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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings imcRtools_1.17.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/imcRtools.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-11 04:54:59 UTC
* checking for file ‘imcRtools/DESCRIPTION’ ... OK
* this is package ‘imcRtools’ version ‘1.17.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘imcRtools’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.generateInteractionsPlot: no visible binding for global variable
  ‘weight’
.valid.plotInteractions.input: no visible binding for global variable
  ‘from_label’
.valid.plotInteractions.input: no visible binding for global variable
  ‘to_label’
.valid.plotInteractions.input: no visible global function definition
  for ‘n_distinct’
.valid.plotInteractions.input: no visible global function definition
  for ‘capture.output’
plotInteractions: no visible binding for global variable ‘from_label’
plotInteractions: no visible binding for global variable ‘to_label’
plotInteractions: no visible binding for global variable ‘weight’
plotInteractions: no visible global function definition for
  ‘everything’
readSCEfromTIFF: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  capture.output everything from_label n_distinct read.csv to_label
  weight
Consider adding
  importFrom("utils", "capture.output", "read.csv")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) aggregateNeighbors.Rd:52: Lost braces; missing escapes or markup?
    52 | \code{summarize_by = "metadata"} or "{statistic}_aggregatedExpression" when
       |                                      ^
checkRd: (-1) testInteractions.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testInteractions.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotSpatial.Rd: ggraph
  readImagefromTXT.Rd: Image-class, CytoImageList-class
  readSCEfromTIFF.Rd: SingleCellExperiment-class
  readSCEfromTXT.Rd: SingleCellExperiment-class
  read_cpout.Rd: SpatialExperiment-class, SingleCellExperiment-class
  read_steinbock.Rd: SpatialExperiment-class,
    SingleCellExperiment-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 ... WARNING
Found the following significant warnings:

  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
testInteractions  222.374  2.928 152.671
read_steinbock     16.336  5.607  16.497
plotInteractions    8.911  0.093   6.587
buildSpatialGraph   7.846  1.080   8.590
plotSpatial         5.372  0.186   5.559
* 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:
  Actual noise: warnings.
  ── Failure ('test_plotSpotHeatmap.R:100:5'): plotSpotHeatmap function works. ───
  Expected `... <- NULL` to run silently.
  Actual noise: warnings.
  ── Failure ('test_plotSpotHeatmap.R:102:5'): plotSpotHeatmap function works. ───
  Expected `cur_out <- plotSpotHeatmap(cur_sce, cellwidth = 5)` to run silently.
  Actual noise: warnings.
  ── Failure ('test_plotSpotHeatmap.R:103:5'): plotSpotHeatmap function works. ───
  Expected `... <- NULL` to run silently.
  Actual noise: warnings.
  
  [ FAIL 25 | WARN 21 | SKIP 0 | PASS 2978 ]
  Error:
  ! Test failures.
  Execution halted
* 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, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/imcRtools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL imcRtools
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘imcRtools’ ...
** this is package ‘imcRtools’ version ‘1.17.1’
** 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 (imcRtools)

R version 4.6.0 alpha (2026-04-05 r89794)
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(imcRtools)
Loading required package: SpatialExperiment
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

