search for: hdf5save

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 wanted (R version 2.3.1 under ubuntu edgy). Since the upgrade to ubuntu feisty fawn which ships with R 2.4.1, the code above causes a crash: *** caught segfault *** address 0x11, cause '...

...ue as to what's going on here and maybe can advice me to handle it. Thank you, appreciate any help i can get. Cheers, Budi The example script ==================== library(hdf5) fileName <- "sample.txt" myTable <- read.table(fileName,header=TRUE,sep="\t",as.is=TRUE) hdf5save("test.hdf", "myTable") ======== The data example, the list continue for more than 250,000 rows: sample.txt ======== Date Time f1 f2 f3 f4 f5 20070328 07:56 463 463.07 462.9 463.01 1100 20070328 07:57 463.01 463.01 463.01 463.01 200 ....

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, wi...

...x64. Please let us know if you have any thoughts or tips that can help us debug this. Thanks, David ************ Using default transfer plist in vector_io: permuting About to write *** caught segfault *** address e8554000, cause 'memory not mapped' Traceback: 1: .External("do_hdf5save", call, sys.frame(sys.parent()), fileout, ..., PACKAGE = "hdf5") 2: hdf5save(hdf5_Fstat, "Fstat", "geneNames", "genotype") aborting ... ************ We've tried many things to debug it: * dbx Runtime Checking (RTC) is not detecting any (meaningfu...

I'm an R newbie, so please forgive if this question has been asked and answered many times before on this mailing list. I can't find anything in the manual (Notes or R), the FAQ or on CRAN, so... Has anyone implemented an interface so R can read NCSA's HDF? -- Terry J. Westley, Principal Engineer Veridian Engineering, Calspan Operations P.O. Box 400, Buffalo, NY 14225 twestley at

...ed for long. And, even if I quit, the NCSA folk have bent over forwards and backwards to make the hdf5 libraries build on many many platforms. This data storage format has many things to recommend it, none of which I am technically qualified to explain to you :) But, in R you can make use of hdf5save to store the data in a format that might be communicated to another platform without corruption. If you have a newish copy of Swarm on your system, then you can make hdf5 datasets that have vector, or "time series" sorts of data in them. High precision storage of floating point numbe...

Hi Everyone, I have updated my R version from 2.7 to 2.8 (patch) and since then I can not open HDF5 files that I saved previously with the command hdf5save from the hdf5 library. As anyone had that problem yet? Any help would be appreciated. Thanks Emmanuel ------------------------------------------- Dr. Emmanuel Devred Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, Nova Scotia, B2Y 4A2, Canada Ph: (1) 902 426-4681 Fax: (1) 90...

Hi, I've been playing with R for only a few days, so I'm not terribly familiar with it yet. Has anyone ever done any work using HDF or NetCDF files with R? Both file formats have libraries which can be linked to a program to read and write data to these formats. Is this sort of thing possible with R? We are planning to use the HDF format to store experimental data collected by some

...R-0.63.2/src/main/names.c Tue Jan 26 16:15:07 1999 @@ -472,7 +472,7 @@ #endif {"parse", do_parse, 0, 11, 4, PP_FUNCALL}, {"save", do_save, 0, 111, 3, PP_FUNCALL}, -{"load", do_load, 0, 111, 1, PP_FUNCALL}, +{"load", do_load, 0, 111, 2, PP_FUNCALL}, {"hdf5save", do_hdf5save, 0, 0, -1, PP_FUNCALL}, {"hdf5load", do_hdf5load, 0, 11, 2, PP_FUNCALL}, {"deparse", do_deparse, 0, 11, 2, PP_FUNCALL}, diff -r --unified R-0.63.2.orig/src/main/saveload.c R-0.63.2/src/main/saveload.c --- R-0.63.2.orig/src/main/saveload.c Tue Nov 10 19:23:5...

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

...ames.c *** src/main/names.c 2000/01/27 05:41:22 1.119 --- src/main/names.c 2000/01/29 00:23:18 *************** *** 515,522 **** {"parse", do_parse, 0, 11, 4, PP_FUNCALL}, {"save", do_save, 0, 111, 4, PP_FUNCALL}, {"load", do_load, 0, 111, 2, PP_FUNCALL}, - {"hdf5save", do_hdf5save, 0, 0, -1, PP_FUNCALL}, - {"hdf5load", do_hdf5load, 0, 11, 2, PP_FUNCALL}, {"deparse", do_deparse, 0, 11, 2, PP_FUNCALL}, {"dput", do_dput, 0, 111, 2, PP_FUNCALL}, {"dump", do_dump, 0, 111, 2, PP_FUNCALL}, --- 515,520 ---- Index: src...