[Bioc-devel] BiocFileCache for developers

[Sean Davis]

On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:

> So having a user argument might be best.  Or defining a unique cache
> location for your package would be another option.
>

The R package development policies actually has a statement that may be
helpful in thinking about this. Your mileage may vary in the
interpretation....


>    - - Packages should not write in the users’ home filespace, nor
>    anywhere else on the file system apart from the R session’s temporary
>    directory (or during installation in the location pointed to by TMPDIR:
>    and such usage should be cleaned up). Installing into the system’s R
>    installation (e.g., scripts to its bin directory) is not allowed.
>
>    Limited exceptions may be allowed in interactive sessions if the
>    package obtains confirmation from the user.
>
>
https://cran.r-project.org/web/packages/policies.html

Sean



>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Sean
> Davis <seandavi at gmail.com>
> *Sent:* Friday, December 1, 2017 11:06:39 AM
> *To:* Michael Love
> *Cc:* bioc-devel at r-project.org
> *Subject:* Re: [Bioc-devel] BiocFileCache for developers
>
> On Fri, Dec 1, 2017 at 10:28 AM, Michael Love <michaelisaiahlove at gmail.com
> >
> wrote:
>
> > hi,
> >
> > I'm writing a function which currently uses BiocFileCache to store a
> > small data.frame and one or more TxDb objects, so that these objects
> > are persistent and available across sessions (or possible available to
> > multiple users).
> >
> > In the simplest case, I would call
> >
> > bfc <- BiocFileCache()
> >
> > inside my function, which will check the default location:
> >
> > user_cache_dir(appname = "BiocFileCache")
> >
> > In general, should developers also support the user specifying a
> > specific location for the BiocFileCache? So functions using
> > BiocFileCache should have an argument that overrides the above
> > location?
> >
>
> On some systems, the user home directory is not large (such as on HPC
> systems) or has strong quotas. The default user_cache_dir may not be the
> best choice there.
>
> Sean
>
>
> >
> > thanks,
> > Mike
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> --
> Sean Davis, MD, PhD
> Center for Cancer Research
> National Cancer Institute
> National Institutes of Health
> Bethesda, MD 20892
> https://seandavi.github.io/
> https://twitter.com/seandavis12
>
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-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

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