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CHECK report for CellScore on malbec2

This page was generated on 2019-10-16 12:13:17 -0400 (Wed, 16 Oct 2019).

Package 234/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellScore 1.4.0
Nancy Mah
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CellScore
Branch: RELEASE_3_9
Last Commit: a9f9288
Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 2019)
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

Summary

Package: CellScore
Version: 1.4.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CellScore.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CellScore_1.4.0.tar.gz
StartedAt: 2019-10-16 00:22:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:27:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 305.6 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-3.9-bioc/R/bin/R CMD check --install=check:CellScore.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CellScore_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CellScore.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.0’
* 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                42.405  1.116  43.616
heatmapOnOffMarkers            29.398  0.552  30.026
extractTransitions             27.389  0.428  27.848
ScatterplotCellScoreComponents 26.821  0.435  27.463
RugplotCellScore               25.767  0.240  26.065
PlotCosineSimHeatmap           20.919  0.160  21.087
CosineSimScore                 19.113  0.348  19.478
CellScore                      18.115  0.238  18.797
BoxplotCellScore               17.317  0.312  17.777
PcaStandards                   15.416  0.156  15.581
BarplotOnOff                   11.410  0.814  13.643
OnOff                           9.245  0.244   9.500
* 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-3.9-bioc/R/bin/R CMD INSTALL CellScore
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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
BarplotOnOff11.410 0.81413.643
BoxplotCellScore17.317 0.31217.777
CellScore18.115 0.23818.797
CellScoreReport42.405 1.11643.616
CosineSimScore19.113 0.34819.478
OnOff9.2450.2449.500
PcaStandards15.416 0.15615.581
PlotCosineSimHeatmap20.919 0.16021.087
RugplotCellScore25.767 0.24026.065
ScatterplotCellScoreComponents26.821 0.43527.463
extractTransitions27.389 0.42827.848
heatmapOnOffMarkers29.398 0.55230.026
rugplotDonorTargetTest0.0000.0000.001
scatterplotDonorTargetTest0.0000.0000.001