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CHECK report for SubCellBarCode on merida1

This page was generated on 2021-05-05 12:15:34 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the SubCellBarCode package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1811/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.6.0  (landing page)
Taner Arslan
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/SubCellBarCode
Branch: RELEASE_3_12
Last Commit: 41ba24b
Last Changed Date: 2020-10-27 11:46:11 -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: SubCellBarCode
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SubCellBarCode_1.6.0.tar.gz
StartedAt: 2021-05-05 07:21:49 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 07:25:58 -0400 (Wed, 05 May 2021)
EllapsedTime: 249.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SubCellBarCode.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:SubCellBarCode.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SubCellBarCode_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/SubCellBarCode.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 ‘SubCellBarCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SubCellBarCode’ version ‘1.6.0’
* 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 ‘SubCellBarCode’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
applyThresholdCompartment    18.091  0.279  18.407
computeThresholdCompartment  15.841  0.106  15.992
applyThresholdNeighborhood   14.787  0.150  14.953
computeThresholdNeighborhood 13.840  0.094  13.949
svmExternalData              11.912  0.056  12.011
candidateRelocatedProteins    9.670  0.288   9.983
svmClassification             9.497  0.065   9.575
* 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

SubCellBarCode.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SubCellBarCode
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SubCellBarCode’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SubCellBarCode)

Tests output


Example timings

SubCellBarCode.Rcheck/SubCellBarCode-Ex.timings

nameusersystemelapsed
applyThresholdCompartment18.091 0.27918.407
applyThresholdNeighborhood14.787 0.15014.953
calRowMean0.0200.0010.020
calculateCoveredProtein0.1540.0020.156
candidateRelocatedProteins9.6700.2889.983
compareCls0.0280.0010.030
computeThresholdCompartment15.841 0.10615.992
computeThresholdNeighborhood13.840 0.09413.949
convert2symbol0.0020.0000.002
hcc827Ctrl0.0050.0000.006
hcc827CtrlPSMCount0.0120.0000.012
hcc827GEF0.0030.0010.004
hcc827GEFClass0.0010.0000.001
hcc827GefPSMCount0.0010.0000.002
hcc827exon0.0060.0020.007
loadData0.0020.0010.002
markerQualityControl0.5050.0090.516
mergeCls0.0090.0010.010
mergeProbability0.0070.0010.007
plotBarcode0.5670.0050.593
plotMultipleProtein0.2820.0010.284
replacePrediction0.0050.0000.005
sankeyPlot0.0410.0010.042
sumProbability0.0080.0000.009
svmClassification9.4970.0659.575
svmExternalData11.912 0.05612.011
tsneVisualization0.2420.0030.246