Philippe Hauchamps
| Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/CytoPipeline |
| git_branch: devel |
| git_last_commit: 365c1dd |
| git_last_commit_date: 2024-05-28 05:37:41 -0400 (Tue, 28 May 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-06 11:38 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 486/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CytoPipeline 1.5.1 (landing page) Philippe Hauchamps
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CytoPipeline package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CytoPipeline.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CytoPipeline |
| Version: 1.5.1 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CytoPipeline_1.5.1.tar.gz |
| StartedAt: 2024-07-05 21:59:37 -0400 (Fri, 05 Jul 2024) |
| EndedAt: 2024-07-05 22:04:19 -0400 (Fri, 05 Jul 2024) |
| EllapsedTime: 282.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CytoPipeline.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CytoPipeline.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CytoPipeline_1.5.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CytoPipeline.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.5.1’
* 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 26.717 1.048 27.801
interactingWithCytoPipelineCache 13.677 0.280 13.957
inspectCytoPipelineObjects 9.471 0.203 9.676
* 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-3.20-bioc/meat/CytoPipeline.Rcheck/00check.log’
for details.
CytoPipeline.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CytoPipeline ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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)
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-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-3.20-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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-3.20-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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-3.20-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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] ...
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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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 30.75% of the measurements
The algorithm removed 30.75% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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] ...
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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|++++++++++++++++++++++++++++++++++++++++++ | 85%
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|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
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|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 24.38% of the measurements
The algorithm removed 24.38% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read]: found in cache!
Proceeding with step 2 [remove_margins]: found in cache!
Proceeding with step 3 [compensate]: found in cache!
Proceeding with step 4 [flowframe_aggregate]: found in cache!
Proceeding with step 5 [scale_transform_estimate]: found in cache!
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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-3.20-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] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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] ...
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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|++++++++++++++++++++++++++++++++++++++++++ | 85%
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|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
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|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
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|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 30.75% of the measurements
The algorithm removed 30.75% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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] ...
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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|++++++++ | 15%
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|++++++++++ | 20%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
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|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
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|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 24.38% of the measurements
The algorithm removed 24.38% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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] ...
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%
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|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
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|++++++++++ | 20%
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|++++++++++++ | 25%
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|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
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|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
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|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
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|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 30.75% of the measurements
The algorithm removed 30.75% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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] ...
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%
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|+++++ | 10%
|
|++++++++ | 15%
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|++++++++++ | 20%
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|++++++++++++ | 25%
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|+++++++++++++++ | 30%
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|++++++++++++++++++ | 35%
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|++++++++++++++++++++ | 40%
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|++++++++++++++++++++++ | 45%
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|+++++++++++++++++++++++++ | 50%
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|++++++++++++++++++++++++++++ | 55%
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|++++++++++++++++++++++++++++++ | 60%
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|++++++++++++++++++++++++++++++++ | 65%
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|+++++++++++++++++++++++++++++++++++ | 70%
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|++++++++++++++++++++++++++++++++++++++ | 75%
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|++++++++++++++++++++++++++++++++++++++++ | 80%
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|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
MAD analysis removed 24.38% of the measurements
The algorithm removed 24.38% of the measurements
Proceeding with step 8 [transform] ...
#####################################################
### running SCALE TRANSFORMATION processing steps ###
#####################################################
Proceeding with step 1 [flowframe_read] ...
Proceeding with step 2 [remove_margins] ...
Removing margins from file : Donor1.fcs
Removing margins from file : Donor2.fcs
Proceeding with step 3 [compensate] ...
Proceeding with step 4 [flowframe_aggregate] ...
Proceeding with step 5 [scale_transform_estimate] ...
|
| | 0%
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|=================================== | 50%
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|======================================================================| 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-3.20-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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-3.20-bioc/R/site-library/CytoPipeline/extdata/Donor1.fcs...
#####################################################
Proceeding with step 1 [flowframe_read] ...
#####################################################
### NOW PRE-PROCESSING FILE /home/biocbuild/bbs-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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-3.20-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
COL NAMES MARKER MAPPING: Channel, Marker, Used
COL NAMES MARKER MAPPING: Channel, Marker, Used
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Removing margins from file : Donor1.fcs
Applying PeacoQC method...
Starting quality control analysis for Donor1.fcs
Calculating peaks
|
| | 0%
|
|++ | 5%
|
|+++++ | 10%
|
|++++++++ | 15%
|
|++++++++++ | 20%
|
|++++++++++++ | 25%
|
|+++++++++++++++ | 30%
|
|++++++++++++++++++ | 35%
|
|++++++++++++++++++++ | 40%
|
|++++++++++++++++++++++ | 45%
|
|+++++++++++++++++++++++++ | 50%
|
|++++++++++++++++++++++++++++ | 55%
|
|++++++++++++++++++++++++++++++ | 60%
|
|++++++++++++++++++++++++++++++++ | 65%
|
|+++++++++++++++++++++++++++++++++++ | 70%
|
|++++++++++++++++++++++++++++++++++++++ | 75%
|
|++++++++++++++++++++++++++++++++++++++++ | 80%
|
|++++++++++++++++++++++++++++++++++++++++++ | 85%
|
|+++++++++++++++++++++++++++++++++++++++++++++ | 90%
|
|++++++++++++++++++++++++++++++++++++++++++++++++ | 95%
|
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
Applying flowAI method...
