[Bioc-devel] AnnotationHub Update.

[Jim Java]

We've updated the release version of the AnnotationHub package to address
some of the issues raised in this thread:

https://stat.ethz.ch/pipermail/bioc-devel/2015-September/007966.html.

In v. 2.3.2:

  • The 'cache(x)' semantics remain the same (i.e. download all the
resources in hub 'x'), but we've clarified in the man page that the only
relevant assignment is 'cache(x) <- NULL', which removes all local
resources corresponding to the records in 'x' from the cache.

  • 'cache(x)' now prints out the URLs of AnnotationHub resources before
downloading, or notes that they're being retrieved from the local cache.

  • The new 'removeCache()' function removes the local AnnotationHub
database and all its related resources. After calling this function, the
user will have to download any AnnotationHub resources again. (This is
sometimes necessary if the database files become corrupted for whatever
reason.)

  • 'hubOption("PROXY")' returns a request object from httr::use_proxy().
The request object describes a proxy connection allowing Internet access,
usually through a restrictive firewall. Setting this option with
'setHubOption("PROXY", value)' sends all AnnotationHub requests through the
proxy. Default: NULL.

  • In 'setHubOption("PROXY", value)', value can be one of NULL, a request
object returned by httr::use_proxy(), or a well-formed URL as character(1).
The URL can be completely specified by
http://username:password@proxy.dom.com:8080; username:password and port
(e.g. :8080) are optional.

  • AnnotationHub resources whose further manipulation requires the
GenomicRanges or rtracklayer package now have the package loaded beforehand.

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