convertHub: Convert old Hub to new Hub structure

Description Usage Arguments Value Author(s) See Also Examples

View source: R/Hub-utils.R

Description

The Hub class was updated to utilize BiocFileCache to allow for file level caching control. This update changed the way files were stored and named. As a convenience for AnnotationHub and ExperimentHub we have provided this helper function to try to re-download files and add them into the BiocFileCache tracking database.

Usage

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convertHub(oldcachepath=NULL,
           newcachepath=NULL,
           hubType=c("AnnotationHub", "ExperimentHub"),
           proxy=getAnnotationHubOption("PROXY"),
           max.downloads=getAnnotationHubOption("MAX_DOWNLOADS"),
           force=FALSE, verbose=TRUE)

Arguments

oldcachepath

character(1) complete file path location of the old hub to be converted. If left as NULL, will use the default path of the old code, which for unix systems was in a user's home directory "~\" and for windows users was in a user's AppData directory "~\AppData".

newcachepath

character(1) complete file path to the new location for the cache. If left as NULL, will use the new default path which utilizes the rappdir::user_cache_dir to deterime the appropriate caching location.

hubType

Either AnnotationHub or ExperimentHub. By default assumes AnnotationHub.

proxy

proxy connection allowing Internet access, usually through a restrictive firewall. Default: NULL.

max.downloads

numeric(1). The integer number of downloads allowed before triggering a warning. This is to help avoid accidental download of a large number of AnnotationHub members

force

logical(1). Force re-download of a resource rather than using a cached version.

verbose

logical(1). Print out status messages.

Value

character(1). File path of new cache location. If verbose also prints status messages for downloading files and any files that were not redownloaded.

Author(s)

Lori Shepherd

See Also

AnnotationHub, getAnnotationHubOption, getInfoOnIds

Examples

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# To transition over from old default to new default location
## Not run: convertHub()

Bioconductor/AnnotationHub documentation built on Dec. 2, 2019, 10:48 p.m.