##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:visiumStitched.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings visiumStitched_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/visiumStitched.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘visiumStitched/DESCRIPTION’ ... OK
* this is package ‘visiumStitched’ version ‘1.2.0’
* 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 ‘visiumStitched’ 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
.fit_to_array_lsap: no visible binding for global variable ‘key’
.fit_to_array_lsap: no visible binding for global variable
  ‘capture_area’
.fit_to_array_lsap: no visible binding for global variable
  ‘pxl_row_in_fullres’
.fit_to_array_lsap: no visible binding for global variable
  ‘pxl_col_in_fullres’
.map_lsap: no visible binding for global variable ‘pxl_col_in_fullres’
.map_lsap: no visible binding for global variable ‘pxl_row_in_fullres’
.map_lsap: no visible binding for global variable
  ‘pxl_col_in_fullres_rounded’
.map_lsap: no visible binding for global variable
  ‘pxl_row_in_fullres_rounded’
Undefined global functions or variables:
  capture_area key pxl_col_in_fullres pxl_col_in_fullres_rounded
  pxl_row_in_fullres pxl_row_in_fullres_rounded
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
build_SpatialExperiment 31.545  1.851  33.594
add_array_coords        11.373  1.806  13.407
merge_overlapping        7.919  0.494   8.555
prep_fiji                6.456  1.334   7.894
rescale_fiji_inputs      6.410  0.998   7.707
as.Seurat                4.878  0.327   5.519
* 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/visiumStitched.Rcheck/00check.log’
for details.