############################################################################## ############################################################################## ### ### 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ILoReg.Rcheck’ * using R version 4.3.1 (2023-06-16) * 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 Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ILoReg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ILoReg’ version ‘1.10.0’ * 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 20.952 0.636 33.125 SelectTopGenes 17.518 0.514 25.746 ClusteringScatterPlot 15.045 0.407 23.662 GeneHeatmap 14.307 0.442 22.436 AnnotationScatterPlot 13.755 0.454 21.750 GeneScatterPlot 12.053 0.351 18.852 FindGeneMarkers 11.012 0.351 17.411 RunUMAP 10.122 0.268 15.855 CalcSilhInfo 9.608 0.333 15.244 RunTSNE 9.331 0.312 14.817 VlnPlot 8.847 0.255 13.901 SilhouetteCurve 8.368 0.367 12.689 MergeClusters 8.466 0.250 13.372 RunPCA 8.462 0.251 13.354 PCAElbowPlot 8.133 0.254 12.884 HierarchicalClustering 8.010 0.265 12.720 SelectKClusters 7.972 0.289 12.754 RenameAllClusters 7.987 0.242 12.589 RenameCluster 7.953 0.241 12.578 RunParallelICP 7.816 0.243 12.371 * 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-3.17-bioc-mac-arm64/meat/ILoReg.Rcheck/00check.log’ for details.