[Bioc-devel] BiocFileCache for developers

[Shepherd, Lori]

Unfortunately I think there are a number of packages that don't necessarily adhere to this.


Bioconductor packages we try to always make sure any example or vignette code follows this policy.


I think the exception case may be made if it deals with main functionality of package code and if it is noted prominently in the package documentation.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Sean Davis <seandavi at gmail.com>
Sent: Friday, December 1, 2017 11:23:39 AM
To: Shepherd, Lori
Cc: Michael Love; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] BiocFileCache for developers


On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto: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<mailto:bioc-devel-bounces at r-project.org>> on behalf of Sean Davis <seandavi at gmail.com<mailto:seandavi at gmail.com>>
Sent: Friday, December 1, 2017 11:06:39 AM
To: Michael Love
Cc: bioc-devel at r-project.org<mailto: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<mailto: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<mailto: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


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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