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import(methods)
import(BiocGenerics)
import(RSQLite)
import(S4Vectors)
import(BiocVersion)
import(BiocManager)
import(BiocFileCache)
importFrom(tools, R_user_dir)
importFrom(rappdirs, user_cache_dir)
importFrom(stats, setNames)
importFrom(grDevices, rgb)
importFrom(utils, packageVersion, read.csv, read.delim, unzip,
capture.output, read.table, .DollarNames
)
importFrom(httr,
GET, content, parse_url, progress, write_disk,
stop_for_status, status_code, use_proxy, HEAD, headers
)
importFrom(yaml, yaml.load)
importMethodsFrom(AnnotationDbi, dbconn, dbfile)
importFrom(AnnotationDbi, dbFileConnect)
importFrom(dplyr,"%>%")
importFrom(dplyr,collect)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClasses(
Hub,
AnnotationHub, AnnotationHubResource
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in AnnotationHub
###
exportMethods(
names, length, "$", "[", subset, "[[", as.list, c,
show, fileName, mcols, dbconn, dbfile
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics defined in AnnotationHub + export corresponding
### methods
###
export(
cache, "cache<-", query,
hubUrl, hubCache, hubDate,
snapshotDate, "snapshotDate<-",
getHub, listResources, loadResources,
package, convertHub, removeResources,
isLocalHub, "isLocalHub<-", getInfoOnIds
)
exportMethods(
cache, "cache<-", query, removeResources,
hubUrl, hubCache, hubDate,
snapshotDate, "snapshotDate<-",
getHub, isLocalHub, "isLocalHub<-", getInfoOnIds
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
.Hub, AnnotationHub,
removeCache,
getAnnotationHubOption, setAnnotationHubOption,
possibleDates, mcols,
.httr_proxy, .hub_option_key, .db_close,
recordStatus, DispatchClassList, refreshHub
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(.DollarNames, Hub)
S3method(as.list, Hub)
### Also export them thru the export() directive so that (a) they can be
### called directly, (b) tab-completion on the name of the generic shows them,
### and (c) methods() doesn't asterisk them.
export(
.DollarNames.Hub,
as.list.Hub
)
|
