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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.2.3’
* 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 ‘SpatialFeatureExperiment’ 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘spdep:::minmax.listw’
  See the note in ?`:::` about the use of this operator.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                      user system elapsed
spatialGraphs                                        9.365  1.066  23.452
SFE-image                                            6.378  2.055  17.027
dimGeometries                                        7.648  0.367  17.502
removeEmptySpace                                     6.973  0.774  16.939
cbind-SpatialFeatureExperiment-method                7.022  0.320  15.960
findVisiumGraph                                      6.616  0.603  15.829
findSpatialNeighbors-SpatialFeatureExperiment-method 6.337  0.506  15.572
crop                                                 5.870  0.195  12.109
SFE-transform                                        5.242  0.264  11.899
SpatialFeatureExperiment-coercion                    3.654  0.206   7.923
sampleIDs                                            3.337  0.230   7.684
addVisiumSpotPoly                                    3.415  0.124   7.416
updateObject                                         3.134  0.247   7.468
bbox-SpatialFeatureExperiment-method                 3.147  0.159   7.046
show-SpatialFeatureExperiment-method                 3.028  0.239   7.254
annotOp                                              3.019  0.181   6.945
annotPred                                            2.945  0.165   6.898
annotSummary                                         2.934  0.164   6.823
unit-SpatialFeatureExperiment-method                 2.854  0.235   6.887
SpatialFeatureExperiment-subset                      2.747  0.223   6.551
annotGeometries                                      2.706  0.203   6.726
changeSampleIDs                                      2.327  0.161   5.005
read10xVisiumSFE                                     2.320  0.105   5.010
saveRDS-SpatialFeatureExperiment-method              2.348  0.069   5.102
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.