[Bioc-devel] Error in HDF5 - Package submission - Not detected locally
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. Best, Mike On Sat, 14 Sep 2019 at 23:26, Tiago Lubiana Alves <
tiago.lubiana.alves at 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 Bioinform?tica, FCF/USP *Computational Systems Biology Laboratory (CSBL)* Telefone (laborat?rio): +55 (11) 2648-0240 Telefone (pessoal): +55 (11) 954258000 [[alternative HTML version deleted]]
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