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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:SpaceMarkers.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings SpaceMarkers_2.3.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/SpaceMarkers.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* 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: 2026-05-06 08:32:53 UTC
* checking for file ‘SpaceMarkers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpaceMarkers’ version ‘2.3.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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 ‘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 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 ... NOTE
.calc_IM_scores: no visible global function definition for ‘p.adjust’
.calc_threshold: no visible global function definition for ‘quantile’
.calculate_all_fc_scores: no visible binding for global variable
  ‘p.adjust’
.calculate_all_fc_scores: no visible global function definition for
  ‘median’
.calculate_fc_score: no visible global function definition for
  ‘quantile’
.calculate_fc_score: no visible global function definition for
  ‘wilcox.test’
.directed_SpaceMarkers: no visible global function definition for
  ‘combn’
.prepare_circos_data_logic: no visible global function definition for
  ‘ave’
SpaceMarkersExperiment: no visible global function definition for ‘as’
load10X: no visible global function definition for ‘as’
plot_im_scores: no visible binding for global variable ‘Gene’
plot_spatial: no visible binding for global variable ‘x’
plot_spatial: no visible binding for global variable ‘y’
plot_spatial: no visible global function definition for ‘as.raster’
plot_spatial: no visible binding for global variable ‘x_c’
plot_spatial: no visible binding for global variable ‘y_c’
plot_spatial_data_over_image: no visible binding for global variable
  ‘x’
plot_spatial_data_over_image: no visible binding for global variable
  ‘y’
plot_spatial_data_over_image: no visible global function definition for
  ‘as.raster’
plot_spatial_data_over_image: no visible binding for global variable
  ‘x_c’
plot_spatial_data_over_image: no visible binding for global variable
  ‘y_c’
calculate_gene_set_score,ANY : <anonymous>: no visible global function
  definition for ‘weighted.mean’
calculate_gene_set_specificity,ANY: no visible binding for global
  variable ‘weighted.mean’
calculate_lr_scores,ANY : <anonymous>: no visible global function
  definition for ‘weighted.mean’
Undefined global functions or variables:
  Gene as as.raster ave combn median p.adjust quantile weighted.mean
  wilcox.test x x_c y y_c
Consider adding
  importFrom("grDevices", "as.raster")
  importFrom("methods", "as")
  importFrom("stats", "ave", "median", "p.adjust", "quantile",
             "weighted.mean", "wilcox.test")
  importFrom("utils", "combn")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
get_interacting_genes          24.558  3.966  30.619
get_pairwise_interacting_genes 19.145  2.730  22.663
get_spatial_params_morans_i    15.739  2.655   4.630
find_pattern_hotspots           6.819  0.462   7.570
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/SpaceMarkers.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL SpaceMarkers
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘SpaceMarkers’ ...
** this is package ‘SpaceMarkers’ version ‘2.3.1’
** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(SpaceMarkers)
> 
> test_check("SpaceMarkers")
pattern_pairs not provided. Calculating all 
            possible pairs.
Using user provided optParams.
Using user provided hotspot regions.
Calculating genes of interest for Pattern_1 and Pattern_2
pattern_pairs not provided. Calculating all 
            possible pairs.
Using user provided optParams.
Using user provided hotspot regions.
Calculating genes of interest for Pattern_1 and Pattern_2
Only one method can be used at a time. Using Szymkiewicz-Simpson
Only one method can be used at a time. Using Szymkiewicz-Simpson
number of iterations= 50 
number of iterations= 91 
number of iterations= 507 
number of iterations= 70 
number of iterations= 50 
number of iterations= 91 
number of iterations= 32 
number of iterations= 45 
Processed pattern pair: Pattern_1 and Pattern_2

number of iterations= 50 
number of iterations= 91 
number of iterations= 32 
number of iterations= 45 
Only one method can be used at a time. Using relative-abundance
number of iterations= 50 
number of iterations= 91 
number of iterations= 32 
number of iterations= 45 
Processed pattern pair: Pattern_1 and Pattern_2

number of iterations= 50 
number of iterations= 91 
number of iterations= 32 
number of iterations= 45 
Processed pattern pair: Pattern_1 and Pattern_2

number of iterations= 50 
number of iterations= 91 
number of iterations= 32 
number of iterations= 45 
Processed pattern pair: P1 and P2

spatial_patterns(x) <- value: rownames(value) not set; assuming rows are in colnames(x) order.
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.
Only one method can be used at a time. Using Szymkiewicz-Simpson
Only one method can be used at a time. Using Szymkiewicz-Simpson
Only one method can be used at a time. Using Szymkiewicz-Simpson
Only one method can be used at a time. Using Szymkiewicz-Simpson
resolution: fullres
resolution: fullres
Reading spot diameter from specified .json file
resolution: fullres
Loading required namespace: CoGAPS
resolution: lowres
resolution: lowres
resolution: lowres
resolution: lowres
Version not provided. Trying to infer.
probe_set.csv or .parquet not found.Assuming version 1.0.
[ FAIL 0 | WARN 6 | SKIP 2 | PASS 265 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-SpaceMarkersExperiment-pipeline.R:617:5',
  'test-SpaceMarkersExperiment-pipeline.R:635:5'

[ FAIL 0 | WARN 6 | SKIP 2 | PASS 265 ]
> 
> proc.time()
   user  system elapsed 
 86.072   9.504  85.454