Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:51 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 tokay2


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? here 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 1416/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 2.6.0  (landing page)
Hai Fang
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/Pi
git_branch: RELEASE_3_14
git_last_commit: 0c06e8e
git_last_commit_date: 2021-10-26 12:30:09 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Pi
Version: 2.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pi.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Pi_2.6.0.tar.gz
StartedAt: 2022-01-21 00:34:34 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 00:38:58 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 263.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Pi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pi.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Pi_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Pi.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Pi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pi' version '2.6.0'
* 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 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 'C:/Users/biocbuild/bbs-3.14-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/Pi.Rcheck/00check.log'
for details.



Installation output

Pi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Pi_2.6.0.tar.gz && rm -rf Pi.buildbin-libdir && mkdir Pi.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pi.buildbin-libdir Pi_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Pi_2.6.0.zip && rm Pi_2.6.0.tar.gz Pi_2.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1207k  100 1207k    0     0  2681k      0 --:--:-- --:--:-- --:--:-- 2684k

install for i386

* 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
  converting help for package 'Pi'
    finding HTML links ... done
    EG                                      html  
    GS                                      html  
    aOnto                                   html  
    cTarget                                 html  
    dTarget                                 html  
    eGSEA                                   html  
    eTarget                                 html  
    eTerm                                   html  
    iSubg                                   html  
    ls_eTerm                                html  
    pNode                                   html  
    pPerf                                   html  
    sGS                                     html  
    sTarget                                 html  
    xAggregate                              html  
    xCheckParallel                          html  
    xCircos                                 html  
    xColormap                               html  
    xCombineNet                             html  
    xContour                                html  
    xConverter                              html  
    xCorrelation                            html  
    xDAGanno                                html  
    xDefineEQTL                             html  
    xDefineHIC                              html  
    xDefineNet                              html  
    xDefineOntology                         html  
    xEnrichForest                           html  
    xEnrichViewer                           html  
    xEnricher                               html  
    xEnricherGenes                          html  
    xGGnetwork                              html  
    xGR                                     html  
    xGR2nGenes                              html  
    xGR2xGeneScores                         html  
    xGR2xGenes                              html  
    xGRscores                               html  
    xGRsort                                 html  
    xGSEAbarplot                            html  
    xGSEAconciser                           html  
    xGSEAdotplot                            html  
    xGSsimulator                            html  
    xGeneID2Symbol                          html  
    xHeatmap                                html  
    xLayout                                 html  
    xLiftOver                               html  
    xMEabf                                  html  
    xMLcaret                                html  
    xMLcompare                              html  
    xMLdensity                              html  
    xMLdotplot                              html  
    xMLfeatureplot                          html  
    xMLglmnet                               html  
    xMLparameters                           html  
    xMLrandomforest                         html  
    xMLrename                               html  
    xMLzoom                                 html  
    xPieplot                                html  
    xPier                                   html  
    xPierABF                                html  
    xPierABFheatmap                         html  
    xPierAnno                               html  
    xPierCor                                html  
    xPierCross                              html  
    xPierEvidence                           html  
    xPierGRs                                html  
    xPierGSEA                               html  
    xPierGenes                              html  
    xPierMRS                                html  
    xPierManhattan                          html  
    xPierMatrix                             html  
    xPierPathways                           html  
    xPierROCR                               html  
    xPierSNPs                               html  
    xPierSNPsAdv                            html  
    xPierSNPsAdvABF                         html  
    xPierSubnet                             html  
    xPierTrack                              html  
    xPierTrackAdv                           html  
    xPredictCompare                         html  
    xPredictROCR                            html  
    xRDataLoader                            html  
    xRWR                                    html  
    xSM2DF                                  html  
    xSNP2cGenes                             html  
    xSNP2eGenes                             html  
    xSNP2nGenes                             html  
    xSNPlocations                           html  
    xSNPscores                              html  
    xSparseMatrix                           html  
    xSubneterGenes                          html  
    xSymbol2GeneID                          html  
    xVisEvidence                            html  
    xVisEvidenceAdv                         html  
    xVisKernels                             html  
    xVisNet                                 html  
** 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

install for x64

* installing *source* package 'Pi' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ROCR::plot' by 'graphics::plot' when loading 'Pi'
* MD5 sums
packaged installation of 'Pi' as Pi_2.6.0.zip
* DONE (Pi)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Pi' successfully unpacked and MD5 sums checked

