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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpaceMarkers.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpaceMarkers_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpaceMarkers.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘SpaceMarkers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpaceMarkers’ version ‘1.5.0’
* 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 ‘SpaceMarkers’ 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 ... NOTE
plotIMScores: no visible binding for global variable ‘Gene’
plotOverlapScores: no visible binding for global variable ‘pattern1’
plotOverlapScores: no visible binding for global variable ‘pattern2’
plotOverlapScores: no visible binding for global variable
  ‘overlapScore’
Undefined global functions or variables:
  Gene overlapScore pattern1 pattern2
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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
getInteractingGenes         312.980  7.935 122.240
getPairwiseInteractingGenes 102.986  3.135 106.826
getSpatialParamsMoransI     102.562  2.954   5.151
plotIMScores                101.406  3.119 105.405
plotOverlapScores            96.924  1.732   1.381
findPatternHotspots          58.859  0.546  62.399
getIMScores                   6.389  1.444 108.722
load10XCoords                 0.063  0.046   6.541
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpaceMarkers.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpaceMarkers
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SpaceMarkers’ ...
** this is package ‘SpaceMarkers’ version ‘1.5.0’
** using staged installation
** R
** data
** 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 (SpaceMarkers)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(SpaceMarkers)
> 
> test_check("SpaceMarkers")
Using user provided optParams.
hotspots does not have refPattern column or dimension 
    does not match with data.
Pattern_1 and Pattern_2 do not sufficiently interact.
                Skipping statistical test for genes.
No interacting genes found. Returning 
            result with only hotspots.
No interacting genes found. Returning 
            result with only hotspots.
Reading spot diameter from specified .json file
Loading required namespace: CoGAPS
Version not provided. Trying to infer.
probe_set.csv or .parquet not found.Assuming version 1.0.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 67 ]
> 
> proc.time()
   user  system elapsed 
 46.815   2.888  40.319