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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ILoReg.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ILoReg_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ILoReg.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.9.0’
* 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 documentation object 'FindAllGeneMarkers':
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 documentation object 'FindGeneMarkers':
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 documentation object 'RunICP':
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 documentation object 'RunParallelICP':
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     27.072  0.315  30.717
SelectTopGenes         25.263  0.167  27.227
AnnotationScatterPlot  19.267  0.116  21.487
ClusteringScatterPlot  18.528  0.040  20.109
GeneHeatmap            18.205  0.235  18.902
GeneScatterPlot        17.356  0.096  19.176
FindGeneMarkers        13.840  0.088  14.533
CalcSilhInfo           13.271  0.104  15.676
RunTSNE                13.024  0.028  13.240
RunUMAP                12.997  0.012  13.024
VlnPlot                11.830  0.009  11.839
RenameCluster          11.470  0.008  11.492
SilhouetteCurve        11.453  0.020  11.483
HierarchicalClustering 10.759  0.016  11.397
PCAElbowPlot           10.759  0.008  10.770
RunPCA                 10.723  0.000  10.980
MergeClusters          10.689  0.016  11.942
RenameAllClusters      10.645  0.009  10.655
RunParallelICP         10.546  0.008  10.560
SelectKClusters        10.301  0.000  10.592
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ILoReg.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ILoReg.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ILoReg
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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)