getExperimentHubOption: Get and set options for default ExperimentHub behavior.

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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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 Experiment Hub. 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 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:[email protected]:8080; username:password and port (e.g. :8080) are optional.

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

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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 May 6, 2019, 3:05 a.m.