similar to: hdf5 package segfault when processing large data

I've installed hdf5 [library & includes] here locally, last week. [see ?hdf5save in R] There is a remaining compilation / linking problem for me: The hdf5 library uses "compress2" a routine defined in Gnu's zlib, but not available in the zlib that comes with X11R6.3 (which we have installed). Now unfortunately, the final link statement for R (0.65) [for me, with hdf5

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

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

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'

*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 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, 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

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

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 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

Hello everybody, I'm using hdf5 files to store results from intermediate calculations. These are usually part of a list, called "res". As I want the hdf-files to contain all the members of res in its top "directory", I used to do attach(res) do.call("hdf5save", args=c(fileout=file.path(dir, ofile), as.list(names(res)))) detach(res) which did what I

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 ->

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

--=-=-= 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

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

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

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

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

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 -- View this message in context: