##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DOtools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DOtools_0.99.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DOtools.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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     25.919  0.304  26.234
DO.CellComposition 10.269  5.115  10.603
DO.MultiDGE         7.252  0.026   7.279
DO.SplitBarGSEA     6.935  0.053  10.760
DO.enrichR          6.700  0.088  10.258
DO.CellTypist       4.997  0.722  18.732
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘DOtools.Rmd’ using rmarkdown

                    oooo  oooo      .                           o8o               .
                     888   888    .o8                           `"'             .o8
 .ooooo.   .ooooo.   888   888  .o888oo oooo    ooo oo.ooooo.  oooo   .oooo.o .o888oo
d88'  "Y8 d88   88b  888   888    888     88.  .8    888   88b  888  d88(  "8   888
888       888ooo888  888   888    888      88..8     888   888  888  `"Y88b.    888
888   .o8 888    .o  888   888    888 .    `888'     888   888  888  o.  )88b   888 .
 Y8bod8P  `Y8bod8P' o888o o888o   "888"     .8'      888bod8P' o888o 8""888P'   "888"
                                        .o..P'       888
                                        `Y8P'       o888o             @Teichmann lab
⚙️ Configuration:
	🛠️ indata: /tmp/Rtmpi3TUFD/file154c9a1ed3aaa1/ad.h5ad
	🛠️ model: Healthy_COVID19_PBMC.pkl
	🛠️ transpose-input: False
	🛠️ gene-file: None
	🛠️ cell-file: None
	🛠️ mode: best_match
	🛠️ p-thres: 0.5
	🛠️ majority-voting: True
	🛠️ outdir: /tmp/Rtmpi3TUFD/file154c9a1ed3aaa1
	🛠️ prefix: 
	🛠️ xlsx: False
	🛠️ plot-results: False
	🛠️ quiet: False
	🛠️ over-clustering: leiden0.3
	🛠️ min-prop: 0.0
📁 Input file is '/tmp/Rtmpi3TUFD/file154c9a1ed3aaa1/ad.h5ad'
⏳ Loading data
⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate
🔬 Input data has 2807 cells and 800 genes
🔗 Matching reference genes in the model
🧬 609 features used for prediction
⚖️ Scaling input data
🖋️ Predicting labels
✅ Prediction done!
🗳️ Majority voting the predictions
✅ Majority voting done!
[INFO] Your data doesn't have replicates! Artificial replicates will be simulated to run scanpro.
[INFO] Simulation may take some minutes...
[INFO] Generating 3 replicates and running 100 simulations...
[INFO] Finished 100 simulations in 4.22 seconds

                    oooo  oooo      .                           o8o               .
                     888   888    .o8                           `"'             .o8
 .ooooo.   .ooooo.   888   888  .o888oo oooo    ooo oo.ooooo.  oooo   .oooo.o .o888oo
d88'  "Y8 d88   88b  888   888    888     88.  .8    888   88b  888  d88(  "8   888
888       888ooo888  888   888    888      88..8     888   888  888  `"Y88b.    888
888   .o8 888    .o  888   888    888 .    `888'     888   888  888  o.  )88b   888 .
 Y8bod8P  `Y8bod8P' o888o o888o   "888"     .8'      888bod8P' o888o 8""888P'   "888"
                                        .o..P'       888
                                        `Y8P'       o888o             @Teichmann lab
⚙️ Configuration:
	🛠️ indata: /tmp/Rtmpi3TUFD/file154c9a4c3aeaec/ad.h5ad
	🛠️ model: Healthy_COVID19_PBMC.pkl
	🛠️ transpose-input: False
	🛠️ gene-file: None
	🛠️ cell-file: None
	🛠️ mode: best_match
	🛠️ p-thres: 0.5
	🛠️ majority-voting: True
	🛠️ outdir: /tmp/Rtmpi3TUFD/file154c9a4c3aeaec
	🛠️ prefix: 
	🛠️ xlsx: False
	🛠️ plot-results: False
	🛠️ quiet: False
	🛠️ over-clustering: annotation_recluster
	🛠️ min-prop: 0.0
📁 Input file is '/tmp/Rtmpi3TUFD/file154c9a4c3aeaec/ad.h5ad'
⏳ Loading data
⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate
🔬 Input data has 1799 cells and 800 genes
🔗 Matching reference genes in the model
🧬 609 features used for prediction
⚖️ Scaling input data
🖋️ Predicting labels
✅ Prediction done!
🗳️ Majority voting the predictions
✅ Majority voting done!

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Quitting from DOtools.Rmd:525-547 [GO analysis2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `scan()`:
! line 9 did not have 2 elements
---
Backtrace:
    ▆
 1. └─DOtools::DO.enrichR(...)
 2.   └─enrichR::enrichr(genes = df_up[[gene_column]], databases = go_catgs)
 3.     └─base::lapply(...)
 4.       └─enrichR (local) FUN(X[[i]], ...)
 5.         └─utils::read.table(...)
 6.           └─base::scan(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
line 9 did not have 2 elements
--- failed re-building ‘DOtools.Rmd’

SUMMARY: processing the following file failed:
  ‘DOtools.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DOtools.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DOtools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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

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'

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    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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    IQR, mad, sd, var, xtabs

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    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'

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    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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    %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

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    anyMissing, rowMedians


Attaching package: 'SummarizedExperiment'

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    Assays

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    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
2025-10-24 23:23:44 - 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
2025-10-24 23:23:45 - 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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Using condition, orig.ident as id variables
Normalizing layer: counts
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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
2025-10-24 23:23:58 - 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
2025-10-24 23:24:00 - 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
2025-10-24 23:24:02 - 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
2025-10-24 23:24:03 - 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
2025-10-24 23:24:05 - 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
2025-10-24 23:24:08 - 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
2025-10-24 23:24:09 - 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
2025-10-24 23:24:11 - 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
2025-10-24 23:24:11 - 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
2025-10-24 23:24:14 - 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
2025-10-24 23:24:16 - 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
2025-10-24 23:24:18 - 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
2025-10-24 23:24:19 - 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'

