[Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Mike Smith gr|mbough @end|ng |rom gm@||@com
Mon Sep 16 10:38:47 CEST 2019

Hi Tiago,

I suspect what has happened here is that when create the mini_pbmc3k
object, you're doing this by subsetting the PBMC, 3k scRNA-seq data from
ExperimenHub. The assay data for that are are actually stored in an HDF5
file which will be downloaded and stored in your ExperimentHub cache on
your local machine. When you take the subset for your new object it still
points to the same HDF5 file, and when you save mini_pbmc3k all it actually
saves is the location of the HDF5 rather than putting the data in the
object. This works locally, but naturally the BioC build server doesn't
have the original HDF5 in exactly the same location, and so it fails.

Is there a reason you don't want to use the whole dataset and make the
first section of the vignette demonstrate how to download it via
ExperimentHub? Alternatively there is a way to transform from an HDF5 back
SingleCellExperiment to using the data in memory, but I can't remember it
right now - hopefully someone else will be along shortly.

This also seems like the perfect opportunity to point out that our next
BioC Developers' Forum (
https://stat.ethz.ch/pipermail/bioc-devel/2019-September/015499.html) will
have a discussion on object serilaisation which should cover exactly this
type of issue.


On Sat, 14 Sep 2019 at 23:26, Tiago Lubiana Alves <
tiago.lubiana.alves using usp.br> wrote:

> Hello,
> I am having a problem with a package submission build.
> This is the package issue:
> https://github.com/Bioconductor/Contributions/issues/1241
> And this is the ERROR:
> HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
>   #000: C:/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/src/H5F.c line 509
> in H5Fopen(): unable to open file
>     major: File accessibilty
>     minor: Unable to open file
>   #001: C:/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/src/H5Fint.c line
> 1498 in H5F_open(): unable to open file: time = Fri Sep 13 15:05:35
> 2019
> , name = '/home/lubianat/.cache/ExperimentHub/5486ffbe0e3_1605',
> tent_flags = 0
> (...)
> Quitting from lines 46-51 (fcoex.Rmd)
> Error: processing vignette 'fcoex.Rmd' failed with diagnostics:
> failed to open file '/home/lubianat/.cache/ExperimentHub/5486ffbe0e3_1605'
> --- failed re-building 'fcoex.Rmd'
> It looks like something is pointing in the wrong direction, but I have not
> been able to figure out exactly what. I've tried re-saving the data file
> ("mini_pbmc3k"), which is loaded in the vignette chunk of the error, but
> that did not help.
> Does anyone have a suggestion of what might be happening?
> Thank you very much for your time,
> Best,
> Tiago
> Tiago Lubiana
> Mestrando em Bioinformática, FCF/USP
> *Computational Systems Biology Laboratory (CSBL)*
> Telefone (laboratório): +55 (11) 2648-0240
> Telefone (pessoal): +55 (11) 954258000
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