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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:spatialLIBD.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings spatialLIBD_1.10.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/spatialLIBD.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘spatialLIBD/DESCRIPTION’ ... OK
* this is package ‘spatialLIBD’ version ‘1.10.1’
* 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 ‘spatialLIBD’ 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 R 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
registration_pseudobulk: no visible global function definition for
  ‘spatialCoords<-’
Undefined global functions or variables:
  spatialCoords<-
* 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 LazyData ... 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
add_images     21.204  2.041  26.493
vis_gene       21.009  2.172  23.782
img_update_all 19.709  1.806  21.924
vis_gene_p     18.948  1.931  22.412
vis_grid_clus  18.266  2.380  21.296
vis_grid_gene  17.921  2.160  20.672
vis_clus       18.000  2.062  20.618
vis_clus_p     17.748  1.764  20.203
check_spe      17.755  1.687  20.067
cluster_export 17.305  1.716  19.875
cluster_import 17.399  1.441  19.409
geom_spatial   17.075  1.708  19.416
sce_to_spe     17.278  1.444  19.406
add_key        16.532  1.534  18.854
img_update     16.332  1.432  18.538
img_edit       16.268  1.488  18.400
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘TenX_data_download.Rmd’ using ‘UTF-8’... OK
  ‘spatialLIBD.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/spatialLIBD.Rcheck/00check.log’
for details.