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This page was generated on 2022-06-24 12:06:30 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for PeacoQC on palomino3


To the developers/maintainers of the PeacoQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PeacoQC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1428/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PeacoQC 1.6.0  (landing page)
Annelies Emmaneel
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/PeacoQC
git_branch: RELEASE_3_15
git_last_commit: 2fa1046
git_last_commit_date: 2022-04-26 12:06:05 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: PeacoQC
Version: 1.6.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PeacoQC.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PeacoQC_1.6.0.tar.gz
StartedAt: 2022-06-24 03:31:56 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 03:34:21 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 144.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PeacoQC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PeacoQC.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PeacoQC_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/PeacoQC.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'PeacoQC/DESCRIPTION' ... OK
* this is package 'PeacoQC' version '1.6.0'
* 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 whether package 'PeacoQC' 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 ... NOTE
BuildBackgroundQCPlot: no visible binding for global variable 'x_min'
BuildBackgroundQCPlot: no visible binding for global variable 'x_max'
BuildBackgroundQCPlot: no visible binding for global variable 'y_min'
BuildBackgroundQCPlot: no visible binding for global variable 'y_max'
BuildBackgroundQCPlot: no visible binding for global variable
  'fill_blocks'
BuildChannelPlots: no visible binding for global variable 'Cells'
BuildManualPartPlot: no visible binding for global variable 'minimum'
BuildManualPartPlot: no visible binding for global variable 'x_min'
BuildManualPartPlot: no visible binding for global variable 'x_max'
BuildManualPartPlot: no visible binding for global variable 'y_min'
BuildManualPartPlot: no visible binding for global variable 'y_max'
BuildPeaksPlot: no visible binding for global variable 'Bin'
BuildPeaksPlot: no visible binding for global variable 'Peak'
BuildPeaksPlot: no visible binding for global variable 'Cluster'
BuildTimePlot: no visible binding for global variable 'x_min'
BuildTimePlot: no visible binding for global variable 'x_max'
BuildTimePlot: no visible binding for global variable 'y_min'
BuildTimePlot: no visible binding for global variable 'y_max'
BuildTimePlot: no visible binding for global variable 'fill_blocks'
Undefined global functions or variables:
  Bin Cells Cluster Peak fill_blocks minimum x_max x_min y_max y_min
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'PeacoQC':
PeacoQC
  Code: function(ff, channels, determine_good_cells = "all", plot = 20,
                 save_fcs = TRUE, output_directory = ".",
                 name_directory = "PeacoQC_results", report = TRUE,
                 events_per_bin = FindEventsPerBin(remove_zeros, ff,
                 channels, min_cells, max_bins, step), min_cells = 150,
                 max_bins = 500, step = 500, MAD = 6, IT_limit = 0.6,
                 consecutive_bins = 5, remove_zeros = FALSE, suffix_fcs
                 = "_QC", force_IT = 150, peak_removal = (1/3),
                 min_nr_bins_peakdetection = 10, time_channel_parameter
                 = "Time", ...)
  Docs: function(ff, channels, determine_good_cells = "all", plot = 20,
                 save_fcs = TRUE, output_directory = ".",
                 name_directory = "PeacoQC_results", report = TRUE,
                 events_per_bin = FindEventsPerBin(remove_zeros, ff,
                 channels, min_cells, max_bins, step), min_cells = 150,
                 max_bins = 500, step = 500, MAD = 6, IT_limit = 0.6,
                 consecutive_bins = 5, remove_zeros = FALSE, suffix_fcs
                 = "_QC", force_IT = 150, peak_removal = (1/3),
                 min_nr_bins_peakdetection = 10, ...)
  Argument names in code not in docs:
    time_channel_parameter
  Mismatches in argument names:
    Position: 21 Code: time_channel_parameter Docs: ...

Codoc mismatches from documentation object 'PlotPeacoQC':
PlotPeacoQC
  Code: function(ff, channels, output_directory = ".", display_cells =
                 2000, manual_cells = NULL, title_FR = NULL,
                 display_peaks = TRUE, prefix = "PeacoQC_", time_unit =
                 100, time_channel_parameter = "Time", ...)
  Docs: function(ff, channels, output_directory = ".", display_cells =
                 2000, manual_cells = NULL, title_FR = NULL,
                 display_peaks = TRUE, prefix = "PeacoQC_", time_unit =
                 100, ...)
  Argument names in code not in docs:
    time_channel_parameter
  Mismatches in argument names:
    Position: 10 Code: time_channel_parameter Docs: ...

* 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
PlotPeacoQC    13.68   0.19   14.88
PeacoQC         5.88   0.19    7.67
PeacoQCHeatmap  5.06   0.09    5.16
* 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/PeacoQC.Rcheck/00check.log'
for details.



Installation output

PeacoQC.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PeacoQC
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'PeacoQC' ...
** using staged installation
** R
** 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 (PeacoQC)

Tests output


Example timings

PeacoQC.Rcheck/PeacoQC-Ex.timings

nameusersystemelapsed
PeacoQC5.880.197.67
PeacoQCHeatmap5.060.095.16
PlotPeacoQC13.68 0.1914.88
RemoveDoublets0.030.000.03
RemoveMargins0.160.000.16