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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:COTAN.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings COTAN_2.6.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'COTAN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COTAN' version '2.6.1'
* 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 whether package 'COTAN' 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 ... NOTE
'library' or 'require' call to 'torch' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'ggplot2:::ggname'
  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
mergeUniformCellsClusters : fromMergedName: warning in
  vapply(currentClNames, function(clName, mergedName) {: partial
  argument match of 'FUN.VAL' to 'FUN.VALUE'
mergeUniformCellsClusters : fromMergedName: warning in
  return(str_detect(mergedName, clName)): partial argument match of
  'FUN.VAL' to 'FUN.VALUE'
mergeUniformCellsClusters : fromMergedName: warning in }, FUN.VAL =
  logical(1L), mergedClName): partial argument match of 'FUN.VAL' to
  'FUN.VALUE'
ECDPlot: no visible binding for global variable '.'
GDIPlot: no visible binding for global variable 'sum.raw.norm'
GDIPlot: no visible binding for global variable 'GDI'
UMAPPlot: no visible binding for global variable 'x'
UMAPPlot: no visible binding for global variable 'y'
UMAPPlot: no visible binding for global variable 'types'
calculateCoex_Legacy: no visible binding for global variable
  'expectedNN'
calculateCoex_Legacy: no visible binding for global variable
  'expectedNY'
calculateCoex_Legacy: no visible binding for global variable
  'expectedYN'
calculateCoex_Legacy: no visible binding for global variable
  'expectedYY'
calculateCoex_Legacy: no visible binding for global variable
  'observedYY'
calculateCoex_Legacy: no visible binding for global variable '.'
calculateG: no visible binding for global variable 'observedNN'
calculateG: no visible binding for global variable 'observedNY'
calculateG: no visible binding for global variable 'observedYN'
calculateG: no visible binding for global variable 'observedYY'
calculateG: no visible binding for global variable 'expectedNN'
calculateG: no visible binding for global variable 'expectedNY'
calculateG: no visible binding for global variable 'expectedYN'
calculateG: no visible binding for global variable 'expectedYY'
calculatePartialCoex: no visible binding for global variable
  'expectedNN'
calculatePartialCoex: no visible binding for global variable
  'expectedNY'
calculatePartialCoex: no visible binding for global variable
  'expectedYN'
calculatePartialCoex: no visible binding for global variable
  'expectedYY'
calculatePartialCoex: no visible binding for global variable
  'observedYY'
calculatePartialCoex: no visible binding for global variable '.'
cellSizePlot: no visible binding for global variable '.'
cellsUniformClustering: no visible binding for global variable
  'objSeurat'
cellsUniformClustering: no visible binding for global variable
  'usedMaxResolution'
cellsUniformClustering: no visible binding for global variable
  'permMap'
checkClusterUniformity: no visible binding for global variable
  'pcaCellsPlot'
checkClusterUniformity: no visible binding for global variable '.'
