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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EGSEA_1.39.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/EGSEA.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EGSEA/DESCRIPTION’ ... OK
* this is package ‘EGSEA’ version ‘1.39.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘EGSEA’ 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
buildGeneSetDBIdx: no visible binding for global variable ‘GOTERM’
buildMSigDBIdx: no visible binding for global variable ‘msigdb’
generateSummaryPlots: no visible binding for global variable ‘x.data’
generateSummaryPlots: no visible binding for global variable ‘y.data’
generateSummaryPlots: no visible binding for global variable ‘gsSize’
generateSummaryPlots: no visible binding for global variable ‘id’
generateSummaryPlots: no visible binding for global variable ‘sig’
loadArrayData: no visible binding for global variable ‘arraydata’
loadKeggData: no visible binding for global variable ‘kegg.pathways’
Undefined global functions or variables:
  GOTERM arraydata gsSize id kegg.pathways msigdb sig x.data y.data
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'egsea-main.Rd':
  ‘[limma]{ebayes}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘EGSEA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: egsea
> ### Title: Core functions to perform ensemble of gene set enrichment
> ###   analysis (EGSEA)
> ### Aliases: egsea egsea,egsea-main egsea.cnt egsea.cnt,egsea-main
> ###   egsea.ora egsea.ora,egsea-main egsea.ma
> 
> ### ** Examples
> 
> # Example of egsea
> library(EGSEAdata)
> data(il13.data)
> v = il13.data$voom
> contrasts = il13.data$contra
> gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", 
+ msigdb.gsets="none", 
+          kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
[1] "Building KEGG pathways annotation object ... "
> # set report = TRUE to generate the EGSEA interactive report
> gsa = egsea(voom.results=v, contrasts=contrasts,  gs.annots=gs.annots, 
+          symbolsMap=v$genes, baseGSEAs=egsea.base()[-c(2,5,6,9,12)], 
+ 			display.top = 5, sort.by="avg.rank", 
+ 			report.dir="./il13-egsea-report", 
+          num.threads = 2, report = FALSE)
EGSEA analysis has started
##------ Wed Dec 17 19:40:34 2025 ------##
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and kegg collection
...safe*....zscore*.
 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: solve.default(crossprod(Z), crossprod(Z, X))
 2: solve(crossprod(Z), crossprod(Z, X))
 3: .lineartest(Y, Z, X, offset, dir, perms, fromGLM = TRUE)
 4: .glmtest(response, Z = null, X = alternative, offset = offset,     family = "binomial", dir = directional, perms = permutations)
 5: gt(factor(group), data.log.sel, subsets = args$gs.annot@idx,     permutations = 10000)
 6: FUN(X[[i]], ...)
 7: lapply(X = X, FUN = FUN, ...)
 8: mclapply(args.all, runglobaltest.contrast, mc.cores = num.workers)
 9: runglobaltest(voom.results = voom.results, contrast = contrast,     gs.annot = gs.annot, num.workers = num.threads, verbose = verbose)
10: runbaseGSEA(method = args$baseGSEA, args$voom.results, args$contrast,     args$gs.annot, num.threads = args$num.threads, verbose = args$verbose)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch({    temp.result <- runbaseGSEA(method = args$baseGSEA, args$voom.results,         args$contrast, args$gs.annot, num.threads = args$num.threads,         verbose = args$verbose)    if (args$verbose)         message(paste0("Running ", toupper(args$baseGSEA), " on all ",             "contrasts ... COMPLETED"))    else {        message(args$baseGSEA, "*", appendLF = FALSE)    }    return(temp.result)}, error = function(e) {    message(toupper(args$baseGSEA), " encountered an error -> ",         e)})
15: FUN(X[[i]], ...)
16: lapply(X = S, FUN = FUN, ...)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
21: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
22: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
23: FUN(X[[i]], ...)
24: lapply(seq_len(cores), inner.do)
25: mclapply(args.all, runbaseGSEAParallelWorker, mc.cores = num.workers)
26: runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops,     baseGSEAs = baseGSEAs, combineMethod = combineMethod, combineWeights = NULL,     gs.annot = gs.annot, logFC = logFC, logFC.cutoff = logFC.cutoff,     fdr.cutoff = fdr.cutoff, vote.bin.width = vote.bin.width,     keep.base = keep.base, num.workers = num.threads, verbose = verbose)
27: egsea.main(voom.results, contrasts, gs.annots, baseGSEAs, combineMethod,     combineWeights, sort.by, report.dir, kegg.dir, logFC, symbolsMap,     minSize, display.top, logFC.cutoff, fdr.cutoff, sum.plot.cutoff,     sum.plot.axis, vote.bin.width, keep.base, verbose, num.threads,     report, keep.limma, keep.set.scores, interactive)
28: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
29: suppressWarnings(return(egsea.main(voom.results, contrasts, gs.annots,     baseGSEAs, combineMethod, combineWeights, sort.by, report.dir,     kegg.dir, logFC, symbolsMap, minSize, display.top, logFC.cutoff,     fdr.cutoff, sum.plot.cutoff, sum.plot.axis, vote.bin.width,     keep.base, verbose, num.threads, report, keep.limma, keep.set.scores,     interactive)))
30: egsea(voom.results = v, contrasts = contrasts, gs.annots = gs.annots,     symbolsMap = v$genes, baseGSEAs = egsea.base()[-c(2, 5, 6,         9, 12)], display.top = 5, sort.by = "avg.rank", report.dir = "./il13-egsea-report",     num.threads = 2, report = FALSE)
An irrecoverable exception occurred. R is aborting now ...
camera*..gage*...gsva*..ora*
Error in runegsea(voom.results = voom.results, contrast = contrast, limma.tops = limma.tops,  : 
  ERROR: One of the base methods failed on this dataset (safe).
Remove it and try again.
See error messages for more information.
Calls: egsea
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
EGSEAResults-methods 28.633  1.863  39.613
egsea-index          16.391  1.940  19.553
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/EGSEA.Rcheck/00check.log’
for details.