Your message dated Tue, 9 Feb 2021 19:34:49 +0000 with message-id <4e4549c1-d4ce-4ba5-7251-c98c95b03...@shayandoust.me> and subject line Re: Bug#963675: Info received (Further details) has caused the Debian Bug report #963675, regarding r-bioc-rhdf5: h5read fails to read any dataset to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 963675: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963675 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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
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--- Begin Message ---Dear Rob Moss, Thank you for the initial report. It seems like this bug has indeed been fixed, to which you've also verified. Kind regards, Shayan Doust
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