Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:41 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 500/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CytoPipeline 1.4.0 (landing page) Philippe Hauchamps
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | 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 | ![]() | ||||||||
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. |
Package: CytoPipeline |
Version: 1.4.0 |
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_1.4.0.tar.gz |
StartedAt: 2024-08-12 02:58:44 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 03:10:01 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 677.5 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_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CytoPipeline.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 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 56.530 2.825 77.891 interactingWithCytoPipelineCache 29.721 1.481 41.987 inspectCytoPipelineObjects 20.640 1.031 29.236 ggplotEvents 9.365 0.166 12.040 qualityControlFlowAI 6.480 0.411 9.448 * 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 ‘/Users/biocbuild/bbs-3.19-bioc/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/4.4-x86_64/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CytoPipeline/extdata/Donor1.fcs... ##################################################### ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/Resources/library/CytoPipeline/extdata/Donor1.fcs... ##################################################### ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CytoPipeline/extdata/Donor1.fcs... ##################################################### ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/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] ... ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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] ... ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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] ... ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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] ... | | | 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/4.4-x86_64/Resources/library/CytoPipeline/extdata/Donor1.fcs... ##################################################### ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/Resources/library/CytoPipeline/extdata/Donor1.fcs... ##################################################### Proceeding with step 1 [flowframe_read] ... ##################################################### ### NOW PRE-PROCESSING FILE /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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 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 153.456 7.511 242.138
CytoPipeline.Rcheck/CytoPipeline-Ex.timings
name | user | system | elapsed | |
CytoPipelineClass | 0.081 | 0.012 | 0.124 | |
CytoProcessingStep | 0.008 | 0.002 | 0.013 | |
aggregateAndSample | 0.372 | 0.024 | 0.523 | |
appendCellID | 0.221 | 0.012 | 0.314 | |
applyScaleTransforms | 0.444 | 0.020 | 0.581 | |
areFluoCols | 0.222 | 0.015 | 0.332 | |
areSignalCols | 0.233 | 0.009 | 0.316 | |
compensateFromMatrix | 2.791 | 0.103 | 3.698 | |
computeScatterChannelsLinearScale | 0.370 | 0.021 | 0.495 | |
estimateScaleTransforms | 0.386 | 0.016 | 0.525 | |
execute | 56.530 | 2.825 | 77.891 | |
exportCytoPipeline | 0.030 | 0.003 | 0.037 | |
findTimeChannel | 0.231 | 0.007 | 0.313 | |
getAcquiredCompensationMatrix | 0.160 | 0.006 | 0.209 | |
getChannelNamesFromMarkers | 0.234 | 0.011 | 0.315 | |
getFCSFileName | 0.224 | 0.011 | 0.305 | |
getTransfoParams | 0.240 | 0.010 | 0.326 | |
ggplotEvents | 9.365 | 0.166 | 12.040 | |
ggplotFilterEvents | 1.359 | 0.051 | 1.797 | |
ggplotFlowRate | 2.073 | 0.036 | 2.658 | |
handlingProcessingSteps | 0.012 | 0.004 | 0.020 | |
inspectCytoPipelineObjects | 20.640 | 1.031 | 29.236 | |
interactingWithCytoPipelineCache | 29.721 | 1.481 | 41.987 | |
qualityControlFlowAI | 6.480 | 0.411 | 9.448 | |
qualityControlPeacoQC | 1.661 | 0.052 | 2.304 | |
readRDSObject | 0.442 | 0.017 | 0.641 | |
readSampleFiles | 0.194 | 0.008 | 0.253 | |
removeChannels | 0.230 | 0.010 | 0.295 | |
removeDeadCellsManualGate | 0.240 | 0.008 | 0.319 | |
removeDebrisManualGate | 0.243 | 0.010 | 0.337 | |
removeDoubletsCytoPipeline | 0.281 | 0.009 | 0.426 | |
removeMarginsPeacoQC | 0.535 | 0.026 | 0.801 | |
resetCellIDs | 0.220 | 0.013 | 0.340 | |
runCompensation | 0.266 | 0.017 | 0.376 | |
singletsGate | 1.745 | 0.072 | 2.539 | |
subsample | 0.231 | 0.008 | 0.322 | |
updateMarkerName | 0.239 | 0.014 | 0.402 | |
writeFlowFrame | 0.512 | 0.038 | 0.830 | |