##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings DelayedMatrixStats_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedMatrixStats.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘DelayedMatrixStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DelayedMatrixStats’ version ‘1.29.1’
* 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 ‘DelayedMatrixStats’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Missing object imported by a ':::' call: ‘DelayedArray:::.reduce_array_dimensions’
Unexported objects imported by ':::' calls:
  ‘DelayedArray:::.get_ans_type’ ‘DelayedArray:::BLOCK_colVars’
  ‘DelayedArray:::BLOCK_rowVars’ ‘DelayedArray:::RleArraySeed’
  ‘DelayedArray:::get_Nindex_lengths’ ‘DelayedArray:::set_dim’
  ‘DelayedArray:::set_dimnames’ ‘DelayedArray:::subset_by_Nindex’
  ‘DelayedArray:::to_linear_index’
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  colAlls.Rd: DelayedMatrix-class
  colAnyNAs.Rd: DelayedMatrix-class
  colAvgsPerRowSet.Rd: DelayedMatrix-class
  colCollapse.Rd: DelayedMatrix-class
  colCounts.Rd: DelayedMatrix-class
  colCummaxs.Rd: DelayedMatrix-class
  colDiffs.Rd: DelayedMatrix-class
  colIQRDiffs.Rd: DelayedMatrix-class
  colIQRs.Rd: DelayedMatrix-class
  colLogSumExps.Rd: DelayedMatrix-class
  colMads.Rd: DelayedMatrix-class
  colMeans2.Rd: DelayedMatrix-class
  colMedians.Rd: DelayedMatrix-class
  colOrderStats.Rd: DelayedMatrix-class
  colProds.Rd: DelayedMatrix-class
  colQuantiles.Rd: DelayedMatrix-class
  colRanks.Rd: DelayedMatrix-class
  colSums2.Rd: DelayedMatrix-class
  colTabulates.Rd: DelayedMatrix-class
  colVars.Rd: DelayedMatrix-class
  colWeightedMads.Rd: DelayedMatrix-class
  colWeightedMeans.Rd: DelayedMatrix-class
  colWeightedMedians.Rd: DelayedMatrix-class
  colWeightedVars.Rd: DelayedMatrix-class
  from_DelayedArray_to_simple_seed_class.Rd: DelayedArray-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  34: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  35: source_file(path, env = env(env), desc = desc, error_call = error_call)
  36: FUN(X[[i]], ...)
  37: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  38: doTryCatch(return(expr), name, parentenv, handler)
  39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  40: tryCatchList(expr, classes, parentenv, handlers)
  41: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  42: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  43: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  44: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  45: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  46: test_check("DelayedMatrixStats")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedMatrixStats.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL DelayedMatrixStats
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘DelayedMatrixStats’ ...
** this is package ‘DelayedMatrixStats’ version ‘1.29.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DelayedMatrixStats)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(DelayedMatrixStats)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep

> 
> test_check("DelayedMatrixStats")

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call2("C_viewMeans_RleViews", trim(x), na.rm, PACKAGE = "IRanges")
 2: viewMeans(x = views, na.rm = na.rm)
 3: viewMeans(x = views, na.rm = na.rm)
 4: candidate(S, ..., useNames = useNames)
 5: .smart_seed_dispatcher(x, generic = MatrixGenerics::colMeans2,     blockfun = .DelayedMatrix_block_colMeans2, force_block_processing = force_block_processing,     rows = rows, cols = cols, na.rm = na.rm, ..., useNames = useNames)
 6: .local(x, rows, cols, na.rm, ..., useNames = useNames)
 7: (new("standardGeneric", .Data = function (x, rows = NULL, cols = NULL,     na.rm = FALSE, ..., useNames = TRUE) standardGeneric("colMeans2"), generic = "colMeans2", package = "MatrixGenerics",     group = list(), valueClass = character(0), signature = "x",     default = NULL, skeleton = (function (x, rows = NULL, cols = NULL,         na.rm = FALSE, ..., useNames = TRUE)     stop(gettextf("invalid call in method dispatch to '%s' (no default method)",         "colMeans2"), domain = NA))(x, rows, cols, na.rm, ...,         useNames = useNames)))(dots[[1L]][[66L]])
 8: (new("standardGeneric", .Data = function (x, rows = NULL, cols = NULL,     na.rm = FALSE, ..., useNames = TRUE) standardGeneric("colMeans2"), generic = "colMeans2", package = "MatrixGenerics",     group = list(), valueClass = character(0), signature = "x",     default = NULL, skeleton = (function (x, rows = NULL, cols = NULL,         na.rm = FALSE, ..., useNames = TRUE)     stop(gettextf("invalid call in method dispatch to '%s' (no default method)",         "colMeans2"), domain = NA))(x, rows, cols, na.rm, ...,         useNames = useNames)))(dots[[1L]][[66L]])
 9: mapply(FUN = f, ..., SIMPLIFY = FALSE)
10: Map(dmg_f, DelayedMatrix_list)
11: eval(code, test_env)
12: eval(code, test_env)
13: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
21: test_code(desc, code, env = parent.frame(), reporter = reporter)
22: test_that("Default arguments", {    check.attributes <- checkAttributes(DelayedMatrix_list)    expecteds <- Map(mg_f, matrix_list)    observeds <- Map(dmg_f, DelayedMatrix_list)    Map(expect_equal, observeds, expecteds, check.attributes = check.attributes)})
23: testDefaultArgs(filtered_matrix_list, filtered_DelayedMatrix_list)
24: eval(code, test_env)
25: eval(code, test_env)
26: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
34: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
35: source_file(path, env = env(env), desc = desc, error_call = error_call)
36: FUN(X[[i]], ...)
37: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
38: doTryCatch(return(expr), name, parentenv, handler)
39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
40: tryCatchList(expr, classes, parentenv, handlers)
41: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
42: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
43: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
44: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
45: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
46: test_check("DelayedMatrixStats")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)