r - Saving in hdf5save creates an unreadable file -

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i'm trying save array hdf5 file using r, having no luck.

to try , diagnose problem ran example(hdf5save). created hdf5 file read h5dump.

when ran r code manually, found didn't work. code ran same ran in example script (except change of filename avoid overwriting). here code:

(m <- cbind(a = 1, diag(4))) ll <- list(a=1:10, b=letters[1:8]); l2 <- list(c="c", l=ll); pp <- pi hdf5save("ex2.hdf", "m","pp","ll","l2") rm(m,pp,ll,l2)  # , reload them: hdf5load("ex2.hdf",verbosity=3) m        # read "ex1.hdf"; buglet: dimnames dropped str(ll) str(l2)

and here error message h5dump:

h5dump error: unable open file "ex2.hdf"

does have ideas? i'm @ loss.

thanks

i have had problem. not sure of cause , neither hdf5 maintainers. authors of r package have not replied.

alternatives work

in time since answered, hdf5 package has been archived, , suitable alternatives (h5r, rhdf5, , ncdf4) have been created; usingncdf4`:

  1. since netcdf-4 uses hdf5 storage layer, ncdf4 package provides interface both netcdf-4 , hdf5.
  2. the h5r package r>=2.10
  3. the rhdf5 package available on bioconductor.

workarounds 2 functional unsatisfactory workarounds used prior finding alternatives above:

  1. install r 2.7, hdf5 version 1.6.6, r hdf5 v1.6.7, , zlib1g version 1:1.2.3.3 , use when writing files (this solution until migrating ncdf4 library).
  2. use h5totxt @ command line [hdf5utils][1] program (requires using bash , rewriting r code)

a minimal, reproducible demonstration of issue:

here reproducible example sends error

first r session

library(hdf5) dat <- 1:10 hdf5save("test.h5","dat") q() n # not save workspace

second r session:

library(hdf5) hdf5load("test.h5")

output:

hdf5-diag: error detected in hdf5 library version: 1.6.10 thread 47794540500448.  trace follows.  #000: h5f.c line 2072 in h5fopen(): unable open file    major(04): file interface    minor(17): unable open file  #001: h5f.c line 1852 in h5f_open(): unable read superblock    major(04): file interface    minor(24): read failed  #002: h5fsuper.c line 114 in h5f_read_superblock(): unable find file signature    major(04): file interface    minor(19): not hdf5 file  #003: h5f.c line 1304 in h5f_locate_signature(): unable find valid file signature    major(05): low-level i/o layer    minor(29): unable initialize object error in hdf5load("test.h5") : unable open hdf file: test.h5

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