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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:netSmooth.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings netSmooth_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/netSmooth.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-07 07:38:48 UTC
* checking for file ‘netSmooth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netSmooth’ version ‘1.31.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netSmooth’ 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* 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 ... NOTE
checkRd: (-1) human.ppi.Rd:7: Lost braces; missing escapes or markup?
     7 | \format{A square matrix where A_{ij}=1 if gene i interacts with gene j}
       |                                 ^
checkRd: (-1) mouse.ppi.Rd:7: Lost braces; missing escapes or markup?
     7 | \format{A square matrix where A_{ij}=1 if gene i interacts with gene j}
       |                                 ^
checkRd: (-1) randomWalkByMatrixInv-matrix-method.Rd:29: Lost braces; missing escapes or markup?
    29 |   f_{ss} = (1 - alpha) * (I - alpha * A)^{-1} * f_0
       |     ^
checkRd: (-1) randomWalkByMatrixInv-matrix-method.Rd:29: Lost braces; missing escapes or markup?
    29 |   f_{ss} = (1 - alpha) * (I - alpha * A)^{-1} * f_0
       |                                          ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'projectFromNetworkRecombine-matrix-method.Rd':
  ‘filepath’

Documented arguments not in \usage in Rd file 'smoothAndRecombine-matrix-method.Rd':
  ‘filepath’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
pickDimReduction 5.161  0.163   5.329
robustClusters   4.752  0.337   5.098
* 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:
  49: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  50: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
  51: FUN(X[[i]], ...)
  52: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
  53: doTryCatch(return(expr), name, parentenv, handler)
  54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  55: tryCatchList(expr, classes, parentenv, handlers)
  56: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  57: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
  58: 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, shuffle = shuffle,     error_call = error_call)
  59: 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, shuffle = shuffle)
  60: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  61: test_check("netSmooth")
  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, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/netSmooth.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL netSmooth
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘netSmooth’ ...
** this is package ‘netSmooth’ version ‘1.31.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (netSmooth)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 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(netSmooth)
Loading required package: scater
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
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: GenomicRanges
Loading required package: stats4
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 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: Seqinfo
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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: scuttle
Loading required package: ggplot2
Loading required package: clusterExperiment

Attaching package: 'clusterExperiment'

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

    plotHeatmap

> 
> test_check("netSmooth")

 *** caught segfault ***
address 0x5b847e40, cause 'memory not mapped'

Traceback:
 1: .Call2("C_h5mread", filepath, name, starts, counts, noreduce,     as.vector, as.integer, as.sparse, method, use.H5Dread_chunk,     PACKAGE = "h5mread")
 2: h5mread(filepath, name, starts = index, as.vector = FALSE, as.integer = as.integer,     as.sparse = as.sparse)
 3: .h5mread2(x@filepath, x@name, index, as.integer = as_int)
 4: extract_array(x@seed, index)
 5: extract_array(x@seed, index)
 6: .nextMethod(x = x, index = index)
 7: callNextMethod()
 8: extract_array(x, Nindex)
 9: extract_array(x, Nindex)
10: read_block_as_dense(x, viewport)
11: read_block_as_dense(x, viewport)
12: .read_block(x, viewport, as.sparse = as.sparse)
13: read_block(x, viewport, as.sparse = NA)
14: FUN(init, viewport, ...)
15: FUN(viewport, init, ...)
16: gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
17: sinkApply(sink, FUN, x, verbose, verbose_read_block, grid = grid,     verbose = FALSE)
18: BLOCK_write_to_sink(sink, x, verbose = verbose)
19: writeHDF5Array(DelayedArray::DelayedArray(original_expression),     filepath = filepath, with.dimnames = TRUE)
20: projectFromNetworkRecombine(gene_expression, gene_expression_in_A_space_smooth,     filepath)
21: projectFromNetworkRecombine(gene_expression, gene_expression_in_A_space_smooth,     filepath)
22: smoothAndRecombine(x, adjMatrix, alpha, normalizeAdjMatrix = normalizeAdjMatrix,     filepath = filepath)
23: smoothAndRecombine(x, adjMatrix, alpha, normalizeAdjMatrix = normalizeAdjMatrix,     filepath = filepath)
24: .local(x, ...)
25: netSmooth(singleHDF5, smallPPI, alpha = 0.5)
26: netSmooth(singleHDF5, smallPPI, alpha = 0.5)
27: eval(code, test_env)
28: eval(code, test_env)
29: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(expr, restarts[[1L]])
36: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
37: test_code(code, parent.frame())
38: test_that("netSmooth accepts DelayedMatrix objects", {    sink(ifelse(.Platform$OS.type == "unix", "/dev/null", "NUL"))    singleHDF5 <- as(assay(smallscRNAseq), "HDF5Array")    netSmooth(singleHDF5, smallPPI, alpha = 0.5)    netSmooth(singleHDF5, smallPPI, alpha = "auto", autoAlphaMethod = "entropy")    sink()})
39: eval(code, test_env)
40: eval(code, test_env)
41: withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt)
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
46: doWithOneRestart(return(expr), restart)
47: withOneRestart(expr, restarts[[1L]])
48: withRestarts(tryCatch(withCallingHandlers({    eval(code, test_env)    new_expectations <- the$test_expectations > starting_expectations    if (snapshot_skipped) {        skip("On CRAN")    }    else if (!new_expectations && skip_on_empty) {        skip_empty()    }}, expectation = handle_expectation, packageNotFoundError = function(e) {    if (on_cran()) {        skip(paste0("{", e$package, "} is not installed."))    }}, snapshot_on_cran = function(cnd) {    snapshot_skipped <<- TRUE    invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message,     error = handle_error, interrupt = handle_interrupt), error = handle_fatal),     end_test = function() {    })
49: test_code(code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
50: source_file(path, env = env(env), desc = desc, shuffle = shuffle,     error_call = error_call)
51: FUN(X[[i]], ...)
52: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle,     error_call = error_call)
53: doTryCatch(return(expr), name, parentenv, handler)
54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
55: tryCatchList(expr, classes, parentenv, handlers)
56: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
57: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, shuffle = shuffle, error_call = error_call))
58: 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, shuffle = shuffle,     error_call = error_call)
59: 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, shuffle = shuffle)
60: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
61: test_check("netSmooth")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)