Tests output


Example timings

Pi.Rcheck/examples_i386/Pi-Ex.timings

nameusersystemelapsed
EG000
GS000
aOnto000
cTarget000
dTarget000
eGSEA000
eTarget000
eTerm000
iSubg000
ls_eTerm000
pNode000
pPerf000
sGS000
sTarget000
xAggregate000
xCheckParallel000
xCircos000
xColormap0.020.000.01
xCombineNet0.020.000.02
xContour0.040.010.06
xConverter0.050.000.05
xCorrelation000
xDAGanno000
xDefineEQTL000
xDefineHIC000
xDefineNet000
xDefineOntology000
xEnrichForest000
xEnrichViewer000
xEnricher000
xEnricherGenes000
xGGnetwork000
xGR000
xGR2nGenes000
xGR2xGeneScores000
xGR2xGenes000
xGRscores000
xGRsort000
xGSEAbarplot000
xGSEAconciser000
xGSEAdotplot000
xGSsimulator000
xGeneID2Symbol000
xHeatmap000
xLayout000
xLiftOver000
xMEabf000
xMLcaret000
xMLcompare000
xMLdensity000
xMLdotplot000
xMLfeatureplot000
xMLglmnet000
xMLparameters000
xMLrandomforest000
xMLrename000
xMLzoom000
xPieplot000
xPier000
xPierABF000
xPierABFheatmap000
xPierAnno000
xPierCor000
xPierCross000
xPierEvidence000
xPierGRs000
xPierGSEA000
xPierGenes000
xPierMRS000
xPierManhattan000
xPierMatrix000
xPierPathways000
xPierROCR000
xPierSNPs000
xPierSNPsAdv000
xPierSNPsAdvABF000
xPierSubnet000
xPierTrack000
xPierTrackAdv000
xPredictCompare000
xPredictROCR000
xRDataLoader000
xRWR000
xSM2DF0.010.000.01
xSNP2cGenes000
xSNP2eGenes000
xSNP2nGenes000
xSNPlocations000
xSNPscores000
xSparseMatrix0.020.000.02
xSubneterGenes000
xSymbol2GeneID000
xVisEvidence000
xVisEvidenceAdv000
xVisKernels0.110.030.17
xVisNet000

Pi.Rcheck/examples_x64/Pi-Ex.timings

nameusersystemelapsed
EG000
GS000
aOnto000
cTarget000
dTarget000
eGSEA000
eTarget000
eTerm000
iSubg000
ls_eTerm000
pNode000
pPerf000
sGS000
sTarget000
xAggregate000
xCheckParallel000
xCircos000
xColormap0.010.000.02
xCombineNet000
xContour0.030.000.03
xConverter0.030.000.08
xCorrelation000
xDAGanno000
xDefineEQTL000
xDefineHIC000
xDefineNet000
xDefineOntology000
xEnrichForest000
xEnrichViewer000
xEnricher000
xEnricherGenes000
xGGnetwork000
xGR000
xGR2nGenes000
xGR2xGeneScores000
xGR2xGenes000
xGRscores000
xGRsort000
xGSEAbarplot000
xGSEAconciser000
xGSEAdotplot000
xGSsimulator000
xGeneID2Symbol000
xHeatmap000
xLayout000
xLiftOver000
xMEabf000
xMLcaret000
xMLcompare000
xMLdensity000
xMLdotplot0.010.000.02
xMLfeatureplot000
xMLglmnet000
xMLparameters000
xMLrandomforest000
xMLrename000
xMLzoom000
xPieplot000
xPier000
xPierABF000
xPierABFheatmap000
xPierAnno000
xPierCor000
xPierCross000
xPierEvidence000
xPierGRs000
xPierGSEA000
xPierGenes000
xPierMRS000
xPierManhattan000
xPierMatrix000
xPierPathways000
xPierROCR000
xPierSNPs000
xPierSNPsAdv000
xPierSNPsAdvABF000
xPierSubnet000
xPierTrack000
xPierTrackAdv000
xPredictCompare000
xPredictROCR000
xRDataLoader000
xRWR000
xSM2DF0.010.000.01
xSNP2cGenes000
xSNP2eGenes000
xSNP2nGenes000
xSNPlocations000
xSNPscores000
xSparseMatrix0.020.000.02
xSubneterGenes000
xSymbol2GeneID000
xVisEvidence000
xVisEvidenceAdv000
xVisKernels0.130.020.15
xVisNet000