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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bumphunter_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/bumphunter.Rcheck’
* using R version 4.5.2 Patched (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 ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.52.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'S4Vectors', 'IRanges', 'Seqinfo', 'GenomicRanges', 'foreach',
  'iterators', 'parallel', 'locfit'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘bumphunter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
  bootstraps
* checking Rd files ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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 ‘bumphunter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bumphunter
> ### Title: Bumphunter
> ### Aliases: bumphunter bumphunter-methods bumphunter,matrix-method
> ###   bumphunterEngine print.bumps
> 
> ### ** Examples
> 
> dat <- dummyData()
> # Enable parallelization
> require(doParallel)
Loading required package: doParallel
> registerDoParallel(cores = 2)
> # Find bumps
> bumps <- bumphunter(dat$mat, design=dat$design, chr=dat$chr, pos=dat$pos,
+                     cluster=dat$cluster, coef=2, cutoff= 0.28, nullMethod="bootstrap",
+                     smooth=TRUE, B=250, verbose=TRUE,
+                     smoothFunction=loessByCluster)
[bumphunterEngine] Parallelizing using 2 workers/cores (backend: doParallelMC, version: 1.0.17).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
Loading required package: rngtools
[bumphunterEngine] Performing 250 bootstraps.

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

 *** caught segfault ***
address 0x110, cause 'invalid permissions'

Traceback:
 1: backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X), t(matstar)))
 2: FUN(newX[, i], ...)
 3: apply(bootstraps, 2, function(bootIndex) {    matstar <- null + resids[, bootIndex]    nullbetas <- backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X),         t(matstar)))[coef, ]    if (useWeights) {        sigma <- rowSums(t(tcrossprod(diag(nrow(design)) - tcrossprod(qr.Q(qr.X)),             matstar))^2)        sigma <- sqrt(sigma/(nrow(design) - qr.X$rank))        outList <- list(coef = nullbetas, sigma = sigma)    }    else {        outList <- nullbetas    }    return(outList)})
 4: eval(c.expr, envir = args, enclos = envir)
 5: eval(c.expr, envir = args, enclos = envir)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
10: FUN(X[[i]], ...)
11: lapply(X = S, FUN = FUN, ...)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
18: FUN(X[[i]], ...)
19: lapply(seq_len(cores), inner.do)
20: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,     mc.silent = silent, mc.cores = cores)
21: e$fun(obj, substitute(ex), parent.frame(), e$data)
22: (function (obj, ex) {    e <- getDoPar()    e$fun(obj, substitute(ex), parent.frame(), e$data)})(list(args = iter(bootIndexes, by = "column", chunksize = chunksize)(.doRNG.stream = list(    c(10407L, -902622907L, -1811262142L, 1742512091L, -5955232L,     994941409L, 131442222L), c(10407L, 29783153L, 233190138L,     -13027976L, 2106844339L, -1477538752L, 1959762265L))), argnames = c("bootstraps", ".doRNG.stream"), evalenv = <environment>, specified = character(0),     combineInfo = list(fun = new("standardGeneric", .Data = function (...,         deparse.level = 1)     standardGeneric("cbind"), generic = "cbind", package = "BiocGenerics", 
Traceback:
 1: backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X), t(matstar)))
 2: FUN(newX[, i], ...)        group = list(), valueClass = character(0), signature = "...", 