checkClusterUniformity: no visible binding for global variable
  'bGroupGenesPlot'
checkClusterUniformity: no visible binding for global variable
  'UDEPLot'
checkClusterUniformity: no visible binding for global variable 'nuPlot'
checkClusterUniformity: no visible binding for global variable
  'zoomedNuPlot'
cleanPlots: no visible binding for global variable 'PC1'
cleanPlots: no visible binding for global variable 'PC2'
cleanPlots: no visible binding for global variable 'n'
cleanPlots: no visible binding for global variable 'means'
cleanPlots: no visible binding for global variable 'nu'
clustersMarkersHeatmapPlot: no visible binding for global variable
  'condName'
clustersMarkersHeatmapPlot: no visible binding for global variable
  'conditions'
clustersSummaryPlot: no visible binding for global variable 'keys'
clustersSummaryPlot: no visible binding for global variable 'values'
clustersSummaryPlot: no visible binding for global variable
  'CellNumber'
clustersSummaryPlot: no visible binding for global variable 'ExpGenes'
clustersSummaryPlot: no visible binding for global variable 'Cluster'
clustersSummaryPlot: no visible binding for global variable 'Condition'
establishGenesClusters: no visible binding for global variable
  'secondaryMarkers'
establishGenesClusters: no visible binding for global variable 'GCS'
establishGenesClusters: no visible binding for global variable
  'rankGenes'
expectedContingencyTables: no visible binding for global variable
  'expectedN'
expectedPartialContingencyTables: no visible binding for global
  variable 'expectedNN'
expectedPartialContingencyTables: no visible binding for global
  variable 'expectedN'
genesSizePlot: no visible binding for global variable '.'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'group'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'y'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'x'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'width'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'violinwidth'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'xmax'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'xminv'
geom_flat_violin : <anonymous>: no visible binding for global variable
  'xmaxv'
heatmapPlot: no visible binding for global variable 'obj'
heatmapPlot: no visible binding for global variable 'type'
heatmapPlot: no visible binding for global variable 'g2'
heatmapPlot: no visible binding for global variable 'coex'
mergeUniformCellsClusters : fromMergedName: no visible binding for
  global variable 'clName1'
mergeUniformCellsClusters : fromMergedName: no visible binding for
  global variable 'clName2'
mergeUniformCellsClusters : testPairListMerge: no visible binding for
  global variable 'cl1'
mergeUniformCellsClusters : testPairListMerge: no visible binding for
  global variable 'cl2'
mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible
  binding for global variable 'clName1'
mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible
  binding for global variable 'clName2'
mergeUniformCellsClusters : mergeAllClusters: no visible binding for
  global variable 'clName1'
mergeUniformCellsClusters : mergeAllClusters: no visible binding for
  global variable 'clName2'
mergeUniformCellsClusters: no visible binding for global variable
  'permMap'
mitochondrialPercentagePlot: no visible binding for global variable '.'
mitochondrialPercentagePlot: no visible binding for global variable
  'mit.percentage'
observedContingencyTables: no visible binding for global variable
  'observedY'
observedPartialContingencyTables: no visible binding for global
  variable 'observedYY'
observedPartialContingencyTables: no visible binding for global
  variable 'observedY'
scatterPlot: no visible binding for global variable '.'
scatterPlot: no visible binding for global variable '.x'
calculateCoex,COTAN: no visible binding for global variable 'useTorch'
coerce,COTAN-scCOTAN: no visible binding for global variable 'rawNorm'
coerce,COTAN-scCOTAN: no visible binding for global variable 'nu'
coerce,COTAN-scCOTAN: no visible binding for global variable 'lambda'
coerce,COTAN-scCOTAN: no visible binding for global variable 'a'
coerce,COTAN-scCOTAN: no visible binding for global variable 'hk'
coerce,COTAN-scCOTAN: no visible binding for global variable 'clusters'
coerce,COTAN-scCOTAN: no visible binding for global variable
  'clusterData'
Undefined global functions or variables:
  . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 UDEPLot a
  bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData clusters coex
  condName conditions expectedN expectedNN expectedNY expectedYN
  expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot
  obj objSeurat observedNN observedNY observedY observedYN observedYY
  pcaCellsPlot permMap rankGenes rawNorm secondaryMarkers sum.raw.norm
  type types useTorch usedMaxResolution values violinwidth width x xmax
  xmaxv xminv y zoomedNuPlot
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
UniformClusters         256.80   1.45  256.91
CalculatingCOEX          78.44   0.90   78.45
HeatmapPlots             55.77   1.31   56.39
ParametersEstimations    44.68   0.82   45.51
HandlingClusterizations  35.00   1.31   35.38
GenesStatistics          14.66   0.18   14.70
COTAN_ObjectCreation     13.44   0.30   13.45
Conversions               7.81   0.16    7.98
RawDataCleaning           5.55   0.08    5.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'outputTestDatasetCreation.R'
  Running 'spelling.R'
  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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck/00check.log'
for details.