* using log directory 'd:/Rcompile/CRANpkg/local/4.5/BaseSet.Rcheck'
* using R Under development (unstable) (2025-02-07 r87707 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'BaseSet/DESCRIPTION' ... OK
* this is package 'BaseSet' version '0.9.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BaseSet' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s] OK
* checking Rd files ... [2s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [10s] 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)
+ }
Warning: multiple methods tables found for 'union'
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: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [11s] OK
  Running 'spelling.R' [0s]
  Running 'testthat.R' [10s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [120s] OK
* checking PDF version of manual ... [34s] OK
* checking HTML version of manual ... [14s] OK
* DONE
Status: 1 ERROR