Quality control for the file: Donor1
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.
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 248 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-gating.R:42:5', 'test-ggplots.R:185:5',
'test-ggplots.R:310:5'
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 248 ]
Deleting unused snapshots:
• gating/singletsgate-default-channels-with-fixed-nmad.svg
• gating/singletsgate-selected-channels.svg
• gating/singletsgates-one-after-the-other-fig1.svg
• gating/singletsgates-one-after-the-other-fig2.svg
• ggplots/ggplotevents-2d-x-linear-y-logicle.svg
• ggplots/ggplotevents-2d-x-logicle-y-linear.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-bins.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-by-markers.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-not-run.svg
• ggplots/ggplotevents-2d-x-logicle-y-logicle-translist-run.svg
• ggplots/ggplotfilterevents-2d-5000-points.svg
• ggplots/ggplotfilterevents-2d-all-points-interactive.svg
• ggplots/ggplotfilterevents-2d-infinite-nb-of-points.svg
• ggplots/ggplotfilterevents-2d-small-size.svg
• ggplots/ggplotfilterevents-2d-translist-not-run.svg
• ggplots/ggplotfilterevents-2d-translist-run.svg
>
> proc.time()
user system elapsed
72.143 3.269 85.305
CytoPipeline.Rcheck/CytoPipeline-Ex.timings
| name | user | system | elapsed | |
| CytoPipelineClass | 0.034 | 0.000 | 0.035 | |
| CytoProcessingStep | 0.005 | 0.000 | 0.004 | |
| aggregateAndSample | 0.198 | 0.003 | 0.203 | |
| appendCellID | 0.120 | 0.008 | 0.129 | |
| applyScaleTransforms | 0.234 | 0.000 | 0.235 | |
| areFluoCols | 0.152 | 0.004 | 0.156 | |
| areSignalCols | 0.125 | 0.004 | 0.128 | |
| compensateFromMatrix | 1.759 | 0.275 | 2.036 | |
| computeScatterChannelsLinearScale | 0.178 | 0.009 | 0.187 | |
| estimateScaleTransforms | 0.193 | 0.000 | 0.194 | |
| execute | 26.717 | 1.048 | 27.801 | |
| exportCytoPipeline | 0.012 | 0.000 | 0.012 | |
| findTimeChannel | 0.129 | 0.000 | 0.129 | |
| getAcquiredCompensationMatrix | 0.065 | 0.000 | 0.065 | |
| getChannelNamesFromMarkers | 0.125 | 0.004 | 0.129 | |
| getFCSFileName | 0.123 | 0.000 | 0.124 | |
| getTransfoParams | 0.137 | 0.003 | 0.141 | |
| ggplotEvents | 4.339 | 0.071 | 4.263 | |
| ggplotFilterEvents | 0.706 | 0.004 | 0.711 | |
| ggplotFlowRate | 0.873 | 0.016 | 0.890 | |
| handlingProcessingSteps | 0.004 | 0.000 | 0.005 | |
| inspectCytoPipelineObjects | 9.471 | 0.203 | 9.676 | |
| interactingWithCytoPipelineCache | 13.677 | 0.280 | 13.957 | |
| qualityControlFlowAI | 3.699 | 0.304 | 4.004 | |
| qualityControlPeacoQC | 0.641 | 0.036 | 0.678 | |
| readRDSObject | 0.214 | 0.004 | 0.218 | |
| readSampleFiles | 0.072 | 0.004 | 0.076 | |
| removeChannels | 0.126 | 0.000 | 0.127 | |
| removeDeadCellsManualGate | 0.109 | 0.008 | 0.117 | |
| removeDebrisManualGate | 0.090 | 0.000 | 0.089 | |
| removeDoubletsCytoPipeline | 0.104 | 0.000 | 0.104 | |
| removeMarginsPeacoQC | 0.262 | 0.000 | 0.263 | |
| resetCellIDs | 0.129 | 0.000 | 0.130 | |
| runCompensation | 0.136 | 0.000 | 0.136 | |
| singletsGate | 0.958 | 0.008 | 0.966 | |
| subsample | 0.123 | 0.000 | 0.123 | |
| updateMarkerName | 0.125 | 0.000 | 0.125 | |
| writeFlowFrame | 0.272 | 0.000 | 0.272 | |