[Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub
Woah, I missed the part where you said that there would be an error. This does not sound good. Users are going to flip out, especially when EHub and AHub are not visible dependencies (e.g., scRNAseq, celldex). It also sounds completely unnecessary for EHub and AHub given that the new cache can just be populated by fresh downloads. Similarly, BiocFileCache::bfcrpath should not be affected, and people using that shouldn't be getting an error. Why not just move the old default cache into the new location automatically? This seems like the simplest solution given that everyone accessing BFC resources should be doing so through the BFC API. And most files are not position-dependent, unless people are putting shared libraries in there. But even if you can't, an error is just too much. We use BiocFileCache a lot in our company infrastructure and the brown stuff will hit the fan if we have to find every old default cache and delete it. The package should handle this for us. -A
On Wed, Apr 7, 2021 at 4:46 AM Kern, Lori <Lori.Shepherd at roswellpark.org> wrote:
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 at r-project.org> on behalf of Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
Sent: Wednesday, April 7, 2021 4:10 AM
To: bioc-devel at r-project.org <bioc-devel at 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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