/usr/lib/R/site-library/AnnotationHub/NAMESPACE is in r-bioc-annotationhub 2.6.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | import(methods)
import(BiocGenerics)
import(RSQLite)
import(S4Vectors)
importFrom(stats, setNames)
importFrom(grDevices, rgb)
importFrom(utils, packageVersion, read.csv, read.delim, unzip,
read.table, capture.output, .DollarNames
)
importFrom(httr,
GET, content, parse_url, progress, write_disk,
stop_for_status, status_code, use_proxy
)
importFrom(interactiveDisplayBase, display)
importFrom(BiocInstaller, biocVersion, isDevel)
importFrom(yaml, yaml.load)
importMethodsFrom(AnnotationDbi, dbconn, dbfile)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 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, display, 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
)
exportMethods(
cache, "cache<-", query,
hubUrl, hubCache, hubDate,
snapshotDate, "snapshotDate<-",
getHub, listResources, loadResources,
package
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
.Hub, AnnotationHub, display,
removeCache,
getAnnotationHubOption, setAnnotationHubOption,
possibleDates, mcols,
.httr_proxy, .hub_option_key, .db_close,
recordStatus
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 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
)
|