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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SpatialFeatureExperiment_1.9.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.9.7’
* 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 ‘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 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 whether startup messages can be suppressed ... 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 ... NOTE
.seu_to_sfe: warning in do.call(setdiff, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe: warning in do.call(intersect, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe : <anonymous>: warning in do.call(setdiff, arg = assays_n):
  partial argument match of 'arg' to 'args'
.filter_polygons: no visible binding for global variable ‘ID_row’
.no_raw_bytes: no visible binding for global variable ‘xoa_version’
.no_raw_bytes: no visible binding for global variable ‘major_version’
.no_raw_bytes: no visible binding for global variable ‘minor_version’
.no_raw_bytes: no visible binding for global variable
  ‘instrument_version’
.read10xVisium: no visible global function definition for
  ‘spatialCoordsNames<-’
addTxTech: no visible binding for global variable ‘gene_col’
addTxTech: no visible binding for global variable ‘cell_col’
addTxTech: no visible binding for global variable ‘fn’
aggregateTx: no visible global function definition for ‘tail’
aggregateTxTech: no visible binding for global variable ‘gene_col’
aggregateTxTech: no visible binding for global variable ‘cell_col’
aggregateTxTech: no visible binding for global variable ‘fn’
aggregateTxTech: no visible binding for global variable ‘xoa_version’
aggregateTxTech: no visible binding for global variable ‘major_version’
aggregateTxTech: no visible binding for global variable ‘minor_version’
aggregateTxTech: no visible binding for global variable
  ‘instrument_version’
findVisiumHDGraph: no visible binding for global variable ‘..cols’
formatTxTech: no visible binding for global variable ‘gene_col’
formatTxTech: no visible binding for global variable ‘cell_col’
formatTxTech: no visible binding for global variable ‘fn’
readVizgen: no visible binding for global variable ‘img_df’
readXenium: no visible binding for global variable ‘xoa_version’
readXenium: no visible binding for global variable ‘major_version’
readXenium: no visible binding for global variable ‘minor_version’
readXenium: no visible binding for global variable ‘instrument_version’
readXenium: no visible binding for global variable ‘img_df’
Undefined global functions or variables:
  ..cols ID_row cell_col fn gene_col img_df instrument_version
  major_version minor_version spatialCoordsNames<- tail xoa_version
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BioFormatsImage.Rd: Image
  ExtImage.Rd: Image
  Img-set-SpatialExperiment-method.Rd: addImg
  SpatRasterImage.Rd: rast, SpatRaster
  SpatialFeatureExperiment-class.Rd: SpatialExperiment,
    SingleCellExperiment
  SpatialFeatureExperiment-coercion.Rd: SpatialExperiment, DataFrame
  SpatialFeatureExperiment.Rd: DataFrame, SpatialExperiment,
    SingleCellExperiment
  aggregate-SpatialFeatureExperiment-method.Rd: BiocParallelParam
  annotOp.Rd: st_intersection
  annotPred.Rd: st_intersects
  annotSummary.Rd: st_intersects
  colFeatureData.Rd: reducedDimNames
  crop.Rd: st_intersection, st_difference
  findSpatialNeighbors-SpatialFeatureExperiment-method.Rd: nb2listw,
    BiocParallelParam, BiocNeighborParam, KmknnParam, VptreeParam
  formatTxSpots.Rd: BiocParallelParam
  formatTxTech.Rd: BiocParallelParam
  getParams.Rd: reducedDimNames
  readCosMX.Rd: BiocParallelParam
  readVizgen.Rd: SpatRaster, BiocParallelParam
  readXenium.Rd: BiocParallelParam
  saveRDS-SpatialFeatureExperiment-method.Rd: wrap
  spatialGraphs.Rd: SpatialExperiment
  st_any_pred.Rd: st_intersects
  updateObject.Rd: objectVersion
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
formatTxSpots                                        17.990  2.189  21.661
Img-set-SpatialExperiment-method                     16.426  1.101  14.840
readXenium                                           10.137  1.197  10.850
rowGeometries                                        10.064  0.894  10.611
findVisiumGraph                                       6.830  1.114   8.810
removeEmptySpace                                      6.854  0.780   7.897
dimGeometries                                         6.529  0.967   7.974
spatialGraphs                                         6.183  0.705   7.364
cbind-SpatialFeatureExperiment-method                 5.633  0.673   6.780
findSpatialNeighbors-SpatialFeatureExperiment-method  5.381  0.694   6.555
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.