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### Running command:
###
###   /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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/imcRtools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘imcRtools/DESCRIPTION’ ... OK
* this is package ‘imcRtools’ version ‘1.10.0’
* 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 ... 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 ... 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 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 ... OK
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
testInteractions   188.171  3.167 287.656
read_steinbock      31.834  5.074  46.412
buildSpatialGraph   13.546  0.627  19.100
plotSpatial          7.403  0.153  10.270
filterPixels         4.574  0.291   6.650
plotSpatialContext   3.643  0.074   5.190
* 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`:   FALSE
  `expected`: TRUE 
  ── Failure ('test_countInteractions.R:396:5'): countInteractions function works ──
  all(cur_out$ct[!is.na(cur_out$ct)] == 1) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test_integration_interactions.R:351:5'): testInteractions gives same results as neighbouRhood ──
  dat_p$p_gt[!is.na(imcRtools_classic$ct)] not equal to imcRtools_classic_perm$p_gt[!is.na(imcRtools_classic$ct)].
  1/22 mismatches
  [8] 0.881 - 0.901 == -0.0198
  
  [ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ]
  Error: Test failures
  Execution halted
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/Resources/library’
* installing *source* package ‘imcRtools’ ...
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: GenomeInfoDb
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")
[ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_aggregateNeighbors.R:36:5'): aggregateNeighbors function works ──
all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_aggregateNeighbors.R:116:5'): aggregateNeighbors function works ──
all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_aggregateNeighbors.R:545:5'): aggregateNeighbors function works ──
all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_countInteractions.R:396:5'): countInteractions function works ──
all(cur_out$ct[!is.na(cur_out$ct)] == 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_integration_interactions.R:351:5'): testInteractions gives same results as neighbouRhood ──
dat_p$p_gt[!is.na(imcRtools_classic$ct)] not equal to imcRtools_classic_perm$p_gt[!is.na(imcRtools_classic$ct)].
1/22 mismatches
[8] 0.881 - 0.901 == -0.0198

[ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ]
Error: Test failures
Execution halted