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This page was generated on 2021-10-22 12:05:06 -0400 (Fri, 22 Oct 2021).

CHECK results for PeacoQC on merida1

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? here 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 1386/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PeacoQC 1.3.3  (landing page)
Annelies Emmaneel
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/PeacoQC
git_branch: master
git_last_commit: 34dfeb5
git_last_commit_date: 2021-08-23 10:24:13 -0400 (Mon, 23 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: PeacoQC
Version: 1.3.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PeacoQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PeacoQC_1.3.3.tar.gz
StartedAt: 2021-10-22 07:22:06 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 07:25:08 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 181.9 seconds
RetCode: 0
Status:   OK  
CheckDir: PeacoQC.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PeacoQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PeacoQC_1.3.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PeacoQC.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PeacoQC/DESCRIPTION’ ... OK
* this is package ‘PeacoQC’ version ‘1.3.3’
* 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 ‘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 ... 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
PlotPeacoQC    18.222  0.191  18.448
PeacoQCHeatmap  8.433  0.041   8.489
PeacoQC         7.669  0.200   7.893
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/PeacoQC.Rcheck/00check.log’
for details.



Installation output

PeacoQC.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PeacoQC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
PeacoQC7.6690.2007.893
PeacoQCHeatmap8.4330.0418.489
PlotPeacoQC18.222 0.19118.448
RemoveDoublets0.0520.0020.054
RemoveMargins0.1520.0160.168