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### Running command:
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###   /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_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpaceMarkers.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘2.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 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’
.prepare_circos_data_logic: no visible global function definition for
  ‘ave’
calculate_gene_set_score : <anonymous>: no visible global function
  definition for ‘weighted.mean’
calculate_gene_set_specificity: no visible binding for global variable
  ‘weighted.mean’
calculate_lr_scores : <anonymous>: no visible global function
  definition for ‘weighted.mean’
plot_im_scores: no visible binding for global variable ‘Gene’
plot_overlap_scores: no visible binding for global variable ‘pattern1’
plot_overlap_scores: no visible binding for global variable ‘pattern2’
plot_overlap_scores: no visible binding for global variable
  ‘overlapScore’
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’
Undefined global functions or variables:
  Gene as.raster ave median overlapScore p.adjust pattern1 pattern2
  quantile weighted.mean wilcox.test x x_c y y_c
Consider adding
  importFrom("grDevices", "as.raster")
  importFrom("stats", "ave", "median", "p.adjust", "quantile",
             "weighted.mean", "wilcox.test")
to your NAMESPACE file.
* 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          43.015  4.258  19.948
plot_im_scores                 31.953  3.289  21.564
get_spatial_parameters         13.207  1.220   0.043
get_spatial_features           13.198  1.199   0.066
get_im_scores                   7.129  1.367  24.128
find_pattern_hotspots           7.704  0.315  14.952
get_pairwise_interacting_genes  4.666  1.259  20.929
get_spatial_params_morans_i     4.063  1.090   5.196
* 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.