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CHECK report for CellScore on merida1

This page was generated on 2020-08-11 12:01:37 -0400 (Tue, 11 Aug 2020).

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 247/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellScore 1.9.0
Nancy Mah
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/CellScore
Branch: master
Last Commit: c066da8
Last Changed Date: 2020-04-27 15:13:55 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CellScore
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2020-08-11 03:44:12 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 03:51:19 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 427.0 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_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CellScore.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.9.0’
* 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                54.702  1.766  56.593
RugplotCellScore               39.960  1.019  41.249
heatmapOnOffMarkers            39.880  1.029  40.964
ScatterplotCellScoreComponents 39.299  0.966  40.311
extractTransitions             39.008  0.950  40.020
PlotCosineSimHeatmap           31.645  0.694  32.378
BoxplotCellScore               25.806  1.036  26.881
CellScore                      24.695  0.716  25.448
CosineSimScore                 23.090  0.546  23.669
PcaStandards                   21.708  0.453  22.188
BarplotOnOff                   14.899  1.262  16.210
OnOff                          11.298  0.638  11.954
* 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
BarplotOnOff14.899 1.26216.210
BoxplotCellScore25.806 1.03626.881
CellScore24.695 0.71625.448
CellScoreReport54.702 1.76656.593
CosineSimScore23.090 0.54623.669
OnOff11.298 0.63811.954
PcaStandards21.708 0.45322.188
PlotCosineSimHeatmap31.645 0.69432.378
RugplotCellScore39.960 1.01941.249
ScatterplotCellScoreComponents39.299 0.96640.311
extractTransitions39.008 0.95040.020
heatmapOnOffMarkers39.880 1.02940.964
rugplotDonorTargetTest0.0010.0000.001
scatterplotDonorTargetTest0.0000.0010.001