############################################################################## ############################################################################## ### ### 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/site-library --timings ILoReg_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ILoReg.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 17.253 0.616 17.868 SelectTopGenes 16.040 0.240 16.280 AnnotationScatterPlot 12.741 0.496 13.237 ClusteringScatterPlot 11.764 0.232 11.996 GeneHeatmap 11.711 0.260 11.971 GeneScatterPlot 10.516 0.148 10.665 CalcSilhInfo 9.735 0.276 10.011 FindGeneMarkers 9.454 0.192 9.647 RunUMAP 9.087 0.060 9.147 RunTSNE 8.018 0.056 8.073 SilhouetteCurve 7.637 0.040 7.676 PCAElbowPlot 7.413 0.080 7.495 VlnPlot 7.448 0.040 7.489 RenameCluster 7.249 0.076 7.324 MergeClusters 6.760 0.044 6.804 RenameAllClusters 6.559 0.124 6.683 HierarchicalClustering 6.604 0.060 6.664 SelectKClusters 6.516 0.036 6.552 RunPCA 6.387 0.017 6.404 RunParallelICP 6.351 0.032 6.384 * 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 ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘ILoReg.Rmd’ using rmarkdown Error: processing vignette 'ILoReg.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ --- failed re-building ‘ILoReg.Rmd’ SUMMARY: processing the following file failed: ‘ILoReg.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING See ‘/home/biocbuild/bbs-3.17-bioc/meat/ILoReg.Rcheck/00check.log’ for details.