Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-10-19 13:23:28 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 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 20.04.5 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: 2022-10-19 06:10:07 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 06:16:47 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 399.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### 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 4.2.1 (2022-06-23)
* 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
EG0.0010.0000.001
GS0.0010.0010.001
aOnto0.0000.0010.001
cTarget0.0000.0000.001
dTarget0.0000.0000.001
eGSEA0.0010.0000.001
eTarget0.0000.0000.001
eTerm000
iSubg000
ls_eTerm0.0000.0000.001
pNode0.0000.0000.001
pPerf000
sGS000
sTarget000
xAggregate000
xCheckParallel000
xCircos0.0000.0000.001
xColormap0.0240.0070.030
xCombineNet000
xContour0.0550.0150.073
xConverter0.0480.0130.060
xCorrelation000
xDAGanno0.0010.0010.000
xDefineEQTL0.0010.0000.000
xDefineHIC0.0010.0000.001
xDefineNet0.0000.0010.001
xDefineOntology000
xEnrichForest000
xEnrichViewer000
xEnricher0.0010.0010.001
xEnricherGenes0.0010.0010.001
xGGnetwork0.0000.0010.001
xGR0.0010.0010.000
xGR2nGenes0.0010.0000.001
xGR2xGeneScores0.0000.0000.001
xGR2xGenes0.0000.0010.001
xGRscores0.0000.0000.001
xGRsort000
xGSEAbarplot0.0010.0000.000
xGSEAconciser0.0010.0000.000
xGSEAdotplot0.0000.0000.001
xGSsimulator0.0000.0010.000
xGeneID2Symbol000
xHeatmap0.0000.0000.001
xLayout0.0000.0010.001
xLiftOver0.0000.0000.001
xMEabf000
xMLcaret0.0000.0010.000
xMLcompare000
xMLdensity0.0010.0000.000
xMLdotplot0.0010.0000.000
xMLfeatureplot000
xMLglmnet000
xMLparameters0.0000.0010.000
xMLrandomforest000
xMLrename0.0000.0010.001
xMLzoom000
xPieplot000
xPier0.0010.0000.001
xPierABF000
xPierABFheatmap0.0000.0000.001
xPierAnno000
xPierCor000
xPierCross0.0000.0010.000
xPierEvidence000
xPierGRs000
xPierGSEA000
xPierGenes0.0000.0000.001
xPierMRS000
xPierManhattan0.0000.0010.001
xPierMatrix000
xPierPathways000
xPierROCR000
xPierSNPs0.0000.0000.001
xPierSNPsAdv0.0000.0010.000
xPierSNPsAdvABF000
xPierSubnet0.0010.0000.001
xPierTrack0.0010.0010.001
xPierTrackAdv0.0000.0000.001
xPredictCompare0.0000.0000.001
xPredictROCR000
xRDataLoader000
xRWR0.0010.0000.001
xSM2DF0.0190.0060.025
xSNP2cGenes000
xSNP2eGenes0.0000.0000.001
xSNP2nGenes000
xSNPlocations0.0000.0010.000
xSNPscores0.0000.0000.001
xSparseMatrix0.0180.0060.024
xSubneterGenes0.0010.0000.001
xSymbol2GeneID000
xVisEvidence000
xVisEvidenceAdv000
xVisKernels0.0280.0130.041
xVisNet0.0000.0000.001