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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialOmicsOverlay_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpatialOmicsOverlay.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK
* this is package ‘SpatialOmicsOverlay’ 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 ‘SpatialOmicsOverlay’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
plotSpatialOverlay: no visible binding for global variable ‘xcoor’
plotSpatialOverlay: no visible binding for global variable ‘ycoor’
plotSpatialOverlay: no visible binding for global variable ‘sampleID’
plotSpatialOverlay: no visible binding for global variable ‘Target’
scaleBarPrinting: no visible binding for global variable ‘X’
scaleBarPrinting: no visible binding for global variable ‘Y’
Undefined global functions or variables:
  Target X Y sampleID xcoor ycoor
* checking Rd files ... OK
* 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
add4ChannelImage        30.309  1.802  27.295
readSpatialOverlay      26.198  1.153  26.698
cropSamples             23.089  1.644  23.619
changeImageColoring     22.423  1.255  22.160
changeColoringIntensity 22.281  1.312  22.283
addImageOmeTiff         21.953  0.989  21.798
cropTissue              21.833  1.065  21.807
recolor                 21.017  1.127  21.408
flipY                   20.141  1.175  20.457
flipX                   20.141  1.046  20.483
createMask              15.598  0.652  16.317
createCoordFile          8.542  0.067   8.779
parseOverlayAttrs        5.308  0.272   5.206
parseScanMetadata        4.946  0.331   4.860
xmlExtraction            4.712  0.400   4.911
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpatialOmicsOverlay.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialOmicsOverlay
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SpatialOmicsOverlay’ ...
** this is package ‘SpatialOmicsOverlay’ version ‘1.10.0’
** 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 (SpatialOmicsOverlay)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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(vdiffr)
> 
> options( java.parameters = "-Xmx4g" )
> library( "RBioFormats" )
BioFormats library version 7.3.0
> 
> library(SpatialOmicsOverlay)
> 
> # #run tests
> test_check("SpatialOmicsOverlay")
WARNING: A restricted method in java.lang.System has been called
WARNING: java.lang.System::load has been called by org.scijava.nativelib.NativeLibraryUtil in an unnamed module (file:/Users/biocbuild/Library/Caches/org.R-project.R/R/RBioFormats/bioformats_package_7.3.0.jar)
WARNING: Use --enable-native-access=ALL-UNNAMED to avoid a warning for callers in this module
WARNING: Restricted methods will be blocked in a future release unless native access is enabled

Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: NanoStringNCTools
Loading required package: S4Vectors
Loading required package: stats4

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: ggplot2
Extracting XML
Parsing XML - scan metadata
Parsing XML - overlay data
Generating Coordinates
Extracting XML
Parsing XML - scan metadata
Parsing XML - overlay data
Generating Coordinates
Calculating and scaling coordinates
Calculating and scaling coordinates
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 422 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 422 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
333.676  15.064 341.065