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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SpatialArtifacts.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SpatialArtifacts_0.99.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SpatialArtifacts.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 08:47:54 UTC
* checking for file ‘SpatialArtifacts/DESCRIPTION’ ... OK
* this is package ‘SpatialArtifacts’ version ‘0.99.8’
* 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 ‘SpatialArtifacts’ 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 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 ... OK
* 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
detectEdgeArtifacts 53.763  0.713  54.482
clumpEdges           5.054  0.090   5.148
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SpatialArtifacts
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘SpatialArtifacts’ ...
** this is package ‘SpatialArtifacts’ version ‘0.99.8’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (SpatialArtifacts)

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.

> # 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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SpatialArtifacts)
> 
> test_check("SpatialArtifacts")
Detecting edges...
  Sample V11L05-335_C1: 74 edge spots detected
Finding problem areas...
Removed intermediate columns: lg10_sum_umi, sum_umi_3MAD_outlier_sample, sum_umi_3MAD_outlier_binary
Edge artifact detection completed!
  Total edge spots: 74
  Total problem area spots: 78
Classifying artifacts spots...
Classification added: edge_artifact_classification

Classification summary:
  not_artifact: 4887 spots
  small_edge_artifact: 74 spots
  small_interior_artifact: 4 spots
Detecting edges...
  Sample V11L05-335_C1: 74 edge spots detected
Finding problem areas...
Removed intermediate columns: lg10_sum_umi, sum_umi_3MAD_outlier_sample, sum_umi_3MAD_outlier_binary
Edge artifact detection completed!
  Total edge spots: 74
  Total problem area spots: 78
    Clustering 9 outlier bins...
    Creating raster: 10 rows * 10 cols
    Applying morphological transformations...
    [16um Mode] Adjusted min_cluster_size: 2 -> 2
    Clustering outlier regions...
    Found 9 clustered cells
    Identified 1 unique clusters
    Kept 1 clusters (>=2 bins): 9 bins total
    No outliers to cluster
    Clustering 9 outlier bins...
    Creating raster: 10 rows * 10 cols
    Applying morphological transformations...
    [16um Mode] Adjusted min_cluster_size: 2 -> 2
    Clustering outlier regions...
    Found 9 clustered cells
    Identified 1 unique clusters
    Kept 1 clusters (>=2 bins): 9 bins total
terra 1.9.11

Attaching package: 'terra'

The following objects are masked from 'package:testthat':

    compare, describe

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
117.963   2.599 122.017