Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 620/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DOtools 0.99.11 (landing page) Mariano Ruz Jurado
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DOtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DOtools.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: DOtools |
Version: 0.99.11 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DOtools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DOtools_0.99.11.tar.gz |
StartedAt: 2025-10-17 08:26:18 -0000 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 08:38:14 -0000 (Fri, 17 Oct 2025) |
EllapsedTime: 716.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DOtools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DOtools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DOtools_0.99.11.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DOtools.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DOtools/DESCRIPTION’ ... OK * this is package ‘DOtools’ version ‘0.99.11’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 35 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DOtools’ 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DO.Integration 29.179 0.707 29.965 DO.CellComposition 19.805 0.665 16.679 DO.enrichR 9.404 0.753 40.512 DO.SplitBarGSEA 8.862 0.456 22.525 DO.MultiDGE 7.817 0.164 8.005 DO.CellTypist 6.196 0.616 35.266 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/DOtools.Rcheck/00check.log’ for details.
DOtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DOtools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘DOtools’ ... ** this is package ‘DOtools’ version ‘0.99.11’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (DOtools)
DOtools.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(DOtools) > > test_check("DOtools") Loading required package: SeuratObject Loading required package: sp 'SeuratObject' was built with package 'Matrix' 1.7.3 but the current version is 1.7.4; it is recomended that you reinstall 'SeuratObject' as the ABI for 'Matrix' may have changed Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:sp': %over% Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'SummarizedExperiment' The following object is masked from 'package:Seurat': Assays The following object is masked from 'package:SeuratObject': Assays Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Using condition, orig.ident as id variables Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables 2025-10-17 08:36:13 - ListTest empty, comparing every sample with each other Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables 2025-10-17 08:36:14 - ListTest empty, comparing every sample with each other Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Using condition, orig.ident as id variables Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables 2025-10-17 08:36:28 - ListTest empty, comparing every sample with each other Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using condition, orig.ident as id variables Using condition, orig.ident as id variables Using group, cluster as id variables 2025-10-17 08:36:31 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:33 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster, celltype as id variables 2025-10-17 08:36:34 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:36 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:39 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:41 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:43 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:43 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. The following grouping variables have 1 value and will be ignored: celltype Using group, cluster, celltype as id variables 2025-10-17 08:36:46 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster, celltype as id variables 2025-10-17 08:36:49 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:51 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Using group, cluster as id variables 2025-10-17 08:36:52 - ListTest empty, comparing every sample with each other Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:GenomicRanges': intersect, setdiff, union The following object is masked from 'package:Seqinfo': intersect The following objects are masked from 'package:IRanges': collapse, desc, intersect, setdiff, slice, union The following objects are masked from 'package:S4Vectors': first, intersect, rename, setdiff, setequal, union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, setequal, union The following object is masked from 