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    combine

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    intersect, setdiff, union

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    intersect

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    collapse, desc, intersect, setdiff, slice, union

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    first, intersect, rename, setdiff, setequal, union

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    combine, intersect, setdiff, setequal, union

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    explain

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    count

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    matches

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    filter, lag

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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
2025-10-24 23:24:23 - 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
2025-10-24 23:24:28 - Running celltypist using model: Healthy_Adult_Heart.pkl
2025-10-24 23:24:28 - Saving celltypist results to temporary folder: /tmp/RtmpV4afpJ/file151daf14b051ca
For native R and reading and writing of H5AD files, an R <AnnData> object, and conversion to <SingleCellExperiment> or <Seurat> objects, check out the anndataR package:
i Install it from Bioconductor with `BiocManager::install("anndataR")`
i See more at <https://bioconductor.org/packages/anndataR/>
This message is displayed once per session.
2025-10-24 23:24:29 - 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.
2025-10-24 23:24:30 - pattern:  ^scale\.data\.
2025-10-24 23:24:30 -  is removed.
2025-10-24 23:24:30 - pattern:  ^none$
2025-10-24 23:24:30 - 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
2025-10-24 23:24:36 - group_fc_ident_2 is set to NULL, using: healthy
2025-10-24 23:24:36 - group_fc_ident_1 is set to NULL, using: disease
2025-10-24 23:24:39 - Sample: sample1
2025-10-24 23:24:39 - Read matrix
2025-10-24 23:24:39 - Create Single Cell Object
2025-10-24 23:24:39 - Setting condition in object to: sample1
2025-10-24 23:24:39 - Get Mitochondrial+Ribosomal content
2025-10-24 23:24:39 - Create QC images
2025-10-24 23:24:45 - Running Normalisation
2025-10-24 23:24:46 - Running Variable Gene Detection
2025-10-24 23:24:46 - Merging objects
2025-10-24 23:24:46 - Running ScaleData
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
2025-10-24 23:24:46 - Run PCA
Splitting 'counts', 'data' layers. Not splitting 'scale.data'. If you would like to split other layers, set in `layers` argument.
2025-10-24 23:24:46 - Sample: sample2
2025-10-24 23:24:46 - Read matrix
2025-10-24 23:24:46 - Create Single Cell Object
2025-10-24 23:24:46 - Setting condition in object to: sample2
2025-10-24 23:24:47 - Get Mitochondrial+Ribosomal content
2025-10-24 23:24:47 - Create QC images
2025-10-24 23:24:50 - Running Normalisation
2025-10-24 23:24:51 - Running Variable Gene Detection
2025-10-24 23:24:51 - Merging objects
2025-10-24 23:24:51 - Running ScaleData
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
2025-10-24 23:24:51 - Run PCA
2025-10-24 23:24:52 - Splitting object for integration with CCAIntegration by orig.ident
2025-10-24 23:24:52 - Calculating highly variable genes
2025-10-24 23:24:52 - Scaling object
2025-10-24 23:24:52 - Running pca, saved in key: PCA
2025-10-24 23:24:52 - Running integration, saved in key: INTEGRATED.CCA
2025-10-24 23:24:52 - Running Nearest-neighbor graph construction
2025-10-24 23:24:52 - Running cluster detection
2025-10-24 23:24:52 - Creating UMAP
2025-10-24 23:24:52 - Splitting object for integration with CCAIntegration by orig.ident
2025-10-24 23:24:52 - Calculating highly variable genes
2025-10-24 23:24:52 - Scaling object
2025-10-24 23:24:52 - Running pca, saved in key: PCA
2025-10-24 23:24:52 - Running integration, saved in key: INTEGRATED.CCA
2025-10-24 23:24:52 - Running integration, saved in key: INTEGRATED.CCA
2025-10-24 23:24:52 - Splitting object for integration with CCAIntegration by orig.ident
2025-10-24 23:24:52 - Calculating highly variable genes
2025-10-24 23:24:52 - Running integration, saved in key: INTEGRATED.CCA
2025-10-24 23:24:52 - Creating conda environment for DOtools
2025-10-24 23:24:52 - Python packages ready for DOtools!
2025-10-24 23:24:52 - Creating conda environment for DOtools
2025-10-24 23:24:54 - Specified 'ident_name': expecting a categorical variable.
2025-10-24 23:24:54 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >3329
2025-10-24 23:24:55 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = <3329
2025-10-24 23:24:56 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = <=2812
2025-10-24 23:24:56 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >=4083
2025-10-24 23:24:57 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >2812 <4083
2025-10-24 23:24:57 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = <5586 >2410
2025-10-24 23:24:58 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = >999999
2025-10-24 23:24:58 - Specified 'ident_thresh': expecting numeric thresholds specified as character, ident_thresh = !=5
2025-10-24 23:24:58 - Specified 'ident_name': expecting a categorical variable.
2025-10-24 23:24:59 - 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
2025-10-24 23:25:12 - 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 /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154
Downloading healthy filtered to /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/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 -> /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/healthy/outs/filtered_feature_bc_matrix.h5 
Downloading healthy raw to /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/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 -> /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/healthy/outs/raw_feature_bc_matrix.h5 
Downloading disease filtered to /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/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 -> /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/disease/outs/filtered_feature_bc_matrix.h5 
Downloading disease raw to /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/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 -> /tmp/RtmpV4afpJ/dotools_test_151daf1ce15154/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 
108.944   2.652 111.337