| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 495/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoPipeline 1.6.0 (landing page) Philippe Hauchamps
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CytoPipeline package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoPipeline.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: CytoPipeline |
| Version: 1.6.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CytoPipeline_1.6.0.tar.gz |
| StartedAt: 2025-04-01 05:35:39 -0000 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 05:40:57 -0000 (Tue, 01 Apr 2025) |
| EllapsedTime: 318.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoPipeline.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CytoPipeline_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CytoPipeline.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘CytoPipeline/DESCRIPTION’ ... OK
* this is package ‘CytoPipeline’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CytoPipeline’ 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
execute 38.021 0.962 39.076
interactingWithCytoPipelineCache 20.246 0.315 20.613
inspectCytoPipelineObjects 13.636 0.256 13.925
ggplotEvents 5.995 0.071 6.078
* 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-3.20-bioc/meat/CytoPipeline.Rcheck/00check.log’
for details.
CytoPipeline.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CytoPipeline ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’ * installing *source* package ‘CytoPipeline’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CytoPipeline)
CytoPipeline.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
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.
> # CytoPipeline - Copyright (C) <2022-2024>
> # <Université catholique de Louvain (UCLouvain), Belgique>
> #
> # Description and complete License: see LICENSE file.
> #
> # This program (CytoPipeline) is free software:
> # you can redistribute it and/or modify it under the terms of the GNU General
> # Public License as published by the Free Software Foundation,
> # either version 3 of the License, or (at your option) any later version.
> #
> # This program is distributed in the hope that it will be useful,
> # but WITHOUT ANY WARRANTY; without even the implied warranty of
> # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> # GNU General Public License for more details (<http://www.gnu.org/licenses/>).
>
> library(testthat)
> library(CytoPipeline)
>
> # launch unit tests
> test_check("CytoPipeline")
Pipeline object for flow cytometry experiment: OMIP021_PeacoQC
No sample file
No pheno data
Scale transformations evaluation queue has no processing step
Flow frames pre-processing evaluation queue has no processing step
Pipeline object for flow cytometry experiment: OMIP021_PeacoQC
Sample files: 2 sample file(s)
No pheno data
Scale transformations evaluation queue has no processing step
Flow frames pre-processing evaluation queue has no processing step
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [scale_transform_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with phenoData ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with phenoData: found in cache => updating it!
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor1.fcs
Calculating peaks
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|++++++++ | 15%
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|++++++++++ | 20%
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|++++++++++++ | 25%
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|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
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|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
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|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
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|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 30.75% of the measurements
The algorithm removed 30.75% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor2.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
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|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 24.38% of the measurements
The algorithm removed 24.38% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
Proceeding with step 3 [compensate]: found in cache!
Proceeding with step 4 [flowframe_aggregate]: found in cache!
Proceeding with step 5 [scale_transform_estimate]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
Proceeding with step 3 [compensate]: found in cache!
Proceeding with step 4 [remove_doublets]: found in cache!
Proceeding with step 5 [remove_debris]: found in cache!
Proceeding with step 6 [remove_dead_cells]: found in cache!
Proceeding with step 7 [perform_QC]: found in cache!
Proceeding with step 8 [transform]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
Proceeding with step 3 [compensate]: found in cache!
Proceeding with step 4 [remove_doublets]: found in cache!
Proceeding with step 5 [remove_debris]: found in cache!
Proceeding with step 6 [remove_dead_cells]: found in cache!
Proceeding with step 7 [perform_QC]: found in cache!
Proceeding with step 8 [transform]: found in cache!
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor1.fcs
Calculating peaks
|
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|++ | 5%
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|+++++ | 10%
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|++++++++ | 15%
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|++++++++++ | 20%
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|++++++++++++ | 25%
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|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
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|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
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|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 30.75% of the measurements
The algorithm removed 30.75% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor2.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
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|++++++++++++ | 25%
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|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
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|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 24.38% of the measurements
The algorithm removed 24.38% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor1.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
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|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 30.75% of the measurements
The algorithm removed 30.75% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [remove_doublets] ...
Proceeding with step 5 [remove_debris] ...
Proceeding with step 6 [remove_dead_cells] ...
Proceeding with step 7 [perform_QC] ...
Applying PeacoQC method...
Starting quality control analysis for Donor2.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
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|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 24.38% of the measurements
The algorithm removed 24.38% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
Proceeding with step 3 [compensate]: found in cache!
Proceeding with step 4 [flowframe_aggregate]: found in cache!
Proceeding with step 5 [scale_transform_estimate]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
Proceeding with step 3 [compensate]: found in cache!
Proceeding with step 4 [remove_doublets]: found in cache!
Proceeding with step 5 [remove_debris]: found in cache!
Proceeding with step 6 [remove_dead_cells]: found in cache!
Proceeding with step 7 [perform_QC]: found in cache!
Proceeding with step 8 [transform]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
Proceeding with step 3 [compensate]: found in cache!
Proceeding with step 4 [remove_doublets]: found in cache!
Proceeding with step 5 [remove_debris]: found in cache!
