[Bioc-devel] AnnotationHub: cleanup

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Tue Sep 15 04:44:52 CEST 2015

I currently have the `pleasure` of dealing with students who have problems
with installing AnnotationHub and/or downloading resources.  Here are some
comments including some possible bug reports.

1) I think it is extremely dangerous that `cache(ahub)` starts by asking to
download all resources!  May I suggest this only happens with a specific
setting like `cache(ahub, download=TRUE)` or something similar.

2) `cache(ahub)` deletes all cached information, except the sqlite
database.  Could we get a way to remove everything?

3) While I can understand the difference between cache and hubCache, I
would suggest that hubCache(ahub) = NULL removes all cached material
included the sqlite database.

4) It seems that AnnotationHub in the release version of Bioconductor
defaults to using https://.  Wasn't full support for https:// introduced in
R 3.2.2; if so, it seems to be a critical bug that it is using https://

5) Perhaps it should be considered that the default hubCache path is
versioned, perhaps with Bioc version, perhaps with something else.  This
might cause problems for people running multiple versions of R.

6) I strongly suggest that the output printed when retrieving an
AnnotationHub resource includes the download url.

7) If you run AnnotationHub without having GenomicRanges / rtracklayer
installed, it downloads the resource and then pangs out with an error.  To
me it seems more natural to pang out with an error immediately, especially
since when it works, it appears from message printing that loading the
library happens prior to download.


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