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CHECK report for CellScore on merida2

This page was generated on 2019-04-09 13:36:29 -0400 (Tue, 09 Apr 2019).

Package 229/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellScore 1.3.0
Nancy Mah
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CellScore
Branch: master
Last Commit: 8da88b5
Last Changed Date: 2018-10-30 11:54:39 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: CellScore
Version: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2019-04-08 23:44:50 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:51:03 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 372.5 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_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CellScore.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellScore/DESCRIPTION’ ... OK
* this is package ‘CellScore’ version ‘1.3.0’
* 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 or elapsed time > 5s
                                 user system elapsed
CellScoreReport                40.088  3.650  44.047
heatmapOnOffMarkers            38.111  2.838  41.391
ScatterplotCellScoreComponents 34.736  2.773  37.993
RugplotCellScore               33.677  2.582  36.600
extractTransitions             33.328  2.722  36.483
PlotCosineSimHeatmap           28.020  1.817  30.156
PcaStandards                   19.886  1.236  21.271
BoxplotCellScore               19.424  1.679  21.262
CosineSimScore                 18.743  1.207  20.159
CellScore                      16.403  1.307  17.738
BarplotOnOff                   12.701  2.008  14.879
OnOff                          11.190  1.433  12.716
* 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/3.6/Resources/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
BarplotOnOff12.701 2.00814.879
BoxplotCellScore19.424 1.67921.262
CellScore16.403 1.30717.738
CellScoreReport40.088 3.65044.047
CosineSimScore18.743 1.20720.159
OnOff11.190 1.43312.716
PcaStandards19.886 1.23621.271
PlotCosineSimHeatmap28.020 1.81730.156
RugplotCellScore33.677 2.58236.600
ScatterplotCellScoreComponents34.736 2.77337.993
extractTransitions33.328 2.72236.483
heatmapOnOffMarkers38.111 2.83841.391
rugplotDonorTargetTest0.0000.0010.001
scatterplotDonorTargetTest0.0010.0010.001