• using R Under development (unstable) (2025-01-24 r87627)
• using platform: aarch64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.4
• 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 ... INFO Packages suggested but not available for checking:   'org.Hs.eg.db', 'reactome.db'
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• checking whether package ‘BaseSet’ can be installed ... [3s/4s] OK See the install log for details.
• checking installed package size ... OK
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• checking for unstated dependencies in examples ... OK
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• checking files in ‘vignettes’ ... OK
• checking examples ... [3s/4s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [5s/5s] OK   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [5s/5s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [14s/17s] OK
• checking PDF version of manual ... [8s/9s] OK
• DONE Status: 1 ERROR
• using check arguments '--no-clean-on-error '