search for: rhdf5

...rently 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 exit >status in: installPkg(fileName, pkg, pkgVer, type, >lib, repEntry, versForce) >3:Installation of package XML had non-zero exit >status >in: installPkg(fileName, pkg, pkgVer, type, lib, >repEntry, versForce) >What can I do? >Thanks in advance! >Line He...

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 must, though. Thanks, Johann [[alternative HTML version deleted]]

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,...

...} } where dataset is a rank one dataspace having a compound datatype defined as: H5T_UNIX_TIME, float, float, float, float I have tried R packages h5r and hdf5 in an attempt to read the file but examining the source of h5r and reading documentation for hdf5 here: http://xweb.geos.ed.ac.uk/~hcp/Rhdf5.html leads me to believe that compound datatypes are not supported by these packages. My guess is that mapping arbitrary type definitions in HDF5 to available types in R might be somewhat tricky. Incidentally, h5dump has trouble displaying the data in the dataset but I think this is to do with t...

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...

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

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

...my case) build approach of passing in make variables like *-CFLAGS and *-LDFLAGS works fine. The only hitch with the Windows install is that I had to drop the `bundle' wrapper, which was useful for Unix in order to give the package a recognizable name with version number (Rhdf5-0.0), but the installed package with R a minimal name (hdf5). 3) The module itself, as an attachment. Index: aclocal.m4 =================================================================== RCS file: /home/rcvs/src/R/aclocal.m4,v retrieving revision 1.30 diff -c -r1.30 aclocal.m4 *** acloca...

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

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 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]]

...ons: - The speed side of the things worries me. Is the idea totally stupid ? - Does anybody out there have experience in doing similar things (and why not dream about it, doing the exact same thing ;) ) with R ? Thanking any kind of help/pointer in advance, L. PS: I know of the package 'rhdf5'. It provides what I am looking for, but I'd like to offer a poor man's solution (should I say 'lazy man')... the package should work 'out of the box' -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD....

...t builds -- Everything from CRAN, including RMySQL, RmSQL, XML, rpvm, rsprng, RMpi, but not ROracle, RSQLite, RQuantlib -- Lindsay packages rmutil, gnlm, stable, growthm repeated, event, ordinal -- Bioconductor packages Biobase, annotate, affy, AnnBuilder, edd, genefilter, geneplotter, rhdf5, marrayTest, marrayClasses, marrayInput, marrayPlots, multtest, ROC, tkWidgets -- snow from Tierney -- deal from gR -- from Devel Dopt, GRASS, PHYLOGR, R2HTML, RPgSQL, dseplus, pls, runstat, multidim, mclust, ensemble, locfit, write-snns -- from OmegaHat gtk, OOP, RGtk, RGtkViewers, RObjectTa...

A friend of mine recently mentioned that he had painlessly imported a data file with 8 columns and 500,000 rows into matlab. When I tried the same thing in R (both Unix and Windows variants) I had little success. The Windows version hung for a very long time, until I eventually more or less ran out of virtual memory; I tried to set the proper memory allocations for the Unix version, but it never

...essed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not including precomputed annotation data packages for Affymetrix GeneChips(tm), KEGG, GO, and LocusLink mappings. -- HELP AND RESOURCES: The packages and mo...

...essed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data (affy, affycomp, gcrma) * diagnostic plots and normalization for cDNA array data (marrayInput, marrayNorm, marrayPlots) * storage and retrieval of large datasets (rhdf5, externalVector, Rdbi, RdbiPgSQL). * facilitate user interaction (tkWidgets, widgetTools) There are currently a total of 48 packages, not including precomputed annotation data packages for Affymetrix GeneChips(tm), KEGG, GO, and LocusLink mappings. -- HELP AND RESOURCES: The packages and mo...

Hi Thanks once again for your help, I do appreciate it..... however.... Here is what I get with your test.... (under tcsh - i normally use bash, but I will keep everything the same) users/mwatson> env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R >options(internet.info=0) >update.packages() trying URL `http://cran.r-project.org/src/contrib/PACKAGES' unable to connect to