LDFLAGS=-L/share/apps/HDF5/lib'
--configure-args='--with-hdf5=/share/apps/HDF5'
2010 Mar 03
1
linking hdf5, requires setting LD_LIBRARY_PATH
I am writing an R package to interface to hdf5 files (yes I know one
exists, the issue will be demonstrated using that package). I tend to like
to build/install things locally so that aspects of the system I am working
on don't cause problems later when attempting to install elsewhere. To
this end, I build and install the hdf5 libraries w/out incident:
tar xzf hdf5-1.8.4.tar.bz2
cd hdf5-1.8.4
2011 Dec 01
2
HDF5 compound data types and h5r/hdf5 R packages
Hi there,
I have a Java process that writes HDF5 files with the following
approximate structure:
group "xxx" {
group "yyy" {
dataset {}
dataset {}
}
group "zzz" {
dataset {}
dataset {}
}
}
where dataset is a rank one dataspace having a compound datatype defined as:
H5T_UNIX_TIME, float, float, float, float
I
2002 Jan 06
0
New RH7.2 rpms for R-hdf5 support available
HDF5 is a high quality data storage format from NCSA
(http://hdf.ncsa.uiuc.edu/index.html) Marcus Daniels of the Swarm
Development Group has made available an R library called hdf5 which
allows loading and saving of data in hdf5 format. The source for his
library is here:
ftp://ftp.swarm.org/pub/swarm/src/testing/hdf5_1.4.7.tar.gz
I prefer to use RPMs to maintain software across many linux
1999 Oct 06
1
uploaded hdf5 and R 0.65.1 RPMs
Dear everybody:
HDF5, a dataset formatting library, and R that is built with it, have
been uploaded to ftp://ftp-fis.iarc.fr/pub/incoming. The R RPM uses the
spec file created by Martyn Plummer as a starting point, and makes only
a few trivial changes.
-rw-rw-r-- 1 ftp 100 3416612 Oct 6 17:45
R-base-with-hdf5-0.65.1-1.i386.rpm
-rw-rw-r-- 1 ftp 100 2300453 Oct 6 17:48
2007 Dec 05
1
Installing hdf5
Hello,
I want to install hdf5 libraries for R and I get the same error as posted
below whether I try install.packages("hdf5") from R command prompt or the
command line installation below. I would appreciate if any one could help me
on this.
[alamj@thor hdf5]$ ./configure --with-hdf5=/bluejay/apps/HDF5-1.6.6/x86_64
checking for gcc... gcc
checking for C compiler default output... a.out
1999 Apr 21
0
R RPMS and HDF5
Greetings
I'm new to R. I became interested in it because my friends at the Swarm
Development Team at the Santa Fe Institute have been using/developing R
to work as a front end for HDF5 datasets.
>From looking at the RPMS for R, I got the idea they were compiled
without support for HDF5. Correct?
If you are interested in the HDF5 data format and R, on my page I have
RPMS for HDF5 and