Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:05:54 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 nebbiolo1


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: 2022-05-17 13:55:01 -0400 (Tue, 17 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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Pi_2.8.0.tar.gz
StartedAt: 2022-05-17 20:54:20 -0400 (Tue, 17 May 2022)
EndedAt: 2022-05-17 20:57:34 -0400 (Tue, 17 May 2022)
EllapsedTime: 193.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Pi_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Pi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.8.0’
* 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 ‘/home/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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Pi.Rcheck/00check.log’
for details.



Installation output

Pi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Pi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
GS000
aOnto0.0000.0000.001
cTarget0.0000.0000.001
dTarget000
eGSEA0.0010.0000.000
eTarget0.0010.0000.000
eTerm000
iSubg000
ls_eTerm0.0000.0000.001
pNode000
pPerf0.0010.0000.000
sGS0.0010.0000.000
sTarget000
xAggregate000
xCheckParallel0.0000.0000.001
xCircos0.0010.0000.001
xColormap0.0110.0040.014
xCombineNet0.0000.0000.001
xContour0.0310.0040.034
xConverter0.0210.0040.025
xCorrelation0.0000.0010.000
xDAGanno0.0000.0010.001
xDefineEQTL0.0000.0000.001
xDefineHIC0.0000.0000.001
xDefineNet0.0000.0000.001
xDefineOntology0.0000.0000.001
xEnrichForest0.0000.0000.001
xEnrichViewer000
xEnricher0.0010.0000.001
xEnricherGenes0.0010.0000.001
xGGnetwork0.0010.0000.002
xGR000
xGR2nGenes0.0000.0010.000
xGR2xGeneScores000
xGR2xGenes0.0000.0000.001
xGRscores000
xGRsort000
xGSEAbarplot000
xGSEAconciser000
xGSEAdotplot0.0000.0000.001
xGSsimulator0.0000.0000.001
xGeneID2Symbol0.0000.0000.001
xHeatmap0.0000.0000.001
xLayout0.0000.0000.001
xLiftOver0.0000.0000.001
xMEabf0.0000.0000.001
xMLcaret0.0000.0000.001
xMLcompare000
xMLdensity0.0010.0010.000
xMLdotplot000
xMLfeatureplot0.0000.0000.001
xMLglmnet0.0000.0000.001
xMLparameters0.0000.0010.000
xMLrandomforest0.0000.0010.000
xMLrename0.0000.0010.001
xMLzoom000
xPieplot0.0000.0010.000
xPier0.0000.0010.000
xPierABF0.0000.0010.000
xPierABFheatmap0.0000.0010.000
xPierAnno0.0000.0010.000
xPierCor0.0000.0000.001
xPierCross000
xPierEvidence0.0010.0000.000
xPierGRs0.0010.0000.000
xPierGSEA0.0000.0010.000
xPierGenes0.0000.0010.000
xPierMRS000
xPierManhattan0.0000.0010.000
xPierMatrix0.0000.0010.000
xPierPathways0.0000.0010.001
xPierROCR0.0000.0010.000
xPierSNPs0.0000.0010.000
xPierSNPsAdv0.0000.0010.001
xPierSNPsAdvABF0.0000.0010.000
xPierSubnet0.0000.0010.001
xPierTrack0.0000.0000.001
xPierTrackAdv0.0010.0000.000
xPredictCompare000
xPredictROCR0.0010.0000.000
xRDataLoader0.0010.0000.000
xRWR0.0000.0010.002
xSM2DF0.0100.0010.011
xSNP2cGenes0.0010.0000.000
xSNP2eGenes000
xSNP2nGenes0.0000.0050.005
xSNPlocations0.0000.0000.001
xSNPscores0.0000.0000.001
xSparseMatrix0.0120.0010.012
xSubneterGenes0.0010.0000.002
xSymbol2GeneID0.0010.0000.001
xVisEvidence0.0010.0000.001
xVisEvidenceAdv000
xVisKernels0.0100.0120.022
xVisNet0.0010.0000.001