        default = new("derivedDefaultMethod", .Data = function (...,             deparse.level = 1)         .Internal(cbind(deparse.level, ...)), target = new("signature",             .Data = "ANY", names = "...", package = "methods"),             defined = new("signature", .Data = "ANY", names = "...",                 package = "methods"), generic = "cbind"), skeleton = (new("derivedDefaultMethod",             .Data = function (..., deparse.level = 1)             .Internal(cbind(deparse.level, ...)), target = new("signature",                 .Data = "ANY", names = "...", package = "methods"),             defined = new("signature", .Data = "ANY", names = "...",                 package = "methods"), generic = "cbind"))(...,             deparse.level = deparse.level)), in.order = TRUE,         has.init = FALSE, init = NULL, final = NULL, multi.combine = FALSE,         max.combine = 2), errorHandling = "stop", packages = c("bumphunter",     "doRNG"), export = NULL, noexport = NULL, options = list(),     verbose = FALSE), {    {        rngtools::RNGseed(.doRNG.stream)    }    {        apply(bootstraps, 2, function(bootIndex) {            matstar <- null + resids[, bootIndex]            nullbetas <- backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X),                 t(matstar)))[coef, ]            if (useWeights) {                sigma <- rowSums(t(tcrossprod(diag(nrow(design)) -                   tcrossprod(qr.Q(qr.X)), matstar))^2)                sigma <- sqrt(sigma/(nrow(design) - qr.X$rank))                outList <- list(coef = nullbetas, sigma = sigma)            }            else {                outList <- nullbetas            }            return(outList)        })    }})
23: do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
24: foreach(bootstraps = iter(bootIndexes, by = "column", chunksize = chunksize),     .combine = "cbind", .packages = "bumphunter") %dorng% {    apply(bootstraps, 2, function(bootIndex) {        matstar <- null + resids[, bootIndex]        nullbetas <- backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X),             t(matstar)))[coef, ]        if (useWeights) {            sigma <- rowSums(t(tcrossprod(diag(nrow(design)) -                 tcrossprod(qr.Q(qr.X)), matstar))^2)            sigma <- sqrt(sigma/(nrow(design) - qr.X$rank))            outList <- list(coef = nullbetas, sigma = sigma)        }        else {            outList <- nullbetas        }        return(outList)    })}
25: bumphunterEngine(object, design = design, chr = chr, pos, cluster = cluster,     coef = coef, cutoff = cutoff, pickCutoff = pickCutoff, pickCutoffQ = pickCutoffQ,     maxGap = maxGap, nullMethod = nullMethod, smooth = smooth,     smoothFunction = smoothFunction, useWeights = useWeights,     B = B, permutations = NULL, verbose = verbose, ...)
26: .local(object, ...)
27: bumphunter(dat$mat, design = dat$design, chr = dat$chr, pos = dat$pos,     cluster = dat$cluster, coef = 2, cutoff = 0.28, nullMethod = "bootstrap",     smooth = TRUE, B = 250, verbose = TRUE, smoothFunction = loessByCluster)
28: bumphunter(dat$mat, design = dat$design, chr = dat$chr, pos = dat$pos,     cluster = dat$cluster, coef = 2, cutoff = 0.28, nullMethod = "bootstrap",     smooth = TRUE, B = 250, verbose = TRUE, smoothFunction = loessByCluster)
An irrecoverable exception occurred. R is aborting now ...
 3: apply(bootstraps, 2, function(bootIndex) {    matstar <- null + resids[, bootIndex]    nullbetas <- backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X),         t(matstar)))[coef, ]    if (useWeights) {        sigma <- rowSums(t(tcrossprod(diag(nrow(design)) - tcrossprod(qr.Q(qr.X)),             matstar))^2)        sigma <- sqrt(sigma/(nrow(design) - qr.X$rank))        outList <- list(coef = nullbetas, sigma = sigma)    }    else {        outList <- nullbetas    }    return(outList)})
 4: eval(c.expr, envir = args, enclos = envir)
 5: eval(c.expr, envir = args, enclos = envir)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch(eval(c.expr, envir = args, enclos = envir), error = function(e) e)
10: FUN(X[[i]], ...)
11: lapply(X = S, FUN = FUN, ...)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: 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))})
16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
18: FUN(X[[i]], ...)
