############################################################################## ############################################################################## ### ### 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_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ILoReg.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ILoReg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ILoReg’ version ‘1.18.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 25 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘ILoReg’ See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ILoReg.Rcheck/00install.out’ for details. * 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 code 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 14.600 1.289 15.950 SelectTopGenes 14.118 1.417 15.556 ClusteringScatterPlot 11.749 1.055 12.904 AnnotationScatterPlot 10.438 0.992 11.510 GeneHeatmap 9.542 1.193 10.776 GeneScatterPlot 8.571 1.082 9.744 RunUMAP 6.528 0.897 7.456 FindGeneMarkers 6.540 0.788 7.358 CalcSilhInfo 6.097 0.968 7.148 RunTSNE 5.620 0.674 6.402 SilhouetteCurve 5.300 0.929 6.257 VlnPlot 5.090 1.093 6.204 RenameAllClusters 4.757 0.917 5.716 MergeClusters 4.783 0.813 5.621 SelectKClusters 4.000 1.507 5.555 RunParallelICP 4.665 0.686 5.370 RenameCluster 3.625 1.568 5.241 PCAElbowPlot 4.030 0.865 5.036 * 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: 2 WARNINGs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ILoReg.Rcheck/00check.log’ for details.