| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:08 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 492/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoPipeline 1.2.0 (landing page) Philippe Hauchamps
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the CytoPipeline package: - 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. |
| Package: CytoPipeline |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoPipeline_1.2.0.tar.gz |
| StartedAt: 2024-04-17 10:58:20 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 11:03:15 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 295.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoPipeline.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoPipeline_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/CytoPipeline.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CytoPipeline/DESCRIPTION’ ... OK
* this is package ‘CytoPipeline’ version ‘1.2.0’
* 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 R 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 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 28.868 1.594 30.695
interactingWithCytoPipelineCache 16.460 0.823 17.477
inspectCytoPipelineObjects 10.674 0.580 11.301
qualityControlFlowAI 5.052 0.314 5.372
ggplotEvents 5.010 0.109 5.151
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/CytoPipeline.Rcheck/00check.log’
for details.
CytoPipeline.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoPipeline ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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>
> # <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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
Proceeding with phenoData ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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] ...
estimating logicle transformations for fluorochrome channels...
Estimating linear transformation for scatter channels : reference marker = BV785 - CD3...
applying specific linear transformation for FSC-A channel...
initial quantiles : q5 = 48809.1266 ; q95 = 182769.1664
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.91e-05 ; b = -5.33e-01
applying FSC-A linear transformation for FSC-H channel...
applying specific linear transformation for SSC-A channel...
initial quantiles : q5 = 41296.8164 ; q95 = 223620.1273
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.40e-05 ; b = -1.80e-01
applying SSC-A linear transformation for SSC-H channel...
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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] ...
estimating logicle transformations for fluorochrome channels...
Estimating linear transformation for scatter channels : reference marker = BV785 - CD3...
applying specific linear transformation for FSC-A channel...
initial quantiles : q5 = 48809.1266 ; q95 = 182769.1664
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.91e-05 ; b = -5.33e-01
applying FSC-A linear transformation for FSC-H channel...
applying specific linear transformation for SSC-A channel...
initial quantiles : q5 = 41296.8164 ; q95 = 223620.1273
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.40e-05 ; b = -1.80e-01
applying SSC-A linear transformation for SSC-H channel...
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 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] ...
estimating logicle transformations for fluorochrome channels...
Estimating linear transformation for scatter channels : reference marker = BV785 - CD3...
applying specific linear transformation for FSC-A channel...
initial quantiles : q5 = 48809.1266 ; q95 = 182769.1664
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.91e-05 ; b = -5.33e-01
applying FSC-A linear transformation for FSC-H channel...
applying specific linear transformation for SSC-A channel...
initial quantiles : q5 = 41296.8164 ; q95 = 223620.1273
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.40e-05 ; b = -1.80e-01
applying SSC-A linear transformation for SSC-H channel...
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 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] ...
estimating logicle transformations for fluorochrome channels...
Estimating linear transformation for scatter channels : reference marker = BV785 - CD3...
applying specific linear transformation for FSC-A channel...
initial quantiles : q5 = 48809.1266 ; q95 = 182769.1664
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.91e-05 ; b = -5.33e-01
applying FSC-A linear transformation for FSC-H channel...
applying specific linear transformation for SSC-A channel...
initial quantiles : q5 = 41296.8164 ; q95 = 223620.1273
target quantiles : q5 = 0.3996 ; q95 = 2.9603
a = 1.40e-05 ; b = -1.80e-01
applying SSC-A linear transformation for SSC-H channel...
|
| | 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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CytoPipeline/extdata/Donor2.fcs...
#####################################################
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4 | PASS 224 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-gating.R:42:5', 'test-ggplots.R:68:5',
'test-ggplots.R:185:5', 'test-ggplots.R:310:5'
[ FAIL 0 | WARN 0 | SKIP 4 | PASS 224 ]
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-1d-fill-and-color.svg
• ggplots/ggplotevents-1d-linear-double.svg
• ggplots/ggplotevents-1d-linear-explicit-range-single.svg
• ggplots/ggplotevents-1d-logicle-single.svg
• ggplots/ggplotevents-1d-logicle-with-explicit-params-single.svg
• ggplots/ggplotevents-1d-sub-sampling.svg
• ggplots/ggplotevents-1d-transformlist-linear-not-run.svg
• ggplots/ggplotevents-1d-transformlist-linear-run.svg
• ggplots/ggplotevents-1d-transformlist-logicle-not-run.svg
• ggplots/ggplotevents-1d-transformlist-logicle-run.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
82.483 4.275 102.779
CytoPipeline.Rcheck/CytoPipeline-Ex.timings
| name | user | system | elapsed | |
| CytoPipelineClass | 0.041 | 0.006 | 0.049 | |
| CytoProcessingStep | 0.005 | 0.001 | 0.005 | |
| aggregateAndSample | 0.252 | 0.012 | 0.264 | |
| appendCellID | 0.186 | 0.006 | 0.194 | |
| applyScaleTransforms | 0.299 | 0.014 | 0.319 | |
| areFluoCols | 0.198 | 0.007 | 0.206 | |
| areSignalCols | 0.221 | 0.007 | 0.231 | |
| compensateFromMatrix | 1.826 | 0.077 | 1.963 | |
| computeScatterChannelsLinearScale | 0.250 | 0.009 | 0.264 | |
| estimateScaleTransforms | 0.272 | 0.011 | 0.288 | |
| execute | 28.868 | 1.594 | 30.695 | |
| exportCytoPipeline | 0.013 | 0.001 | 0.014 | |
| findTimeChannel | 0.180 | 0.007 | 0.189 | |
| getAcquiredCompensationMatrix | 0.073 | 0.004 | 0.078 | |
| getChannelNamesFromMarkers | 0.196 | 0.008 | 0.205 | |
| getFCSFileName | 0.187 | 0.007 | 0.195 | |
| getTransfoParams | 0.213 | 0.010 | 0.233 | |
| ggplotEvents | 5.010 | 0.109 | 5.151 | |
| ggplotFilterEvents | 0.906 | 0.027 | 0.936 | |
| ggplotFlowRate | 1.019 | 0.016 | 1.045 | |
| handlingProcessingSteps | 0.005 | 0.001 | 0.008 | |
| inspectCytoPipelineObjects | 10.674 | 0.580 | 11.301 | |
| interactingWithCytoPipelineCache | 16.460 | 0.823 | 17.477 | |
| qualityControlFlowAI | 5.052 | 0.314 | 5.372 | |
| qualityControlPeacoQC | 0.720 | 0.066 | 0.787 | |
| readRDSObject | 0.309 | 0.007 | 0.345 | |
| readSampleFiles | 0.093 | 0.005 | 0.098 | |
| removeChannels | 0.213 | 0.004 | 0.218 | |
| removeDeadCellsManualGate | 0.110 | 0.005 | 0.115 | |
| removeDebrisManualGate | 0.115 | 0.006 | 0.120 | |
| removeDoubletsCytoPipeline | 0.136 | 0.007 | 0.146 | |
| removeMarginsPeacoQC | 0.336 | 0.023 | 0.368 | |
| resetCellIDs | 0.251 | 0.005 | 0.256 | |
| runCompensation | 0.230 | 0.005 | 0.235 | |
| singletsGate | 1.386 | 0.037 | 1.426 | |
| subsample | 0.208 | 0.006 | 0.214 | |
| updateMarkerName | 0.221 | 0.007 | 0.229 | |
| writeFlowFrame | 0.277 | 0.015 | 0.292 | |