[Bioc-devel] BiocFileCache for developers

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Fri Dec 22 19:17:35 CET 2017

BiocFileCache has been updated to follow this type of behavior

- if location exists use without prompting (default user_cache_dir())

- if doesnt exit

    - prompt user to create

    - if respond N  or not an interactive session uses temporary directory

This is reflected in devel version 1.3.8

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Michael Love <michaelisaiahlove at gmail.com>
Sent: Saturday, December 9, 2017 5:18:08 PM
To: Henrik Bengtsson
Cc: Shepherd, Lori; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] BiocFileCache for developers

thanks Henrik,

I like the explicitness of the `R.cache` approach and I copied it for
my current implementation.

For the BiocFileCache location that should be used for this package
I'm developing, `tximeta`, I'm now using the following logic:

* If run non-interactively, `tximeta` uses a temporary directory.
* If run interactively, and a location has not been previously saved,
  the user is prompted if she wants to use (1) the default directory or
  a (2) temporary directory.
    - If (1), then use the default directory, and save this choice.
    - If (2), then use a temporary directory for the rest of this R
      session, and ask again next R session.
* The prompt above also mentions that a specific function can be used
  to manually set the directory at any time point, and this choice is
* The default directory is given by `rappdirs::user_cache_dir("BiocFileCache")`.
* The choice itself of the BiocFileCache directory that `tximeta`
  should use is saved in a JSON file here

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