Displaying 20 results from an estimated 600 matches similar to: "HDF5 compound data types and h5r/hdf5 R packages"
2012 Nov 27
1
best HDF5 package: h5r or rhdf5?
What is the current best package for manipulating HDF5 data files?
I tried "hdf5" a long time ago, but I ran into memory problems. "h5r" is on
CRAN now, and "rhdf5" is part of bioconductor.
Ideally, I'd like to read simple vectors or tables, either the entire thing
or a subset of rows. I don't need much writing support, but it would be
nice. Compression is a
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
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
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
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
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
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 Mar 16
2
how do we read netcdf / hdf files in R?
Dear R Users,
How do we read netcdf / hdf format files in R ?
Also, can we convert netcdf to hdf format in R?
Great Thanks,
Best Regards,
Yogesh
[[alternative HTML version deleted]]
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
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
2006 Jun 07
2
how to read hdf files under R?
Hi!
I am trying to install in my R environment the rhdf5 package and
library but it seems to have vanished from either the CRAN or
BioConductors sites.
Can you tell me where it would be possible to find it or any R
library (or function) able to read hdf files?
Sincerely,
Nicolas Degallier
UMR 7159 / IRD UR182
Laboratoire d'Oc?anographie et du Climat, Exp?rimentation et
Approches
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'
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
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 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
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
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
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
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
2012 Aug 08
1
Installing HDF5 package
Dear all
I am a new user of R and I have been trying to install the HDF5 package but
I don't seem to find any easily.
I tried looking in the archives but I didn't succeed in installing the
packages there. I guess they must be for Unix
If any body succeeded in installing this library, please give me some hints
on how to do so?
Thank you in advance
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