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### Running command:
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### /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_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ILoReg.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ILoReg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ILoReg’ version ‘1.12.1’
* 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 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 18.944 2.090 21.199
SelectTopGenes 18.120 1.463 19.589
ClusteringScatterPlot 14.969 1.901 17.148
AnnotationScatterPlot 14.186 1.850 16.264
GeneHeatmap 13.332 1.913 15.334
GeneScatterPlot 12.321 1.696 14.128
FindGeneMarkers 9.896 1.647 11.652
RunUMAP 9.896 1.419 11.374
RunTSNE 8.874 1.134 10.118
CalcSilhInfo 8.623 1.352 10.060
PCAElbowPlot 8.272 1.649 9.974
VlnPlot 8.199 1.623 9.856
SilhouetteCurve 8.137 1.512 9.652
RenameAllClusters 7.622 1.610 9.265
MergeClusters 7.607 1.472 9.092
RunPCA 7.434 1.563 9.042
HierarchicalClustering 7.679 1.282 8.991
RenameCluster 7.333 1.526 8.927
RunParallelICP 7.339 1.449 8.809
SelectKClusters 7.600 1.127 8.731
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc-mac-arm64/meat/ILoReg.Rcheck/00check.log’
for details.
