[Bioc-devel] Symbolic links to ExperimentHub files on Windows

[Kern, Lori]

Could you provide the name of your package so we can investigate further?

What dispatchclass do the experimenthub files use?  Is it an issue on windows regardless of location or perhaps an issue with the directory location itself (sometimes having trouble across partitions?)



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Richard Heery <richardheery using gmail.com>
Sent: Monday, September 23, 2024 2:51 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Symbolic links to ExperimentHub files on Windows

Hello all,

My package is failing to build on Windows as one of the functions attempts
to download files from ExperimentHub and then creates a directory with
symbolic links to these files using R.utils::createLink. However, it seems
on Windows that administrative privileges are required to create symbolic
links.

The downloaded files are a HDF5 file and corresponding RDS file for a
HDF5-backed SummarizedExperiment object. The purpose of using symbolic
links to them is so that a directory containing the links can be loaded
using HDF5Array::loadHDF5SummarizedExperiment while leaving the downloaded
files in the ExperimentHub cache.

Without being able to create symbolic links to the files on Windows, the
only alternatives I can think of are to move or copy the files from the
cache into the SummarizedExperiment directory. Neither are ideal solutions
as I would prefer not to move files out of the cache and since the files
may be quite large I would also prefer to avoid copying them.

If anyone has any other suggestions, I would really appreciate it.

Best,

Richard

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