'package:generics': explain The following object is masked from 'package:matrixStats': count The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Using orig.ident, condition as id variables Using condition as id variables Using orig.ident, condition as id variables Using condition as id variables Using orig.ident, condition as id variables Using condition as id variables 2025-10-17 08:36:58 - Bootstrapping method activated with 5 simulated replicates! . Using orig.ident, condition as id variables Using condition as id variables Using orig.ident, condition as id variables Using condition as id variables Using orig.ident, condition as id variables Using condition as id variables Using orig.ident, condition as id variables Using condition as id variables Using orig.ident, condition as id variables Using condition as id variables 2025-10-17 08:37:05 - Running celltypist using model: Healthy_Adult_Heart.pkl 2025-10-17 08:37:05 - Saving celltypist results to temporary folder: /home/biocbuild/tmp/RtmpW6t20C/file1f4de33a1ada61 2025-10-17 08:37:06 - Creating probality plot Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. Scale for fill is already present. Adding another scale for fill, which will replace the existing scale. 2025-10-17 08:37:08 - pattern: ^scale\.data\. 2025-10-17 08:37:08 - is removed. 2025-10-17 08:37:08 - pattern: ^none$ 2025-10-17 08:37:08 - Object has no layers, pattern does not need to be removed from layers. For a (much!) faster implementation of the Wilcoxon Rank Sum Test, (default method for FindMarkers) please install the presto package -------------------------------------------- install.packages('devtools') devtools::install_github('immunogenomics/presto') -------------------------------------------- After installation of presto, Seurat will automatically use the more efficient implementation (no further action necessary). This message will be shown once per session Calculating cluster A Calculating cluster B Calculating cluster C Calculating cluster A Calculating cluster B Calculating cluster C Calculating cluster A Calculating cluster B Calculating cluster C Calculating cluster A Calculating cluster B Calculating cluster C Calculating cluster healthy Calculating cluster disease Calculating cluster A Calculating cluster B Calculating cluster C Calculating cluster A Calculating cluster B Calculating cluster C 2025-10-17 08:37:16 - group_fc_ident_2 is set to NULL, using: healthy 2025-10-17 08:37:16 - group_fc_ident_1 is set to NULL, using: disease 2025-10-17 08:37:20 - Sample: sample1 2025-10-17 08:37:20 - Read matrix 2025-10-17 08:37:21 - Create Single Cell Object 2025-10-17 08:37:21 - Setting condition in object to: sample1 2025-10-17 08:37:21 - Get Mitochondrial+Ribosomal content 2025-10-17 08:37:21 - Create QC images 2025-10-17 08:37:28 - Running Normalisation 2025-10-17 08:37:30 - Running Variable Gene Detection 2025-10-17 08:37:30 - Merging objects 2025-10-17 08:37:30 - Running ScaleData Centering and scaling data matrix | | | 0% | |======================================================================| 100% 2025-10-17 08:37:30 - Run PCA Splitting 'counts', 'data' layers. Not splitting 'scale.data'. If you would like to split other layers, set in `layers` argument. 2025-10-17 08:37:30 - Sample: sample2 2025-10-17 08:37:30 - Read matrix 2025-10-17 08:37:30 - Create Single Cell Object 2025-10-17 08:37:30 - Setting condition in object to: sample2 2025-10-17 08:37:30 - Get Mitochondrial+Ribosomal content 2025-10-17 08:37:30 - Create QC images 2025-10-17 08:37:35 - Running Normalisation 2025-10-17 08:37:37 - Running Variable Gene Detection 2025-10-17 08:37:37 - Merging objects 2025-10-17 08:37:37 - Running ScaleData Centering and scaling data matrix | | | 0% | |======================================================================| 100% 2025-10-17 08:37:37 - Run PCA 2025-10-17 08:37:37 - Splitting object for integration with CCAIntegration by orig.ident 2025-10-17 08:37:37 - Calculating highly variable genes 2025-10-17 08:37:38 - Scaling object 2025-10-17 08:37:38 - Running pca, saved in key: PCA 2025-10-17 08:37:38 - Running integration, saved in key: INTEGRATED.CCA 2025-10-17 08:37:38 - Running Nearest-neighbor graph construction 2025-10-17 08:37:38 - Running cluster detection 2025-10-17 08:37:38 - Creating UMAP 2025-10-17 08:37:38 - Splitting object for integration with CCAIntegration by orig.ident 2025-10-17 08:37:38 - Calculating highly variable genes 2025-10-17 08:37:38 - Scaling object 2025-10-17 08:37:38 - Running pca, saved in key: PCA 2025-10-17 08:37:38 - Running integration, saved in key: INTEGRATED.CCA 2025-10-17 08:37:38 - Running integration, saved in key: INTEGRATED.CCA 2025-10-17 08:37:38 - Splitting object for integration with CCAIntegration by orig.ident 2025-10-17 08:37:38 - Calculating highly variable genes 2025-10-17 08:37:38 - Running integration, saved in key: INTEGRATED.CCA 2025-10-17 08:37:38 - Creating conda environment for DOtools 2025-10-17 08:37:38 - Python packages ready for DOtools! 