Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-04 11:35:54 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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

Package 1547/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.14.0  (landing page)
Hai Fang
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/Pi
git_branch: RELEASE_3_18
git_last_commit: 213330b
git_last_commit_date: 2023-10-24 10:52:52 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for Pi on nebbiolo2


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


Summary

Package: Pi
Version: 2.14.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Pi_2.14.0.tar.gz
StartedAt: 2024-03-04 01:12:56 -0500 (Mon, 04 Mar 2024)
EndedAt: 2024-03-04 01:16:10 -0500 (Mon, 04 Mar 2024)
EllapsedTime: 194.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings Pi_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Pi.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Pi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pi’ version ‘2.14.0’
* 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-3.18-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-3.18-bioc/meat/Pi.Rcheck/00check.log’
for details.



Installation output

Pi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL Pi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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
dTarget000
eGSEA000
eTarget000
eTerm000
iSubg000
ls_eTerm000
pNode000
pPerf000
sGS000
sTarget000
xAggregate0.0000.0000.001
xCheckParallel000
xCircos0.0000.0000.001
xColormap0.010.000.01
xCombineNet000
xContour0.0290.0000.029
xConverter0.0230.0030.026
xCorrelation000
xDAGanno000
xDefineEQTL000
xDefineHIC000
xDefineNet000
xDefineOntology000
xEnrichForest000
xEnrichViewer000
xEnricher0.0000.0000.001
xEnricherGenes000
xGGnetwork0.0010.0000.000
xGR000
xGR2nGenes0.0010.0000.000
xGR2xGeneScores000
xGR2xGenes0.0010.0000.000
xGRscores000
xGRsort000
xGSEAbarplot000
xGSEAconciser0.0000.0000.001
xGSEAdotplot0.0010.0000.000
xGSsimulator000
xGeneID2Symbol000
xHeatmap000
xLayout0.0000.0000.001
xLiftOver000
xMEabf0.0000.0000.001
xMLcaret0.0000.0010.000
xMLcompare000
xMLdensity000
xMLdotplot000
xMLfeatureplot000
xMLglmnet000
xMLparameters000
xMLrandomforest000
xMLrename000
xMLzoom0.0000.0000.001
xPieplot0.0010.0000.000
xPier0.0000.0000.001
xPierABF000
xPierABFheatmap000
xPierAnno000
xPierCor000
xPierCross000
xPierEvidence000
xPierGRs000
xPierGSEA0.0010.0000.000
xPierGenes000
xPierMRS000
xPierManhattan000
xPierMatrix000
xPierPathways000
xPierROCR0.0000.0000.001
xPierSNPs0.0010.0000.000
xPierSNPsAdv000
xPierSNPsAdvABF000
xPierSubnet000
xPierTrack000
xPierTrackAdv000
xPredictCompare000
xPredictROCR000
xRDataLoader000
xRWR0.0010.0000.000
xSM2DF0.0050.0030.008
xSNP2cGenes000
xSNP2eGenes000
xSNP2nGenes000
xSNPlocations0.0000.0000.001
xSNPscores000
xSparseMatrix0.0020.0030.007
xSubneterGenes000
xSymbol2GeneID0.0010.0010.000
xVisEvidence000
xVisEvidenceAdv000
xVisKernels0.0160.0000.016
xVisNet000