19: lapply(seq_len(cores), inner.do)
20: mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,     mc.silent = silent, mc.cores = cores)
21: e$fun(obj, substitute(ex), parent.frame(), e$data)
22: (function (obj, ex) {    e <- getDoPar()    e$fun(obj, substitute(ex), parent.frame(), e$data)})(list(args = iter(bootIndexes, by = "column", chunksize = chunksize)(.doRNG.stream = list(    c(10407L, -902622907L, -1811262142L, 1742512091L, -5955232L,     994941409L, 131442222L), c(10407L, 29783153L, 233190138L,     -13027976L, 2106844339L, -1477538752L, 1959762265L))), argnames = c("bootstraps", ".doRNG.stream"), evalenv = <environment>, specified = character(0),     combineInfo = list(fun = new("standardGeneric", .Data = function (...,         deparse.level = 1)     standardGeneric("cbind"), generic = "cbind", package = "BiocGenerics",         group = list(), valueClass = character(0), signature = "...",         default = new("derivedDefaultMethod", .Data = function (...,             deparse.level = 1)         .Internal(cbind(deparse.level, ...)), target = new("signature",             .Data = "ANY", names = "...", package = "methods"),             defined = new("signature", .Data = "ANY", names = "...",                 package = "methods"), generic = "cbind"), skeleton = (new("derivedDefaultMethod",             .Data = function (..., deparse.level = 1)             .Internal(cbind(deparse.level, ...)), target = new("signature",                 .Data = "ANY", names = "...", package = "methods"),             defined = new("signature", .Data = "ANY", names = "...",                 package = "methods"), generic = "cbind"))(...,             deparse.level = deparse.level)), in.order = TRUE,         has.init = FALSE, init = NULL, final = NULL, multi.combine = FALSE,         max.combine = 2), errorHandling = "stop", packages = c("bumphunter",     "doRNG"), export = NULL, noexport = NULL, options = list(),     verbose = FALSE), {    {        rngtools::RNGseed(.doRNG.stream)    }    {        apply(bootstraps, 2, function(bootIndex) {            matstar <- null + resids[, bootIndex]            nullbetas <- backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X),                 t(matstar)))[coef, ]            if (useWeights) {                sigma <- rowSums(t(tcrossprod(diag(nrow(design)) -                   tcrossprod(qr.Q(qr.X)), matstar))^2)                sigma <- sqrt(sigma/(nrow(design) - qr.X$rank))                outList <- list(coef = nullbetas, sigma = sigma)            }            else {                outList <- nullbetas            }            return(outList)        })    }})
23: do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
24: foreach(bootstraps = iter(bootIndexes, by = "column", chunksize = chunksize),     .combine = "cbind", .packages = "bumphunter") %dorng% {    apply(bootstraps, 2, function(bootIndex) {        matstar <- null + resids[, bootIndex]        nullbetas <- backsolve(qr.R(qr.X), crossprod(qr.Q(qr.X),             t(matstar)))[coef, ]        if (useWeights) {            sigma <- rowSums(t(tcrossprod(diag(nrow(design)) -                 tcrossprod(qr.Q(qr.X)), matstar))^2)            sigma <- sqrt(sigma/(nrow(design) - qr.X$rank))            outList <- list(coef = nullbetas, sigma = sigma)        }        else {            outList <- nullbetas        }        return(outList)    })}
25: bumphunterEngine(object, design = design, chr = chr, pos, cluster = cluster,     coef = coef, cutoff = cutoff, pickCutoff = pickCutoff, pickCutoffQ = pickCutoffQ,     maxGap = maxGap, nullMethod = nullMethod, smooth = smooth,     smoothFunction = smoothFunction, useWeights = useWeights,     B = B, permutations = NULL, verbose = verbose, ...)
26: .local(object, ...)
27: bumphunter(dat$mat, design = dat$design, chr = dat$chr, pos = dat$pos,     cluster = dat$cluster, coef = 2, cutoff = 0.28, nullMethod = "bootstrap",     smooth = TRUE, B = 250, verbose = TRUE, smoothFunction = loessByCluster)
28: bumphunter(dat$mat, design = dat$design, chr = dat$chr, pos = dat$pos,     cluster = dat$cluster, coef = 2, cutoff = 0.28, nullMethod = "bootstrap",     smooth = TRUE, B = 250, verbose = TRUE, smoothFunction = loessByCluster)
An irrecoverable exception occurred. R is aborting now ...
Warning in mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed,  :
  scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected
[bumphunterEngine] Computing marginal bootstrap p-values.
Error in abs(NullBeta) : non-numeric argument to mathematical function
Calls: bumphunter ... bumphunterEngine -> rowSums -> is.data.frame -> greaterOrEqual
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
  Running ‘test-all.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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/bumphunter.Rcheck/00check.log’
for details.