> 
> test_check("imcRtools")
Saving _problems/test_binAcrossPixels-8.R
Saving _problems/test_binAcrossPixels-38.R
Saving _problems/test_binAcrossPixels-52.R
Saving _problems/test_binAcrossPixels-76.R
Saving _problems/test_binAcrossPixels-79.R
Saving _problems/test_binAcrossPixels-81.R
Saving _problems/test_binAcrossPixels-89.R
Saving _problems/test_plotSpotHeatmap-8.R
Saving _problems/test_plotSpotHeatmap-21.R
Saving _problems/test_plotSpotHeatmap-32.R
Saving _problems/test_plotSpotHeatmap-43.R
Saving _problems/test_plotSpotHeatmap-44.R
Saving _problems/test_plotSpotHeatmap-45.R
Saving _problems/test_plotSpotHeatmap-56.R
Saving _problems/test_plotSpotHeatmap-61.R
Saving _problems/test_plotSpotHeatmap-73.R
Saving _problems/test_plotSpotHeatmap-78.R
Saving _problems/test_plotSpotHeatmap-80.R
Saving _problems/test_plotSpotHeatmap-94.R
Saving _problems/test_plotSpotHeatmap-96.R
Saving _problems/test_plotSpotHeatmap-97.R
Saving _problems/test_plotSpotHeatmap-99.R
Saving _problems/test_plotSpotHeatmap-101.R
Saving _problems/test_plotSpotHeatmap-102.R
Saving _problems/test_plotSpotHeatmap-105.R
[ FAIL 25 | WARN 21 | SKIP 0 | PASS 2978 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_binAcrossPixels.R:8:5'): binAcrossPixels function works. ─────
Expected `out <- binAcrossPixels(cur_sce, bin_size = 10)` to run silently.
Actual noise: warnings.
── Failure ('test_binAcrossPixels.R:38:5'): binAcrossPixels function works. ────
Expected `out <- binAcrossPixels(cur_sce, bin_size = 10, statistic = "mean")` to run silently.
Actual noise: warnings.
── Failure ('test_binAcrossPixels.R:52:5'): binAcrossPixels function works. ────
Expected `out <- binAcrossPixels(cur_sce, bin_size = 2)` to run silently.
Actual noise: warnings.
── Failure ('test_binAcrossPixels.R:76:5'): binAcrossPixels function works. ────
Expected `out <- binAcrossPixels(cur_sce, bin_size = 5, spot_id = "test_id")` to run silently.
Actual noise: warnings.
── Failure ('test_binAcrossPixels.R:79:5'): binAcrossPixels function works. ────
Expected `out <- binAcrossPixels(cur_sce, bin_size = 5, assay_type = "test")` to run silently.
Actual noise: warnings.
── Failure ('test_binAcrossPixels.R:81:5'): binAcrossPixels function works. ────
Expected `out <- binAcrossPixels(cur_sce, bin_size = 5, statistic = "mean")` to run silently.
Actual noise: warnings.
── Failure ('test_binAcrossPixels.R:89:5'): binAcrossPixels function works. ────
Expected `out <- binAcrossPixels(cur_sce, bin_size = 3)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:8:5'): plotSpotHeatmap function works. ─────
Expected `cur_out <- plotSpotHeatmap(cur_sce)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:21:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, log = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:32:5'): plotSpotHeatmap function works. ────
Expected `... <- NULL` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:43:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, threshold = 200)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:44:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, threshold = 0)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:45:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, log = FALSE, threshold = 200)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:56:5'): plotSpotHeatmap function works. ────
Expected `cur_out_2 <- plotSpotHeatmap(cur_sce, log = TRUE, threshold = log10(200))` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:61:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, spot_id = "test_spot")` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:73:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, channel_id = "test_channel")` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:78:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, assay_type = "exprs", log = FALSE)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:80:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, statistic = "mean")` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:93:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, order_metals = FALSE, cluster_rows = TRUE)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:95:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, order_metals = FALSE, cluster_cols = TRUE)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:97:5'): plotSpotHeatmap function works. ────
Expected `cur_out <- plotSpotHeatmap(cur_sce, color = viridis::inferno(50))` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:98:5'): plotSpotHeatmap function works. ────
Expected `... <- NULL` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:100:5'): plotSpotHeatmap function works. ───
Expected `... <- NULL` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:102:5'): plotSpotHeatmap function works. ───
Expected `cur_out <- plotSpotHeatmap(cur_sce, cellwidth = 5)` to run silently.
Actual noise: warnings.
── Failure ('test_plotSpotHeatmap.R:103:5'): plotSpotHeatmap function works. ───
Expected `... <- NULL` to run silently.
Actual noise: warnings.

[ FAIL 25 | WARN 21 | SKIP 0 | PASS 2978 ]
Error:
! Test failures.
Execution halted