############################################################################## ############################################################################## ### ### 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_1.12.1.tar.gz ### ############################################################################## ############################################################################## * 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.