[Bioc-devel] BiocFileCache for developers

On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori <

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

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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/
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National Institutes of Health
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[Bioc-devel] BiocFileCache for developers

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