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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imcRtools_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/imcRtools.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-13 22:59:38 UTC
* using option ‘--no-vignettes’
* checking for file ‘imcRtools/DESCRIPTION’ ... OK
* this is package ‘imcRtools’ version ‘1.17.0’
* 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  8.0Mb
  sub-directories of 1Mb or more:
    extdata   7.6Mb
* 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 ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking S3 generic/method consistency ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
.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 ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking Rd \usage sections ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
testInteractions 54.408  3.020  87.684
read_steinbock    6.882  2.717   7.394
* 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: 4 WARNINGs, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/imcRtools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL imcRtools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘imcRtools’ ...
** this is package ‘imcRtools’ version ‘1.17.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package can be loaded from final location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package keeps a record of temporary installation path
* DONE (imcRtools)

R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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

proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
> 
> test_check("imcRtools")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 3003 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 3003 ]
> 
> proc.time()
   user  system elapsed 
217.622  18.550 265.300