[Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

[Kern, Lori]

Mostly to lighten the dependency tree using tools that is built in with R would remove one additional dependency.  Also clarity; the tools directory adds an R folder for distinction that they are used with R packages which seemed like if a user was ever investigating, they would have a better idea where those files came from.



Lori Shepherd

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 Aaron Lun <infinite.monkeys.with.keyboards using gmail.com>
Sent: Wednesday, April 7, 2021 4:10 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

rebook and basilisk are also currently using rappdirs. I would be
interested in the motivation behind the switch for the Hubs and whether
that is applicable to those two packages as well.

-A

On 4/5/21 6:41 AM, Kern, Lori wrote:
> We are in process of making some major updates to the caching in BiocFileCache, AnnotationHub, and ExperimentHub.  Namely, the default caching location will change from using rappdirs::user_cache_dir   to using  tools::R_user_dir  eventually relieving the dependency on rappdirs.  To avoid conflicting default caches, if anyone used an old default caching directory, there will be an error to decide how to deal with the old location before proceeding and documentation in the vignettes for how to resolve.  Currently I have update BiocFileCache, the changes were just pushed to the devel branch and should propagate tonight.  I plan on doing the same for both AnnotationHub and ExperimentHub within the next few days.  We appreciate any feedback or questions with regards to these updates.
>
> This is only relevant to using the default cache location,  if a user manually specified a unique location, used environment variables, or created a package specific cache the code/location is not affected.  Anyone using package specific caching that utilizes rappdirs is encouraged also to consider changing package code to use the now available function in tools.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
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