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CHECK report for CellScore on merida1

This page was generated on 2021-05-06 12:34:30 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CellScore package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 258/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellScore 1.10.0  (landing page)
Nancy Mah
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CellScore
Branch: RELEASE_3_12
Last Commit: a714c29
Last Changed Date: 2020-10-27 11:32:18 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CellScore
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellScore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellScore_1.10.0.tar.gz
StartedAt: 2021-05-06 00:03:54 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:10:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 392.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CellScore.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellScore.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellScore_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CellScore.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellScore/DESCRIPTION’ ... OK
* this is package ‘CellScore’ version ‘1.10.0’
* 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 ‘CellScore’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
CellScoreReport                49.387  1.672  51.128
heatmapOnOffMarkers            38.117  0.918  39.087
ScatterplotCellScoreComponents 35.571  1.015  36.630
extractTransitions             34.829  1.090  35.988
RugplotCellScore               34.670  1.062  35.779
PlotCosineSimHeatmap           29.457  0.618  30.142
BoxplotCellScore               24.652  1.119  25.813
CellScore                      23.703  0.659  24.393
PcaStandards                   21.659  0.469  22.180
CosineSimScore                 20.511  0.456  20.997
BarplotOnOff                   13.385  1.284  14.750
OnOff                          10.678  0.881  11.815
* 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

CellScore.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CellScore
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CellScore’ ...
** 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 (CellScore)

Tests output


Example timings

CellScore.Rcheck/CellScore-Ex.timings

nameusersystemelapsed
BarplotOnOff13.385 1.28414.750
BoxplotCellScore24.652 1.11925.813
CellScore23.703 0.65924.393
CellScoreReport49.387 1.67251.128
CosineSimScore20.511 0.45620.997
OnOff10.678 0.88111.815
PcaStandards21.659 0.46922.180
PlotCosineSimHeatmap29.457 0.61830.142
RugplotCellScore34.670 1.06235.779
ScatterplotCellScoreComponents35.571 1.01536.630
extractTransitions34.829 1.09035.988
heatmapOnOffMarkers38.117 0.91839.087
rugplotDonorTargetTest0.0000.0010.001
scatterplotDonorTargetTest0.0000.0010.001