Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:08:09 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 machv2


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? here 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 1416/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.6.0  (landing page)
Hai Fang
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/Pi
git_branch: RELEASE_3_14
git_last_commit: 0c06e8e
git_last_commit_date: 2021-10-26 12:30:09 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Pi
Version: 2.6.0
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_2.6.0.tar.gz
StartedAt: 2022-01-16 16:23:52 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 16:29:22 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 330.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 1

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_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Pi.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.6.0’
* 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-3.14-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 ... 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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
EG0.0010.0000.000
GS0.0010.0000.001
aOnto000
cTarget0.0000.0000.001
dTarget000
eGSEA000
eTarget0.0000.0010.000
eTerm0.0000.0010.001
iSubg0.0000.0000.001
ls_eTerm000
pNode000
pPerf000
sGS0.0000.0010.001
sTarget0.0000.0010.000
xAggregate0.0000.0010.000
xCheckParallel0.0000.0010.000
xCircos0.0010.0010.002
xColormap0.0220.0070.028
xCombineNet0.0010.0010.000
xContour0.0550.0160.069
xConverter0.0340.0080.041
xCorrelation0.0000.0010.001
xDAGanno0.0010.0020.002
xDefineEQTL000
xDefineHIC0.0000.0000.001
xDefineNet0.0000.0000.001
xDefineOntology0.0000.0000.001
xEnrichForest0.0000.0010.001
xEnrichViewer000
xEnricher0.0000.0010.002
xEnricherGenes0.0000.0010.001
xGGnetwork0.0010.0020.003
xGR0.0000.0000.001
xGR2nGenes0.0000.0010.001
xGR2xGeneScores0.0000.0010.001
xGR2xGenes0.0010.0020.002
xGRscores0.0010.0010.001
xGRsort0.0010.0010.001
xGSEAbarplot0.0000.0010.000
xGSEAconciser0.0000.0000.001
xGSEAdotplot0.0000.0000.001
xGSsimulator0.0000.0000.001
xGeneID2Symbol0.0000.0000.001
xHeatmap0.0000.0000.001
xLayout0.0000.0000.001
xLiftOver0.0000.0010.000
xMEabf0.0010.0010.001
xMLcaret0.0010.0010.001
xMLcompare0.0010.0000.000
xMLdensity000
xMLdotplot0.0000.0010.000
xMLfeatureplot000
xMLglmnet000
xMLparameters000
xMLrandomforest000
xMLrename0.0010.0010.001
xMLzoom0.0000.0010.001
xPieplot0.0000.0010.001
xPier0.0000.0010.000
xPierABF0.0000.0010.000
xPierABFheatmap0.0000.0010.000
xPierAnno0.0010.0010.001
xPierCor0.0000.0000.001
xPierCross0.0000.0000.001
xPierEvidence000
xPierGRs0.0000.0010.000
xPierGSEA0.0000.0010.000
xPierGenes0.0000.0000.001
xPierMRS000
xPierManhattan0.0000.0010.001
xPierMatrix0.0000.0000.001
xPierPathways0.0010.0000.001
xPierROCR000
xPierSNPs0.0010.0000.000
xPierSNPsAdv0.0000.0000.001
xPierSNPsAdvABF000
xPierSubnet0.0010.0000.001
xPierTrack0.0010.0000.001
xPierTrackAdv000
xPredictCompare0.0010.0000.001
xPredictROCR0.0010.0000.001
xRDataLoader0.0010.0010.001
xRWR0.0010.0010.002
xSM2DF0.0170.0040.021
xSNP2cGenes000
xSNP2eGenes000
xSNP2nGenes0.0010.0000.001
xSNPlocations0.0010.0000.001
xSNPscores0.0010.0000.001
xSparseMatrix0.0140.0040.019
xSubneterGenes0.0000.0010.001
xSymbol2GeneID0.0000.0010.001
xVisEvidence0.0000.0010.001
xVisEvidenceAdv000
xVisKernels0.0220.0140.035
xVisNet0.0000.0000.001