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CHECK report for Pi on malbec2

This page was generated on 2020-10-17 11:55:23 -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: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Pi_2.0.3.tar.gz
StartedAt: 2020-10-17 04:06:18 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:15:15 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 536.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Pi.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Pi_2.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/Pi.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Pi
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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
EG000
GS0.0010.0000.000
aOnto000
cTarget000
dTarget000
eGSEA000
eTarget000
eTerm000
iSubg000
ls_eTerm000
pNode000
pPerf000
sGS000
sTarget000
xAggregate000
xCheckParallel000
xCircos0.0000.0000.001
xColormap0.0170.0000.017
xCombineNet0.0010.0000.001
xContour0.0530.0040.056
xCorrelation0.0010.0000.000
xDAGanno0.0010.0000.001
xDefineEQTL000
xDefineHIC000
xDefineNet000
xDefineOntology000
xEnrichForest0.0010.0000.000
xEnrichViewer0.0010.0000.000
xEnricher0.0010.0000.001
xEnricherGenes0.0000.0000.001
xGGnetwork0.0010.0000.001
xGR000
xGR2nGenes000
xGR2xGeneScores000
xGR2xGenes0.0010.0000.000
xGRscores0.0010.0000.000
xGRsort0.0010.0000.000
xGSEAbarplot0.0010.0000.000
xGSEAconciser0.0010.0000.000
xGSEAdotplot0.0010.0000.000
xGSsimulator0.0010.0000.000
xGeneID2Symbol0.0010.0000.000
xHeatmap0.0010.0000.001
xLiftOver0.0010.0000.001
xMEabf0.0010.0000.000
xMLcaret0.0010.0000.000
xMLcompare0.0010.0000.000
xMLdensity0.0010.0000.000
xMLdotplot0.0010.0000.000
xMLfeatureplot0.0010.0000.000
xMLglmnet000
xMLparameters000
xMLrandomforest000
xMLrename0.0010.0000.000
xMLzoom0.0010.0000.000
xPieplot000
xPier0.0010.0000.001
xPierABF000
xPierABFheatmap000
xPierAnno000
xPierCor000
xPierCross000
xPierEvidence000
xPierGRs000
xPierGSEA0.0010.0000.000
xPierGenes0.0010.0000.000
xPierMRS0.0010.0000.000
xPierManhattan0.0010.0000.001
xPierMatrix0.0000.0000.001
xPierPathways0.0000.0000.001
xPierROCR000
xPierSNPs000
xPierSNPsAdv000
xPierSNPsAdvABF000
xPierSubnet0.0010.0000.000
xPierTrack0.0010.0000.000
xPierTrackAdv0.0000.0000.001
xPredictCompare0.0000.0000.001
xPredictROCR0.0000.0000.001
xRDataLoader0.0000.0000.001
xRWR0.0000.0020.002
xSM2DF0.0200.0040.024
xSNP2cGenes000
xSNP2eGenes000
xSNP2nGenes000
xSNPlocations000
xSNPscores000
xSparseMatrix0.0210.0040.024
xSubneterGenes0.0010.0000.000
xSymbol2GeneID000
xVisEvidence000
xVisEvidenceAdv000
xVisKernels0.0220.0000.022
xVisNet0.0000.0010.000