[Bioc-devel] BiocFileCache for developers
On 12/01/2017 11:23 AM, Sean Davis wrote:
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.
Actually, CRAN policies. The CRAN policy is definitely appropriate for vignette and example code, and certainly functions by default should not write to locations where they will potentially overwrite existing resources. The policy makes it impossible to write files that persist across sessions, which is the objective for BiocFileCache. For the original question, I think there's often a case for user_cache_dir(appname="mikes-package-name") Martin
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/ https://twitter.com/seandavis12 [[alternative HTML version deleted]]
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