Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-18 18:00 -0400 (Tue, 18 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1024/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ILoReg 1.14.0 (landing page) Johannes Smolander
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the ILoReg package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ILoReg.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: ILoReg |
Version: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2024-06-17 06:36:45 -0400 (Mon, 17 Jun 2024) |
EndedAt: 2024-06-17 06:48:36 -0400 (Mon, 17 Jun 2024) |
EllapsedTime: 711.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ILoReg.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ILoReg.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ILoReg/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ILoReg’ version ‘1.14.0’ * 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 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 24.370 1.445 30.818 SelectTopGenes 20.814 1.315 25.605 ClusteringScatterPlot 16.763 0.939 21.210 GeneHeatmap 15.302 1.098 19.795 GeneScatterPlot 15.187 1.044 19.629 AnnotationScatterPlot 14.830 0.927 18.457 RunUMAP 11.114 1.034 14.664 FindGeneMarkers 11.001 0.897 14.395 CalcSilhInfo 9.856 0.977 13.165 RunTSNE 8.880 0.756 11.521 VlnPlot 8.590 0.820 11.480 SilhouetteCurve 8.293 1.008 10.864 SelectKClusters 7.444 0.816 10.073 RenameAllClusters 7.364 0.765 9.771 RunParallelICP 7.046 0.744 9.607 PCAElbowPlot 6.858 0.775 9.180 RenameCluster 6.704 0.812 9.048 MergeClusters 6.629 0.871 9.127 RunPCA 6.448 0.829 8.951 HierarchicalClustering 6.474 0.707 8.544 * 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: 1 WARNING See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ILoReg.Rcheck/00check.log’ for details.
ILoReg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ILoReg ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ILoReg’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ILoReg)
ILoReg.Rcheck/ILoReg-Ex.timings
name | user | system | elapsed | |
AnnotationScatterPlot | 14.830 | 0.927 | 18.457 | |
CalcSilhInfo | 9.856 | 0.977 | 13.165 | |
ClusteringScatterPlot | 16.763 | 0.939 | 21.210 | |
FindAllGeneMarkers | 24.370 | 1.445 | 30.818 | |
FindGeneMarkers | 11.001 | 0.897 | 14.395 | |
GeneHeatmap | 15.302 | 1.098 | 19.795 | |
GeneScatterPlot | 15.187 | 1.044 | 19.629 | |
HierarchicalClustering | 6.474 | 0.707 | 8.544 | |
MergeClusters | 6.629 | 0.871 | 9.127 | |
PCAElbowPlot | 6.858 | 0.775 | 9.180 | |
PrepareILoReg | 0.885 | 0.027 | 1.155 | |
RenameAllClusters | 7.364 | 0.765 | 9.771 | |
RenameCluster | 6.704 | 0.812 | 9.048 | |
RunPCA | 6.448 | 0.829 | 8.951 | |
RunParallelICP | 7.046 | 0.744 | 9.607 | |
RunTSNE | 8.880 | 0.756 | 11.521 | |
RunUMAP | 11.114 | 1.034 | 14.664 | |
SelectKClusters | 7.444 | 0.816 | 10.073 | |
SelectTopGenes | 20.814 | 1.315 | 25.605 | |
SilhouetteCurve | 8.293 | 1.008 | 10.864 | |
VlnPlot | 8.59 | 0.82 | 11.48 | |
pbmc3k_500 | 0.003 | 0.002 | 0.008 | |