Last updated on 2025-02-07 08:52:05 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| BaseSet | 2 | 3 | 8 |
| experDesign | 13 | ||
| rtweet | 5 | 8 |
Current CRAN status: ERROR: 2, NOTE: 3, OK: 8
Version: 0.9.0
Check: examples
Result: ERROR
Running examples in ‘BaseSet-Ex.R’ failed
The error most likely occurred in:
> ### Name: tidy
> ### Title: Convert GSEABase classes to a TidySet
> ### Aliases: tidy tidy.GeneSetCollection tidy.GeneSet
>
> ### ** Examples
>
> # Needs GSEABase pacakge from Bioconductor
> if (requireNamespace("GSEABase", quietly = TRUE)) {
+ library("GSEABase")
+ gs <- GeneSet()
+ gs
+ tidy(gs)
+ fl <- system.file("extdata", "Broad.xml", package="GSEABase")
+ gs2 <- getBroadSets(fl) # actually, a list of two gene sets
+ TS <- tidy(gs2)
+ dim(TS)
+ sets(TS)
+ }
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:BaseSet’:
tidy, union
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
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, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:BaseSet’:
active
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:BaseSet’:
select
Loading required package: XML
Loading required package: graph
Attaching package: ‘graph’
The following object is masked from ‘package:XML’:
addNode
The following objects are masked from ‘package:BaseSet’:
complement, intersection
Attaching package: ‘GSEABase’
The following object is masked from ‘package:BaseSet’:
incidence
Error in UseMethod("tidy") :
no applicable method for 'tidy' applied to an object of class "GeneSet"
Calls: tidy
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.9.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘reactome.db’
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 5, OK: 8
Version: 2.0.0
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘auth.R’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64