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CHECK report for Pi on machv2

This page was generated on 2020-10-17 11:59:12 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Pi PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1310/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.0.3
Hai Fang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Pi
Branch: RELEASE_3_11
Last Commit: ae976b7
Last Changed Date: 2020-09-09 11:25:43 -0400 (Wed, 09 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Pi
Version: 2.0.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pi_2.0.3.tar.gz
StartedAt: 2020-10-17 03:56:02 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:06:53 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 650.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Pi.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pi_2.0.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Pi.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pi’ version ‘2.0.3’
* 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 ‘Pi’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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

Pi.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Pi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ROCR::plot' by 'graphics::plot' when loading 'Pi'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ROCR::plot' by 'graphics::plot' when loading 'Pi'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ROCR::plot' by 'graphics::plot' when loading 'Pi'
** testing if installed package keeps a record of temporary installation path
* DONE (Pi)

Tests output


Example timings

Pi.Rcheck/Pi-Ex.timings

nameusersystemelapsed
EG0.0000.0010.001
GS0.0000.0010.001
aOnto0.0010.0010.000
cTarget0.0000.0010.001
dTarget000
eGSEA000
eTarget0.0000.0000.001
eTerm000
iSubg000
ls_eTerm000
pNode0.0000.0010.000
pPerf0.0010.0010.000
sGS000
sTarget000
xAggregate000
xCheckParallel0.0000.0010.000
xCircos0.0010.0010.001
xColormap0.0160.0030.019
xCombineNet0.0010.0000.001
xContour0.0490.0110.059
xCorrelation0.0000.0000.001
xDAGanno0.0000.0010.002
xDefineEQTL0.0010.0010.001
xDefineHIC0.0000.0010.001
xDefineNet0.0010.0010.001
xDefineOntology0.0000.0000.001
xEnrichForest0.0010.0000.001
xEnrichViewer000
xEnricher0.0010.0010.001
xEnricherGenes0.0010.0010.002
xGGnetwork0.0010.0020.003
xGR0.0000.0010.001
xGR2nGenes0.0010.0000.001
xGR2xGeneScores0.0000.0000.001
xGR2xGenes0.0000.0010.001
xGRscores0.0000.0010.001
xGRsort0.0010.0010.001
xGSEAbarplot0.0000.0000.001
xGSEAconciser000
xGSEAdotplot0.0010.0000.000
xGSsimulator000
xGeneID2Symbol0.0000.0010.000
xHeatmap0.0000.0010.001
xLiftOver0.0000.0010.001
xMEabf0.0000.0000.001
xMLcaret0.0000.0000.001
xMLcompare0.0000.0000.001
xMLdensity0.0010.0010.001
xMLdotplot0.0000.0000.001
xMLfeatureplot0.0000.0000.001
xMLglmnet000
xMLparameters000
xMLrandomforest0.0010.0000.000
xMLrename0.0000.0010.001
xMLzoom0.0010.0010.001
xPieplot0.0000.0000.001
xPier0.0010.0000.001
xPierABF0.0000.0000.001
xPierABFheatmap0.0000.0000.001
xPierAnno0.0000.0010.001
xPierCor0.0000.0010.000
xPierCross0.0010.0000.000
xPierEvidence0.0000.0000.001
xPierGRs0.0010.0010.001
xPierGSEA0.0000.0000.001
xPierGenes0.0000.0000.001
xPierMRS0.0010.0000.000
xPierManhattan0.0000.0010.002
xPierMatrix0.0010.0010.001
xPierPathways0.0000.0010.001
xPierROCR0.0010.0000.000
xPierSNPs0.0000.0000.001
xPierSNPsAdv0.0010.0000.000
xPierSNPsAdvABF0.0000.0000.001
xPierSubnet0.0010.0010.002
xPierTrack0.0000.0010.001
xPierTrackAdv0.0010.0010.001
xPredictCompare0.0000.0010.000
xPredictROCR0.0000.0000.001
xRDataLoader0.0000.0000.001
xRWR0.0020.0010.003
xSM2DF0.0260.0040.030
xSNP2cGenes0.0010.0010.000
xSNP2eGenes000
xSNP2nGenes0.0000.0000.001
xSNPlocations0.0000.0000.001
xSNPscores000
xSparseMatrix0.0330.0070.039
xSubneterGenes0.0010.0010.002
xSymbol2GeneID0.0000.0000.001
xVisEvidence0.0010.0000.000
xVisEvidenceAdv000
xVisKernels0.0210.0150.036
xVisNet0.0010.0010.001