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This page was generated on 2024-04-18 11:32:08 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 493/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoPipelineGUI 1.0.0  (landing page)
Philippe Hauchamps
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/CytoPipelineGUI
git_branch: RELEASE_3_18
git_last_commit: 3f95571
git_last_commit_date: 2023-10-24 11:50:58 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for CytoPipelineGUI on kjohnson1


To the developers/maintainers of the CytoPipelineGUI 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.

raw results

Summary

Package: CytoPipelineGUI
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoPipelineGUI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoPipelineGUI_1.0.0.tar.gz
StartedAt: 2024-04-17 11:00:11 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 11:03:27 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 196.3 seconds
RetCode: 0
Status:   OK  
CheckDir: CytoPipelineGUI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CytoPipelineGUI.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CytoPipelineGUI_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/CytoPipelineGUI.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 ‘CytoPipelineGUI/DESCRIPTION’ ... OK
* this is package ‘CytoPipelineGUI’ version ‘1.0.0’
* 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 ‘CytoPipelineGUI’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
CytoPipelineGUI             20.231  1.069  21.386
plotDiffFlowFrame           13.478  0.683  14.210
plotSelectedFlowFrame       12.024  0.588  12.674
plotScaleTransformedChannel 10.692  0.508  11.296
plotSelectedWorkflow        10.143  0.503  10.710
* 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: OK

Installation output

CytoPipelineGUI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoPipelineGUI
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘CytoPipelineGUI’ ...
** using staged installation
** R
** 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 (CytoPipelineGUI)

Tests output

CytoPipelineGUI.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.

> # CytoPipelineGUI - 
> # Copyright (C) <2022> <Université catholique de Louvain (UCLouvain), Belgique>
> #   
> #   Description and complete License: see LICENSE file.
> # 
> # This program (CytoPipelineGUI) 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(CytoPipelineGUI)
Loading required package: CytoPipeline
> 
> test_check("CytoPipelineGUI")
#####################################################
### 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

  |                                                        
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  |+++++++++++++++                                   |  30%
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  |++++++++++++++++++                                |  35%
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  |++++++++++++++++++++                              |  40%
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  |++++++++++++++++++++++                            |  45%
  |                                                        
  |+++++++++++++++++++++++++                         |  50%
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  |++++++++++++++++++++++++++++                      |  55%
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  |++++++++++++++++++++++++++++++                    |  60%
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  |++++++++++++++++++++++++++++++++                  |  65%
  |                                                        
  |+++++++++++++++++++++++++++++++++++               |  70%
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  |++++++++++++++++++++++++++++++++++++++            |  75%
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  |++++++++++++++++++++++++++++++++++++++++          |  80%
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  |++++++++++++++++++++++++++++++++++++++++++        |  85%
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  |+++++++++++++++++++++++++++++++++++++++++++++     |  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%
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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%
  |                                                        
  |+++++++++++++++++++++++++++++++++++               |  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] ...
no sample file passed as argument => defaulting to first sample file
displaying flow frame plot...
displaying flow frame comparison plot...
displaying flow frame comparison plot...
displaying flow frame comparison plot...
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-plots.R:101:5', 'test-plots.R:234:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 7 ]
Deleting unused snapshots:
• plots/pltdiffff-100c-nofixlin-notran.svg
• plots/pltdiffff-allc-fixlin-notran.svg
• plots/pltdiffff-allc-tran.svg
• plots/pltscaletransch-logicle-data-mker.svg
• plots/pltscaletransch-logicle.svg
• plots/pltselff-100c-nofixlin-notran.svg
• plots/pltselff-allc-tran.svg
> 
> proc.time()
   user  system elapsed 
 22.978   1.189  24.860

Example timings

CytoPipelineGUI.Rcheck/CytoPipelineGUI-Ex.timings

nameusersystemelapsed
CytoPipelineGUI20.231 1.06921.386
plotDiffFlowFrame13.478 0.68314.210
plotScaleTransformedChannel10.692 0.50811.296
plotSelectedFlowFrame12.024 0.58812.674
plotSelectedWorkflow10.143 0.50310.710