2025-10-17 08:37:38 - Creating conda environment for DOtools 2025-10-17 08:37:40 - Specified 'ident_name': expecting a categorical variable. 2025-10-17 08:37:41 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >3329 2025-10-17 08:37:42 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = <3329 2025-10-17 08:37:43 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = <=2812 2025-10-17 08:37:44 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >=4083 2025-10-17 08:37:44 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >2812 <4083 2025-10-17 08:37:45 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = <5586 >2410 2025-10-17 08:37:47 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >999999 2025-10-17 08:37:47 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = !=5 2025-10-17 08:37:47 - Specified 'ident_name': expecting a categorical variable. 2025-10-17 08:37:48 - Specified 'ident_name': expecting a categorical variable. SeuV5 TRUE, if object Seuratv4 or below change SeuV5 to FALSE This message is displayed once per session. Using group, orig.ident as id variables Using group, orig.ident, cell_type as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Class of result: ggplot2::ggplot ggplot ggplot2::gg S7_object gg Type of result: object Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables 2025-10-17 08:38:05 - ListTest empty, comparing every sample with each other Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident, cell_type as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Using group, orig.ident as id variables Downloading data to /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810 Downloading healthy filtered to /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/healthy/outs/filtered_feature_bc_matrix.h5 Mock download https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_10k_protein_v3/pbmc_10k_protein_v3_filtered_feature_bc_matrix.h5 -> /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/healthy/outs/filtered_feature_bc_matrix.h5 Downloading healthy raw to /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/healthy/outs/raw_feature_bc_matrix.h5 Mock download https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_10k_protein_v3/pbmc_10k_protein_v3_raw_feature_bc_matrix.h5 -> /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/healthy/outs/raw_feature_bc_matrix.h5 Downloading disease filtered to /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/disease/outs/filtered_feature_bc_matrix.h5 Mock download https://cf.10xgenomics.com/samples/cell-exp/3.0.0/malt_10k_protein_v3/malt_10k_protein_v3_filtered_feature_bc_matrix.h5 -> /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/disease/outs/filtered_feature_bc_matrix.h5 Downloading disease raw to /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/disease/outs/raw_feature_bc_matrix.h5 Mock download https://cf.10xgenomics.com/samples/cell-exp/3.0.0/malt_10k_protein_v3/malt_10k_protein_v3_raw_feature_bc_matrix.h5 -> /home/biocbuild/tmp/RtmpW6t20C/dotools_test_1f4de3740a4810/disease/outs/raw_feature_bc_matrix.h5 [ FAIL 0 | WARN 90 | SKIP 0 | PASS 233 ] [ FAIL 0 | WARN 90 | SKIP 0 | PASS 233 ] > > proc.time() user system elapsed 133.564 6.305 141.396
DOtools.Rcheck/DOtools-Ex.timings
name | user | system | elapsed | |
DO.BarplotClustert | 2.366 | 0.032 | 2.409 | |
DO.BarplotWilcox | 3.402 | 0.095 | 3.507 | |
DO.BoxPlot | 3.757 | 0.148 | 3.924 | |
DO.CellBender | 0.000 | 0.000 | 0.001 | |
DO.CellComposition | 19.805 | 0.665 | 16.679 | |
DO.CellTypist | 6.196 | 0.616 | 35.266 | |
DO.Correlation | 3.057 | 0.351 | 3.417 | |
DO.DietSCE | 1.585 | 0.084 | 1.673 | |
DO.Dotplot | 2.714 | 0.231 | 2.953 | |
DO.FullRecluster | 3.856 | 0.136 | 4.013 | |
DO.Heatmap | 2.951 | 0.083 | 3.168 | |
DO.Import | 0 | 0 | 0 | |
DO.Integration | 29.179 | 0.707 | 29.965 | |
DO.MultiDGE | 7.817 | 0.164 | 8.005 | |
DO.PyEnv | 0.007 | 0.005 | 0.011 | |
DO.SplitBarGSEA | 8.862 | 0.456 | 22.525 | |
DO.Subset | 0.272 | 0.020 | 0.294 | |
DO.TransferLabel | 2.689 | 0.291 | 2.989 | |
DO.UMAP | 4.201 | 0.255 | 4.472 | |
DO.VlnPlot | 2.266 | 0.056 | 2.329 | |
DO.enrichR | 9.404 | 0.753 | 40.512 | |
DO.scVI | 0 | 0 | 0 | |