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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ILoReg_1.13.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ILoReg.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.13.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ILoReg’ 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 ... OK
* 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 ... WARNING
Codoc mismatches from Rd file 'FindAllGeneMarkers.Rd':
FindAllGeneMarkers.SingleCellExperiment
  Code: function(object, clustering.type, test, log2fc.threshold,
                 min.pct, min.diff.pct, min.cells.group,
                 max.cells.per.cluster, return.thresh, only.pos)
  Docs: function(object, clustering.type, test, log2fc.threshold,
                 min.pct, min.diff.pct, min.cells.group,
                 max.cells.per.cluster, pseudocount.use, return.thresh,
                 only.pos)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 9 Code: return.thresh Docs: pseudocount.use
    Position: 10 Code: only.pos Docs: return.thresh
\S4method{FindAllGeneMarkers}{SingleCellExperiment}
  Code: function(object, clustering.type = "manual", test = "wilcox",
                 log2fc.threshold = 0.25, min.pct = 0.1, min.diff.pct =
                 NULL, min.cells.group = 3, max.cells.per.cluster =
                 NULL, return.thresh = 0.01, only.pos = FALSE)
  Docs: function(object, clustering.type = "manual", test = "wilcox",
                 log2fc.threshold = 0.25, min.pct = 0.1, min.diff.pct =
                 NULL, min.cells.group = 3, max.cells.per.cluster =
                 NULL, pseudocount.use = 1, return.thresh = 0.01,
                 only.pos = FALSE)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 9 Code: return.thresh Docs: pseudocount.use
    Position: 10 Code: only.pos Docs: return.thresh

Codoc mismatches from Rd file 'FindGeneMarkers.Rd':
FindGeneMarkers.SingleCellExperiment
  Code: function(object, clusters.1, clusters.2, clustering.type, test,
                 logfc.threshold, min.pct, min.diff.pct,
                 min.cells.group, max.cells.per.cluster, return.thresh,
                 only.pos)
  Docs: function(object, clusters.1, clusters.2, clustering.type, test,
                 logfc.threshold, min.pct, min.diff.pct,
                 min.cells.group, max.cells.per.cluster,
                 pseudocount.use, return.thresh, only.pos)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 11 Code: return.thresh Docs: pseudocount.use
    Position: 12 Code: only.pos Docs: return.thresh
\S4method{FindGeneMarkers}{SingleCellExperiment}
  Code: function(object, clusters.1 = NULL, clusters.2 = NULL,
                 clustering.type = "", test = "wilcox", logfc.threshold
                 = 0.25, min.pct = 0.1, min.diff.pct = NULL,
                 min.cells.group = 3, max.cells.per.cluster = NULL,
                 return.thresh = 0.01, only.pos = FALSE)
  Docs: function(object, clusters.1 = NULL, clusters.2 = NULL,
                 clustering.type = "", test = "wilcox", logfc.threshold
                 = 0.25, min.pct = 0.1, min.diff.pct = NULL,
                 min.cells.group = 3, max.cells.per.cluster = NULL,
                 pseudocount.use = 1, return.thresh = 0.01, only.pos =
                 FALSE)
  Argument names in docs not in code:
    pseudocount.use
  Mismatches in argument names:
    Position: 11 Code: return.thresh Docs: pseudocount.use
    Position: 12 Code: only.pos Docs: return.thresh

Codoc mismatches from Rd file 'RunICP.Rd':
RunICP
  Code: function(normalized.data = NULL, k = 15, d = 0.3, r = 5, C = 5,
                 reg.type = "L1", max.iter = 200, icp.batch.size = Inf)
  Docs: function(normalized.data = NULL, k = 15, d = 0.3, r = 5, C = 5,
                 reg.type = "L1", max.iter = 200)
  Argument names in code not in docs:
    icp.batch.size

Codoc mismatches from Rd file 'RunParallelICP.Rd':
RunParallelICP.SingleCellExperiment
  Code: function(object, k, d, L, r, C, reg.type, max.iter, threads,
                 icp.batch.size)
  Docs: function(object, k, d, L, r, C, reg.type, max.iter, threads)
  Argument names in code not in docs:
    icp.batch.size
\S4method{RunParallelICP}{SingleCellExperiment}
  Code: function(object, k = 15, d = 0.3, L = 200, r = 5, C = 0.3,
                 reg.type = "L1", max.iter = 200, threads = 0,
                 icp.batch.size = Inf)
  Docs: function(object, k = 15, d = 0.3, L = 200, r = 5, C = 0.3,
                 reg.type = "L1", max.iter = 200, threads = 0)
  Argument names in code not in docs:
    icp.batch.size

* 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 LazyData ... 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
FindAllGeneMarkers     24.588  1.461  31.579
SelectTopGenes         21.918  1.252  27.426
ClusteringScatterPlot  16.032  0.946  20.297
GeneHeatmap            15.097  1.087  18.822
AnnotationScatterPlot  13.936  0.882  17.631
GeneScatterPlot        13.858  0.825  17.745
RunUMAP                11.244  0.929  14.555
FindGeneMarkers        10.550  0.877  13.528
VlnPlot                 8.810  0.885  11.494
RunTSNE                 8.581  0.921  10.880
CalcSilhInfo            8.457  0.770  11.145
PCAElbowPlot            7.288  0.774   9.198
SilhouetteCurve         7.199  0.789   9.439
HierarchicalClustering  7.014  0.658   8.909
RunPCA                  6.897  0.775   8.748
RenameCluster           6.455  0.830   8.243
SelectKClusters         6.530  0.715   8.525
MergeClusters           6.506  0.737   8.355
RenameAllClusters       6.429  0.682   8.171
RunParallelICP          6.202  0.778   7.892
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/ILoReg.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ILoReg
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ILoReg’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ILoReg)