similar to: 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

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

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

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

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

The returned values are in the list you assign to test_data, the original x and y are not modified, i.e the returned value for x will be test_data[[1]] and for y will be test_data[[2]]. Using the same variable names in the function and test is perhaps what is leading to confusion. > On 28 Jul 2017, at 09:13, Vijaya Kumar Regati <VijayaKumar.Regati at m3bi.com> wrote: > > Hi, >

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

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

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

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

In my new bash script, I'm doing what I think is a very simple rsync command the way I'm used to doing it. I just do a lot of setup and checking before I get to it. When I run it, it gets very unhappy with me. It's probably something very simple. I need to build the rsync command in a string so that some things can go away - like if my variables DRY_RUN and DELETE are undefined,

Hi all, I upgraded from 1.4.0rc3 to 2.0.0rc1 in my test environment, and while the upgrade itself went smoothly, i appear to be having problems with the (posix-)locks feature. :( The feature is clearly declared in the server config file, and according to the DEBUG-level logs, it is loaded successfully at runtime ; however, when Gluster attempts to lock an object (for the purposes of AFR

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'

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

*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: *

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

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

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

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

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