##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SpatialFeatureExperiment_1.8.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘1.8.4’
* 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 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'
.aggregate_sample_tx: no visible binding for global variable ‘.N’
.aggregate_sample_tx: no visible global function definition for ‘.’
.aggregate_sample_tx: no visible binding for global variable ‘gene’
.aggregate_sample_tx: no visible binding for global variable ‘L1’
.aggregate_sample_tx: no visible binding for global variable ‘grid_id’
.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 binding for global variable ‘.N’
aggregateTx: no visible global function definition for ‘.’
aggregateTx: no visible binding for global variable ‘gene’
aggregateTx: no visible binding for global variable ‘grid_id’
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 .N ID_row L1 cell_col fn gene gene_col grid_id img_df
  instrument_version major_version minor_version spatialCoordsNames<-
  xoa_version
* 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
Img-set-SpatialExperiment-method                     16.235  1.309  14.803
formatTxSpots                                        15.618  1.169  17.174
readXenium                                           10.379  1.212  11.114
rowGeometries                                         9.425  1.024  10.101
removeEmptySpace                                      7.643  0.760   8.654
spatialGraphs                                         6.595  1.161   8.547
findSpatialNeighbors-SpatialFeatureExperiment-method  5.922  0.990   7.371
findVisiumGraph                                       5.982  0.897   7.330
dimGeometries                                         5.871  0.825   7.145
cbind-SpatialFeatureExperiment-method                 4.730  0.515   5.746
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.