Back to Build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-06-06 11:00:38 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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 kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1496/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.13.0  (landing page)
Hai Fang
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/Pi
git_branch: devel
git_last_commit: 27559f8
git_last_commit_date: 2023-04-25 14:49:44 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

Summary

Package: Pi
Version: 2.13.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Pi_2.13.0.tar.gz
StartedAt: 2023-06-06 04:08:41 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 04:12:52 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 250.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Pi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Pi_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Pi.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘Pi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pi’ version ‘2.13.0’
* 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/R/R-4.3.0/bin/R CMD INSTALL Pi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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
EG0.0000.0000.001
GS0.0000.0000.001
aOnto000
cTarget000
dTarget000
eGSEA000
eTarget000
eTerm000
iSubg000
ls_eTerm000
pNode0.0000.0000.001
pPerf000
sGS000
sTarget000
xAggregate0.0010.0000.000
xCheckParallel000
xCircos0.0000.0010.001
xColormap0.0120.0030.015
xCombineNet0.0010.0000.000
xContour0.0310.0040.034
xConverter0.0250.0040.028
xCorrelation000
xDAGanno0.0010.0000.000
xDefineEQTL000
xDefineHIC000
xDefineNet000
xDefineOntology000
xEnrichForest000
xEnrichViewer000
xEnricher000
xEnricherGenes0.0000.0010.001
xGGnetwork0.0000.0010.001
xGR0.0000.0000.001
xGR2nGenes000
xGR2xGeneScores000
xGR2xGenes0.0000.0010.000
xGRscores0.0000.0000.001
xGRsort000
xGSEAbarplot000
xGSEAconciser000
xGSEAdotplot000
xGSsimulator000
xGeneID2Symbol000
xHeatmap000
xLayout000
xLiftOver000
xMEabf000
xMLcaret000
xMLcompare000
xMLdensity000
xMLdotplot0.0000.0000.001
xMLfeatureplot0.0010.0000.000
xMLglmnet000
xMLparameters000
xMLrandomforest000
xMLrename000
xMLzoom000
xPieplot000
xPier000
xPierABF0.0000.0000.001
xPierABFheatmap0.0010.0000.000
xPierAnno000
xPierCor0.0000.0000.001
xPierCross000
xPierEvidence000
xPierGRs0.0000.0000.001
xPierGSEA000
xPierGenes000
xPierMRS0.0000.0000.001
xPierManhattan000
xPierMatrix000
xPierPathways000
xPierROCR000
xPierSNPs000
xPierSNPsAdv000
xPierSNPsAdvABF000
xPierSubnet0.0010.0000.000
xPierTrack000
xPierTrackAdv0.0000.0000.001
xPredictCompare0.0010.0000.000
xPredictROCR000
xRDataLoader000
xRWR0.0010.0000.001
xSM2DF0.0070.0040.011
xSNP2cGenes000
xSNP2eGenes000
xSNP2nGenes0.0000.0000.001
xSNPlocations000
xSNPscores000
xSparseMatrix0.0090.0000.009
xSubneterGenes0.0010.0000.000
xSymbol2GeneID000
xVisEvidence000
xVisEvidenceAdv000
xVisKernels0.0110.0080.019
xVisNet0.0000.0000.001