Proceeding with step 6 [remove_dead_cells]: found in cache!
Proceeding with step 7 [perform_QC]: found in cache!
Proceeding with step 8 [transform]: found in cache!
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor2.fcs
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor2.fcs
no sample file passed as argument => defaulting to first sample file
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/R/R-4.4.3/site-library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
no sample file passed as argument => defaulting to first sample file
Object of class "CytoProcessingStep"
Name: summing step
Function: user-provided function
COL NAMES MARKER MAPPING: Channel, Marker, Used
COL NAMES MARKER MAPPING: Channel, Marker, Used
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Applying PeacoQC method...
Starting quality control analysis for Donor1.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
Applying flowAI method...
Quality control for the file: Donor1
49% of anomalous cells detected in the flow rate check.
0% of anomalous cells detected in signal acquisition check.
3% of anomalous cells detected in the dynamic range check.
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 248 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-gating.R:42:5', 'test-ggplots.R:185:5',
'test-ggplots.R:310:5'
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 248 ]
Deleting unused snapshots:
• gating/singletsgate-default-channels-with-fixed-nmad.svg
• gating/singletsgate-selected-channels.svg
• gating/singletsgates-one-after-the-other-fig1.svg
• gating/singletsgates-one-after-the-other-fig2.svg
• ggplots/ggplotevents-2d-x-linear-y-logicle.svg
• ggplots/ggplotevents-2d-x-logicle-y-linear.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-bins.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-by-markers.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-not-run.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg
• ggplots/ggplotfilterevents-2d-5000-points.svg
• ggplots/ggplotfilterevents-2d-all-points-interactive.svg
• ggplots/ggplotfilterevents-2d-infinite-nb-of-points.svg
• ggplots/ggplotfilterevents-2d-small-size.svg
• ggplots/ggplotfilterevents-2d-translist-not-run.svg
• ggplots/ggplotfilterevents-2d-translist-run.svg
>
> proc.time()
user system elapsed
98.115 2.201 113.732
CytoPipeline.Rcheck/CytoPipeline-Ex.timings
| name | user | system | elapsed | |
| CytoPipelineClass | 0.048 | 0.000 | 0.048 | |
| CytoProcessingStep | 0.006 | 0.000 | 0.006 | |
| aggregateAndSample | 0.240 | 0.012 | 0.253 | |
| appendCellID | 0.152 | 0.000 | 0.153 | |
| applyScaleTransforms | 0.312 | 0.000 | 0.313 | |
| areFluoCols | 0.160 | 0.012 | 0.171 | |
| areSignalCols | 0.160 | 0.000 | 0.161 | |
| compensateFromMatrix | 2.008 | 0.088 | 2.108 | |
| computeScatterChannelsLinearScale | 0.232 | 0.004 | 0.237 | |
| estimateScaleTransforms | 0.253 | 0.000 | 0.254 | |
| execute | 38.021 | 0.962 | 39.076 | |
| exportCytoPipeline | 0.019 | 0.000 | 0.019 | |
| findTimeChannel | 0.152 | 0.000 | 0.153 | |
| getAcquiredCompensationMatrix | 0.09 | 0.00 | 0.09 | |
| getChannelNamesFromMarkers | 0.134 | 0.004 | 0.139 | |
| getFCSFileName | 0.142 | 0.000 | 0.142 | |
| getTransfoParams | 0.145 | 0.000 | 0.146 | |
| ggplotEvents | 5.995 | 0.071 | 6.078 | |
| ggplotFilterEvents | 0.899 | 0.008 | 0.908 | |
| ggplotFlowRate | 1.357 | 0.016 | 1.375 | |
| handlingProcessingSteps | 0.007 | 0.000 | 0.007 | |
| inspectCytoPipelineObjects | 13.636 | 0.256 | 13.925 | |
| interactingWithCytoPipelineCache | 20.246 | 0.315 | 20.613 | |
| qualityControlFlowAI | 1.584 | 0.012 | 1.601 | |
| qualityControlPeacoQC | 1.045 | 0.000 | 1.048 | |
| readRDSObject | 0.304 | 0.004 | 0.308 | |
| readSampleFiles | 0.104 | 0.004 | 0.109 | |
| removeChannels | 0.172 | 0.004 | 0.176 | |
| removeDeadCellsManualGate | 0.158 | 0.004 | 0.163 | |
| removeDebrisManualGate | 0.145 | 0.004 | 0.150 | |
| removeDoubletsCytoPipeline | 0.204 | 0.000 | 0.204 | |
| removeMarginsPeacoQC | 0.328 | 0.004 | 0.333 | |
| resetCellIDs | 0.171 | 0.000 | 0.172 | |
| runCompensation | 0.187 | 0.000 | 0.187 | |
| singletsGate | 1.206 | 0.008 | 1.217 | |
| subsample | 0.184 | 0.000 | 0.184 | |
| updateMarkerName | 0.184 | 0.000 | 0.183 | |
| writeFlowFrame | 0.275 | 0.000 | 0.275 | |