Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-12-09 11:06:36 -0500 (Fri, 09 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4506
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4283
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4312
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 nebbiolo2


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 1482/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.10.0  (landing page)
Hai Fang
Snapshot Date: 2022-12-08 14:00:03 -0500 (Thu, 08 Dec 2022)
git_url: https://git.bioconductor.org/packages/Pi
git_branch: RELEASE_3_16
git_last_commit: a5ca530
git_last_commit_date: 2022-11-01 11:14:29 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Pi
Version: 2.10.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings Pi_2.10.0.tar.gz
StartedAt: 2022-12-08 22:18:26 -0500 (Thu, 08 Dec 2022)
EndedAt: 2022-12-08 22:25:13 -0500 (Thu, 08 Dec 2022)
EllapsedTime: 407.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings Pi_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Pi.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘Pi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pi’ version ‘2.10.0’
* 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-3.16-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 ...
  ‘Pi_vignettes.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/Pi.Rcheck/00check.log’
for details.



Installation output

Pi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Pi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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
GS0.0000.0000.001
aOnto000
cTarget000
dTarget000
eGSEA0.0000.0000.001
eTarget000
eTerm0.0000.0000.001
iSubg000
ls_eTerm000
pNode000
pPerf0.0010.0000.000
sGS000
sTarget000
xAggregate000
xCheckParallel000
xCircos0.0010.0000.000
xColormap0.0130.0100.022
xCombineNet000
xContour0.0530.0050.057
xConverter0.0390.0040.044
xCorrelation0.0010.0000.000
xDAGanno0.0010.0000.000
xDefineEQTL000
xDefineHIC0.0000.0000.001
xDefineNet0.0000.0000.001
xDefineOntology0.0000.0010.000
xEnrichForest0.0000.0010.000
xEnrichViewer000
xEnricher0.0010.0000.000
xEnricherGenes0.0010.0000.000
xGGnetwork0.0010.0000.000
xGR000
xGR2nGenes0.0000.0010.000
xGR2xGeneScores0.0000.0010.000
xGR2xGenes000
xGRscores000
xGRsort000
xGSEAbarplot0.0000.0000.001
xGSEAconciser000
xGSEAdotplot000
xGSsimulator000
xGeneID2Symbol0.0000.0000.001
xHeatmap000
xLayout000
xLiftOver000
xMEabf0.0010.0000.000
xMLcaret000
xMLcompare000
xMLdensity000
xMLdotplot000
xMLfeatureplot000
xMLglmnet000
xMLparameters000
xMLrandomforest0.0000.0000.001
xMLrename0.0000.0010.000
xMLzoom000
xPieplot000
xPier000
xPierABF000
xPierABFheatmap0.0000.0000.001
xPierAnno0.0000.0010.000
xPierCor000
xPierCross000
xPierEvidence000
xPierGRs0.0000.0010.000
xPierGSEA000
xPierGenes000
xPierMRS000
xPierManhattan0.0010.0000.000
xPierMatrix0.0000.0000.001
xPierPathways0.0000.0000.001
xPierROCR000
xPierSNPs000
xPierSNPsAdv000
xPierSNPsAdvABF0.0010.0000.000
xPierSubnet0.0000.0000.001
xPierTrack0.0000.0000.001
xPierTrackAdv000
xPredictCompare000
xPredictROCR000
xRDataLoader0.0000.0000.001
xRWR0.0010.0000.001
xSM2DF0.0200.0040.078
xSNP2cGenes0.0010.0000.001
xSNP2eGenes000
xSNP2nGenes000
xSNPlocations0.0000.0000.001
xSNPscores0.0000.0010.000
xSparseMatrix0.0110.0060.031
xSubneterGenes0.0010.0000.000
xSymbol2GeneID0.0010.0000.000
xVisEvidence000
xVisEvidenceAdv000
xVisKernels0.0340.0000.081
xVisNet0.0010.0000.000