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CHECK report for CellScore on malbec2

This page was generated on 2018-10-17 08:31:15 -0400 (Wed, 17 Oct 2018).

Package 207/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellScore 1.0.0
Nancy Mah
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CellScore
Branch: RELEASE_3_7
Last Commit: 6f5e1d7
Last Changed Date: 2018-04-30 10:35:49 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellScore
Version: 1.0.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CellScore.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CellScore_1.0.0.tar.gz
StartedAt: 2018-10-15 23:03:59 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:07:38 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 219.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CellScore.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CellScore.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CellScore_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CellScore.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellScore/DESCRIPTION’ ... OK
* this is package ‘CellScore’ 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 ‘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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
CellScoreReport                26.504  0.748  27.296
heatmapOnOffMarkers            21.168  0.248  21.436
RugplotCellScore               20.020  0.236  20.273
extractTransitions             19.760  0.256  20.027
ScatterplotCellScoreComponents 19.416  0.384  19.813
PlotCosineSimHeatmap           16.600  0.236  16.849
BoxplotCellScore               13.944  0.304  14.260
CellScore                      13.536  0.192  13.738
PcaStandards                   12.336  0.228  12.572
CosineSimScore                 12.016  0.212  12.240
BarplotOnOff                    7.708  0.772   8.514
OnOff                           6.416  0.236   6.656
* 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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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CellScore
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘CellScore’ ...
** 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
* DONE (CellScore)

Tests output


Example timings

CellScore.Rcheck/CellScore-Ex.timings

nameusersystemelapsed
BarplotOnOff7.7080.7728.514
BoxplotCellScore13.944 0.30414.260
CellScore13.536 0.19213.738
CellScoreReport26.504 0.74827.296
CosineSimScore12.016 0.21212.240
OnOff6.4160.2366.656
PcaStandards12.336 0.22812.572
PlotCosineSimHeatmap16.600 0.23616.849
RugplotCellScore20.020 0.23620.273
ScatterplotCellScoreComponents19.416 0.38419.813
extractTransitions19.760 0.25620.027
heatmapOnOffMarkers21.168 0.24821.436
rugplotDonorTargetTest0.0000.0000.002
scatterplotDonorTargetTest0.0040.0000.002