Setting ExperimentHub Cache Location
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Mike Smith ★ 5.2k
@mike-smith
Last seen 4 hours ago
EMBL Heidelberg / de.NBI

What's the recommended way to set the cache location for ExperimentHub for every R session?

I don't have much space in $HOME, so at the moment I include the following in my .Rprofile

ExperimentHub::setExperimentHubOption('cache', '/place/with/space/ExHub')

For the most part this works nicely except that it also loads several other packages, including BiocInstaller and S4Vectors.  If I then run biocLite() at some point during the session and it tries to update any of these imported packages it will fail with something like:

Package ‘S4Vectors’ version 0.17.32 cannot be unloaded:
Error in unloadNamespace(package)

I then resort to starting a new R --vanilla session to run the installation, and then switch back, but this is also a pain as .Rprofile specifies the location of my library path too.  S4Vectors in particular seems to be changing a lot in devel and I end up having to do this pretty regularly, so I was just wondering if there is some mechanism for setting the cache location without loading those packages until I want to.

experimenthub • 716 views
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@martin-morgan-1513
Last seen 3 months ago
United States

Remove the .Rprofile setting and use the a global option or environment variable EXPERIMENT_HUB_CACHE; see ?getExperimentHubOption

     Default values may also be determined by system and global R
     environment variables visible _before_ the package is loaded. Use
     options or variables preceded by "EXPERIMENT_HUB_", e.g.,
     'options(EXPERIMENT_HUB_MAX_DOWNLOADS=10)' prior to package load
     sets the default number of downloads to 10.

 

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That works great, thanks.

FYI there are references to getExperimentHubCache and setExperimentHubCache in the Description section of ?getExperimentHub that I'm not sure are valid anymore.

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