Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-20 12:08:33 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Pi on merida1


To the developers/maintainers of the Pi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1454/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.8.0  (landing page)
Hai Fang
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/Pi
git_branch: RELEASE_3_15
git_last_commit: 019a211
git_last_commit_date: 2022-04-26 11:35:45 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Pi
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pi_2.8.0.tar.gz
StartedAt: 2022-05-20 05:52:49 -0400 (Fri, 20 May 2022)
EndedAt: 2022-05-20 05:59:31 -0400 (Fri, 20 May 2022)
EllapsedTime: 401.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pi_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/Pi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.8.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ROCR::plot’ by ‘graphics::plot’ when loading ‘Pi’
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/Pi.Rcheck/00install.out’ for details.
* 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 ... WARNING
'::' or ':::' import not declared from: 'pbapply'
* 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: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/Pi.Rcheck/00check.log’
for details.



Installation output

Pi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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
EG0.0010.0010.000
GS0.0010.0000.000
aOnto0.0010.0000.000
cTarget0.0010.0010.000
dTarget0.0010.0000.000
eGSEA0.0010.0010.000
eTarget0.0010.0000.001
eTerm0.0010.0000.000
iSubg0.0010.0000.000
ls_eTerm0.0010.0000.000
pNode0.0010.0000.000
pPerf0.0010.0000.000
sGS000
sTarget000
xAggregate0.0000.0010.000
xCheckParallel0.0000.0000.001
xCircos0.0010.0010.001
xColormap0.0220.0050.026
xCombineNet0.0000.0010.000
xContour0.0560.0110.067
xConverter0.0390.0090.048
xCorrelation0.0010.0000.000
xDAGanno0.0010.0010.002
xDefineEQTL0.0000.0010.000
xDefineHIC0.0000.0000.001
xDefineNet0.0000.0010.001
xDefineOntology000
xEnrichForest0.0000.0000.001
xEnrichViewer000
xEnricher000
xEnricherGenes0.0000.0010.001
xGGnetwork0.0010.0010.002
xGR000
xGR2nGenes0.0000.0000.001
xGR2xGeneScores000
xGR2xGenes0.0000.0010.001
xGRscores0.0000.0000.001
xGRsort0.0010.0000.000
xGSEAbarplot0.0000.0010.000
xGSEAconciser0.0000.0000.001
xGSEAdotplot0.0000.0000.001
xGSsimulator000
xGeneID2Symbol000
xHeatmap0.0010.0010.001
xLayout0.0000.0000.001
xLiftOver0.0000.0000.001
xMEabf0.0000.0010.000
xMLcaret000
xMLcompare0.0010.0000.000
xMLdensity0.0000.0000.001
xMLdotplot000
xMLfeatureplot000
xMLglmnet0.0000.0000.001
xMLparameters000
xMLrandomforest0.0000.0010.000
xMLrename0.0000.0000.001
xMLzoom0.0000.0000.001
xPieplot000
xPier0.0010.0000.000
xPierABF000
xPierABFheatmap000
xPierAnno0.0000.0000.001
xPierCor0.0010.0000.001
xPierCross0.0010.0000.000
xPierEvidence0.0000.0010.000
xPierGRs0.0000.0000.001
xPierGSEA000
xPierGenes0.0000.0000.001
xPierMRS0.0010.0010.001
xPierManhattan0.0010.0000.000
xPierMatrix000
xPierPathways0.0000.0000.001
xPierROCR000
xPierSNPs0.0010.0000.000
xPierSNPsAdv000
xPierSNPsAdvABF000
xPierSubnet0.0000.0000.001
xPierTrack0.0000.0000.001
xPierTrackAdv000
xPredictCompare000
xPredictROCR000
xRDataLoader0.0000.0000.001
xRWR0.0010.0000.001
xSM2DF0.0180.0040.022
xSNP2cGenes0.0010.0010.000
xSNP2eGenes0.0010.0000.001
xSNP2nGenes0.0000.0000.001
xSNPlocations000
xSNPscores0.0000.0000.001
xSparseMatrix0.0160.0060.021
xSubneterGenes0.0000.0010.001
xSymbol2GeneID000
xVisEvidence0.0000.0000.001
xVisEvidenceAdv000
xVisKernels0.0260.0090.035
xVisNet0.0010.0010.001