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

[Aaron Lun]

> There is no guarantee we would be under the right user to have permissions to move the cache automatically and would not want to leave it in a broken state.

Well, can't you try? If people follow your 4.1 instructions and they
don't have permissions, the cache will be broken anyway.

But let's say you can't move it, and your worst-case scenario comes to
pass. EVEN THEN: I would expect a deprecation warning, no error, and
BiocFileCache continuing to pull from the old cache for 6 months.

Every previous non-transparent change to BioC's core infrastructure
has come with a deprecation warning. I don't see why this is any
different. An error is particularly galling given that the package was
working fine before, it's not like you're doing some kind of critical
bugfix.

> This should not affect any cache that is explicitly stated with a different name in the constructor or using environment variables;  only in the case of BiocFileCache() .  Most package specific caches created their own cache in the constructor so it should not cause the ERROR in that case.

If Vince's last email is any indication, and calling ExperimentHub()
or AnnotationHub() causes an error... this will be a disaster. I'm
going to get a lot of emails, unnecessary emails, from users wondering
why scRNAseq and celldex don't work anymore. It'll be like our
AWS-China problems multiplied by 10.

Why not just make a new cache and populate it? Well, I don't really
care what you do, as long as I don't get an error.

-A

> ________________________________
> From: Aaron Lun <infinite.monkeys.with.keyboards using gmail.com>
> Sent: Wednesday, April 7, 2021 11:41 AM
> To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [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 using 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 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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