AnnotationHub and ExperimentHub make "~" directory in my home
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@mikelove
Last seen 3 hours ago
United States

The problem is that a "~" directory is created in my home, when using the *Hub packages.

First of all, this is only an issue for me using R-devel, which I build from source. Using the Mac binary for R 3.3.1 this does not present the problem.

I can trace it to path.expand()'s behavior, which I know is used to create the location of the *Hub cache directories:

> path.expand("~")
[1] "/Users/love/~"

BTW, it seems like adding a slash fixes this:

> path.expand("~/")
[1] "/Users/love/"

One solution that I've used is to put the following lines in my .Rprofile:

options(EXPERIMENT_HUB_CACHE="/Users/love/.ExperimentHub")
options(ANNOTATION_HUB_CACHE="/Users/love/.AnnotationHub")

However, when I build software packages that use the *Hub packages, I believe the init files aren't used and I again end up with a "~" dir in my home.

 

My session info:

R Under development (unstable) (2016-08-22 r71129)
Platform: x86_64-apple-darwin15.5.0 (64-bit)
Running under: OS X El Capitan 10.11.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] ExperimentHub_0.101.12 AnnotationHub_2.5.11   BiocGenerics_0.19.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.6                   IRanges_2.7.14
 [3] digest_0.6.10                 mime_0.5
 [5] R6_2.1.3                      xtable_1.8-2
 [7] DBI_0.5                       stats4_3.4.0
 [9] RSQLite_1.0.0                 BiocInstaller_1.23.6
[11] httr_1.2.1                    S4Vectors_0.11.13
[13] Biobase_2.33.0                shiny_0.13.2
[15] httpuv_1.3.3                  AnnotationDbi_1.35.4
[17] htmltools_0.3.5               interactiveDisplayBase_1.11.3
annotationhub experimenthub • 810 views
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Interesting - looks like it may be due to differences across platforms: with R-devel on linux it works fine for me without the trailing slash: path.expand("~") results in [1] "/home/keith"

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p.s. I still feel that this is not the right system for reporting and tracking bugs.

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I get the same, i.e.

> path.expand("~")
[1] "/Users/jo/~"

and I'm also building my R on Mac from source; what I find interesting is that I get this only in the terminal, when I run R in Emacs (iESS mode) I get "/Users/jo". It wasn't bothering me much since I run all my analyses through emacs, but it would be nice if it could be fixed as you suggest.

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Looks like it depends on the readline support of the terminal which can be checked with capabilities("cledit") (see ?path.expand)

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When I run this I get TRUE:

> capabilities("cledit")
cledit
  TRUE

Note that I do have expansion capabilities, it just tacks on an additional "~".

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@valerie-obenchain-4275
Last seen 23 months ago
United States

I've changed the cache path for ExperimentHub and AnnotationHub to path.expand("~/"). The change was made in devel only so those using release don't have a problem with their existing cache location.

Valerie

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Thanks Valerie!

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