Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-06-07 11:05:33 -0400 (Wed, 07 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" 4628
palomino3Windows Server 2022 Datacenterx644.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" 4379
merida1macOS 12.6.4 Montereyx86_644.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" 4385
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:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Package 1516/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.12.0  (landing page)
Hai Fang
Snapshot Date: 2023-06-06 14:00:07 -0400 (Tue, 06 Jun 2023)
git_url: https://git.bioconductor.org/packages/Pi
git_branch: RELEASE_3_17
git_last_commit: e800362
git_last_commit_date: 2023-04-25 10:49:44 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Pi
Version: 2.12.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Pi_2.12.0.tar.gz
StartedAt: 2023-06-06 23:42:08 -0400 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 23:45:18 -0400 (Tue, 06 Jun 2023)
EllapsedTime: 190.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Pi_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Pi.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84269)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Pi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pi’ version ‘2.12.0’
* 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-3.17-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 loading without being on the library search path ... 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-3.17-bioc/meat/Pi.Rcheck/00check.log’
for details.



Installation output

Pi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Pi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
aOnto000
cTarget000
dTarget0.0010.0000.000
eGSEA000
eTarget000
eTerm0.0010.0000.000
iSubg000
ls_eTerm0.0000.0000.001
pNode000
pPerf000
sGS0.0000.0010.001
sTarget000
xAggregate000
xCheckParallel000
xCircos0.0000.0010.001
xColormap0.0120.0000.012
xCombineNet0.0000.0000.001
xContour0.0290.0000.028
xConverter0.0220.0000.021
xCorrelation0.0010.0000.000
xDAGanno0.0010.0000.001
xDefineEQTL0.0010.0000.000
xDefineHIC000
xDefineNet000
xDefineOntology0.0000.0010.001
xEnrichForest0.0000.0010.000
xEnrichViewer000
xEnricher0.0000.0000.001
xEnricherGenes000
xGGnetwork0.0010.0000.001
xGR0.0000.0000.001
xGR2nGenes0.0000.0000.001
xGR2xGeneScores000
xGR2xGenes0.0000.0010.001
xGRscores0.0000.0010.000
xGRsort000
xGSEAbarplot0.0000.0000.001
xGSEAconciser000
xGSEAdotplot000
xGSsimulator0.0000.0010.001
xGeneID2Symbol000
xHeatmap000
xLayout0.0000.0000.001
xLiftOver0.0000.0000.001
xMEabf000
xMLcaret000
xMLcompare0.0000.0010.001
xMLdensity000
xMLdotplot000
xMLfeatureplot0.0000.0010.000
xMLglmnet0.0000.0010.000
xMLparameters000
xMLrandomforest000
xMLrename0.0000.0010.000
xMLzoom0.0000.0010.000
xPieplot0.0000.0000.001
xPier0.0000.0000.001
xPierABF000
xPierABFheatmap000
xPierAnno0.0010.0000.000
xPierCor0.0010.0010.000
xPierCross0.0000.0000.001
xPierEvidence000
xPierGRs0.0010.0000.000
xPierGSEA0.0010.0000.000
xPierGenes0.0010.0000.000
xPierMRS000
xPierManhattan0.0000.0000.001
xPierMatrix000
xPierPathways0.0000.0010.000
xPierROCR000
xPierSNPs0.0000.0000.001
xPierSNPsAdv0.0000.0000.001
xPierSNPsAdvABF0.0000.0010.000
xPierSubnet0.0000.0010.000
xPierTrack000
xPierTrackAdv000
xPredictCompare000
xPredictROCR0.0000.0010.000
xRDataLoader000
xRWR0.0000.0010.001
xSM2DF0.0090.0000.010
xSNP2cGenes000
xSNP2eGenes000
xSNP2nGenes0.0010.0000.000
xSNPlocations000
xSNPscores0.0000.0010.001
xSparseMatrix0.0050.0030.008
xSubneterGenes0.0010.0000.001
xSymbol2GeneID0.0010.0000.000
xVisEvidence0.0000.0000.001
xVisEvidenceAdv000
xVisKernels0.0120.0070.018
xVisNet0.0000.0000.001