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