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).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 620/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOtools 0.99.11  (landing page)
Mariano Ruz Jurado
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/DOtools
git_branch: devel
git_last_commit: 95e75ee
git_last_commit_date: 2025-10-09 05:46:33 -0400 (Thu, 09 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DOtools on taishan

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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 

Example timings

DOtools.Rcheck/DOtools-Ex.timings

nameusersystemelapsed
DO.BarplotClustert2.3660.0322.409
DO.BarplotWilcox3.4020.0953.507
DO.BoxPlot3.7570.1483.924
DO.CellBender0.0000.0000.001
DO.CellComposition19.805 0.66516.679
DO.CellTypist 6.196 0.61635.266
DO.Correlation3.0570.3513.417
DO.DietSCE1.5850.0841.673
DO.Dotplot2.7140.2312.953
DO.FullRecluster3.8560.1364.013
DO.Heatmap2.9510.0833.168
DO.Import000
DO.Integration29.179 0.70729.965
DO.MultiDGE7.8170.1648.005
DO.PyEnv0.0070.0050.011
DO.SplitBarGSEA 8.862 0.45622.525
DO.Subset0.2720.0200.294
DO.TransferLabel2.6890.2912.989
DO.UMAP4.2010.2554.472
DO.VlnPlot2.2660.0562.329
DO.enrichR 9.404 0.75340.512
DO.scVI000