[R-pkg-team] Bug#963675: r-bioc-rhdf5: h5read fails to read any dataset

[Rob Moss]

Package: r-bioc-rhdf5
Version: 2.32.0+dfsg-1
Severity: important

Dear Maintainer,

I have been using rhdf5 to load data generated by other programs so that I can plot these data using R.

With the current version of rhdf5, I cannot load any dataset from HDF5 files that previously worked fine.

I run the following commands in an R session:

    library(rhdf5)
    data_file <- 'path_to_data_file.hdf5'
    h5ls(data_file)
    df <- h5read(data_file, '/dataset/path')

I expect that h5ls() will list all of the groups and datasets in the HDF5 file, and that h5read() will return a dataframe.

The outcome is that h5ls() does list all of the groups and datasets, but h5read() fails with the following error message:

    Error in H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  : 
      HDF5. Dataset. Read failed.

Running the same R commands on the same HDF5 file works on a second computer, which is running Debian Stable.

I am unable to determine whether or not this failure coincides with the transition to R 4.0.

   * What led up to the situation?
   * What exactly did you do (or not do) that was effective (or
     ineffective)?
   * What was the outcome of this action?
   * What outcome did you expect instead?

Sincerely,
Rob

-- System Information:
Debian Release: bullseye/sid
  APT prefers testing
  APT policy: (900, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.6.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages r-bioc-rhdf5 depends on:
ii  libc6                                  2.30-8
ii  libgcc-s1                              10.1.0-3
ii  libhdf5-103-1                          1.10.6+repack-2
ii  libstdc++6                             10.1.0-3
ii  r-base-core [r-api-4.0]                4.0.1-1
ii  r-bioc-biocgenerics [r-api-bioc-3.11]  0.34.0-1
ii  r-bioc-rhdf5lib                        1.10.0+dfsg1-1

Versions of packages r-bioc-rhdf5 recommends:
pn  r-cran-bit64     <none>
ii  r-cran-testthat  2.3.2-2+b1

Versions of packages r-bioc-rhdf5 suggests:
ii  r-cran-dplyr      0.8.5-1+b1
ii  r-cran-ggplot2    3.3.1+dfsg-1
ii  r-cran-knitr      1.28+dfsg-2
ii  r-cran-rmarkdown  2.2+dfsg-1

-- no debconf information