Displaying 20 results from an estimated 1100 matches similar to: "best HDF5 package: h5r or rhdf5?"
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
2017 Aug 03
1
Use case for HDF5 dataspace interface
1. This relates to the package *rhdf5* and its implementation of the HDF5
dataspace interface. I am asking for an example of how other people who use
this package make use of the HDF5 data space interface exposed by the
library.
Longer answer:
As per my understanding, the dataspace interface exposes data locations
within a dataspace, but even while retrieving data from an hdf5 file using
methods
2017 Aug 01
0
Use case for HDF5 dataspace interface
1. What does this have to do with R?
2. If it concerns computational biology, the Bioconductor Help list
may be a better place to post.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Tue, Aug 1, 2017 at 2:28 AM, Koustav Pal
2017 Aug 01
2
Use case for HDF5 dataspace interface
This question is a clone of my stackoverflow question which never got
answered (o_O). Therefore I am posting it here. I would really like some
inputs if possible.
I am currently building some applications which make use of HDF5 files.
I have already taken a look at the hdfgroup website with regards to
dataspace <https://support.hdfgroup.org/HDF5/doc/H5.user/Dataspaces.html>
and I think I
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
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
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
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'
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:
*
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
2010 Jun 08
2
Extract/format/show for S4 objects
Hi all,
I'm trying to make an integer-backed quarter (as in fraction of year)
class, but I can't quite it to work. I want integer-backed so I don't
have to worry about floating-point effects when doing math, and so that
I can use it as in data.table.
First of all, is there a good reference for this anywhere? All of the
S4 tutorials that I've found have been too high-level, and
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
2003 Sep 15
1
Rgraphviz, rhdf5
>I just installed bioconductor via getBioC.R but there
>is 3 problems: apparently some libraries are missing
>and I don't know which one, and even the XML package
>add a error message like :
>1:Installation of package Rgraphviz had non-zero exit
>status in: installPkg(fileName, pkg, pkgVer, type,
>lib, repEntry, versForce)
>2:Installation of package rhdf5 had non-zero
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 Aug 24
1
hdf5 package segfault when processing large data
Hi there,
I am currently working on something that uses hdf5 library. I think
hdf5 is a great data format, I've used it somewhat extensively in
python via PyTables. I was looking for something similar to that in R.
The closest I can get is this library: hdf5. While it does not work
the same way as PyTables did, but it's good enough to let them
exchange data via hdf5 file.
There is just 1
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
2000 Feb 01
1
hdf5
Dear R-user group
I am currently running R-0.90.1-1 for LinuxPPC on my PowerBook. Few days
ago
I have seen at CRAN that a new R-package exists, namely
R-base-with-hdf5-0.90.1-2.
Sorrowly, I could not find any explanation, what the difference to the
other package is.
I have downloaded the "Introduction to HDF5 Release 1.2" from
hdf.ncsa.uiuc.edu/HDF5.
It seems that HDF5 is a data
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
2010 Aug 06
3
memory use without running gc()
Is there any way to get the current memory used by R without running
gc()?
I'd like to include the memory usage in logging output, but calling gc()
to get that information takes long enough to be noticeable (~ 6 s with ~
20 GB of ram in use), which goes against the point of logging.
Thanks,
Johann