Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 500/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoPipeline 1.4.0  (landing page)
Philippe Hauchamps
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/CytoPipeline
git_branch: RELEASE_3_19
git_last_commit: aa25dc7
git_last_commit_date: 2024-04-30 11:46:57 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CytoPipeline on nebbiolo1

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.

raw results


Summary

Package: CytoPipeline
Version: 1.4.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CytoPipeline_1.4.0.tar.gz
StartedAt: 2024-06-16 22:14:32 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-16 22:19:08 -0400 (Sun, 16 Jun 2024)
EllapsedTime: 276.6 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoPipeline.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CytoPipeline_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CytoPipeline.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CytoPipeline/DESCRIPTION’ ... OK
* this is package ‘CytoPipeline’ version ‘1.4.0’
* 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                          26.456  0.800  27.257
interactingWithCytoPipelineCache 14.681  0.256  14.937
inspectCytoPipelineObjects       10.059  0.191  10.251
qualityControlFlowAI              4.598  0.516   5.115
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/CytoPipeline.Rcheck/00check.log’
for details.


Installation output

CytoPipeline.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CytoPipeline
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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)

Tests output

CytoPipeline.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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.

> # 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/bbs-3.19-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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] ...
Compensating file : Donor1.fcs
Compensating file : Donor2.fcs
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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] ...
Compensating file : Donor1.fcs
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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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/bbs-3.19-bioc/R/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] ...
Compensating file : Donor2.fcs
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

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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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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] ...
Compensating file : Donor1.fcs
Compensating file : Donor2.fcs
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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] ...
Compensating file : Donor1.fcs
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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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/bbs-3.19-bioc/R/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] ...
Compensating file : Donor2.fcs
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

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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] ...
Compensating file : Donor1.fcs
Compensating file : Donor2.fcs
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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] ...
Compensating file : Donor1.fcs
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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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/bbs-3.19-bioc/R/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] ...
Compensating file : Donor2.fcs
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

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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] ...
Compensating file : Donor1.fcs
Compensating file : Donor2.fcs
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/bbs-3.19-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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
Compensating file : Donor1.fcs
Compensating file : Donor1.fcs
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Compensating file : Donor1.fcs
Compensating file : Donor1.fcs
Compensating file : Donor2.fcs
Compensating file : Donor1.fcs
Compensating file : Donor1.fcs
Compensating 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
0% 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. 
Compensating file : Donor1.fcs
Compensating file : Donor2.fcs
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 253 ]

══ 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 253 ]
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 
 69.576   2.768  81.856 

Example timings

CytoPipeline.Rcheck/CytoPipeline-Ex.timings

nameusersystemelapsed
CytoPipelineClass0.0340.0010.035
CytoProcessingStep0.0050.0000.004
aggregateAndSample0.1760.0080.184
appendCellID0.1260.0000.127
applyScaleTransforms0.2170.0120.228
areFluoCols0.1460.0040.149
areSignalCols0.1190.0080.128
compensateFromMatrix1.6440.0441.691
computeScatterChannelsLinearScale0.1660.0080.174
estimateScaleTransforms0.1920.0000.191
execute26.456 0.80027.257
exportCytoPipeline0.0140.0000.015
findTimeChannel0.1270.0040.133
getAcquiredCompensationMatrix0.0630.0070.070
getChannelNamesFromMarkers0.1250.0040.129
getFCSFileName0.1230.0040.127
getTransfoParams0.1250.0080.134
ggplotEvents4.2570.0324.122
ggplotFilterEvents0.7470.0070.755
ggplotFlowRate0.8650.0120.876
handlingProcessingSteps0.0020.0040.006
inspectCytoPipelineObjects10.059 0.19110.251
interactingWithCytoPipelineCache14.681 0.25614.937
qualityControlFlowAI4.5980.5165.115
qualityControlPeacoQC0.6370.0040.642
readRDSObject0.2290.0000.229
readSampleFiles0.0780.0000.078
removeChannels0.1350.0000.135
removeDeadCellsManualGate0.0910.0040.095
removeDebrisManualGate0.0930.0000.092
removeDoubletsCytoPipeline0.1060.0000.107
removeMarginsPeacoQC0.2450.0070.254
resetCellIDs0.1260.0010.127
runCompensation0.1360.0000.137
singletsGate0.9550.0070.963
subsample0.1260.0010.126
updateMarkerName0.1230.0040.128
writeFlowFrame0.2760.0040.280