getExperimentHubOption: Get and set options for default ExperimentHub behavior.

In ExperimentHub: Client to access ExperimentHub resources

Description

These functions get or set options for creation of new ‘ExperimentHub’ instances.

Usage

getExperimentHubOption(arg)
setExperimentHubOption(arg, value)

Arguments

arg	The character(1) hub options to set. see ‘Details’ for current options.
value	The value to be assigned to the hub option.

Details

Supported options include:

“URL”:

character(1). The base URL of the ExperimentHub. Default: https://experimenthub.bioconductor.org

“CACHE”:

character(1). The location of the hub cache. Default: “.ExperimentHub” in the user home directory.

“MAX_DOWNLOADS”:

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

“PROXY”:

request object returned by httr::use_proxy(). The request object describes a proxy connection allowing Internet access, usually through a restrictive firewall. Setting this option sends all ExperimentHub requests through the proxy. Default: NULL.

In setExperimentHubOption("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:[e-mail]:8080; username:password and port (e.g. :8080) are optional.

“LOCAL”:

logical(1). Should the ExperimentHub create a hub consisting only of previously downloaded resources. Default: FALSE.

“ASK”:

logical(1). TRUE/FALSE should the ExperimentHub ask if the hub location should be created. If FALSE, the default location will be used and created if it doesn't exist without asking. If TRUE will ask the user and if in a non interactive session utilize a temporary directoy for the caching. Default: TRUE.

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.

Value

The requested or successfully set option.

Author(s)

Bioconductor Core Team

Examples

getExperimentHubOption("URL")
## Not run: 
setExperimentHubOption("CACHE", "~/.myHub")

## End(Not run)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: AnnotationHub
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
[1] "https://experimenthub.bioconductor.org"

ExperimentHub documentation built on April 17, 2021, 6:01 p.m.