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CHECK report for Pi on merida1

This page was generated on 2019-04-16 11:59:57 -0400 (Tue, 16 Apr 2019).

Package 1156/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 1.10.0
Hai Fang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Pi
Branch: RELEASE_3_8
Last Commit: 4801867
Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Pi
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pi_1.10.0.tar.gz
StartedAt: 2019-04-16 01:54:29 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:00:50 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 380.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Pi.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pi_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Pi.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pi’ version ‘1.10.0’
* 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 ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
xPierCor: no visible global function definition for 'xCorrelation'
Undefined global functions or variables:
  xCorrelation
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/Pi.Rcheck/00check.log’
for details.



Installation output

Pi.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Pi’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Pi)

Tests output


Example timings

Pi.Rcheck/Pi-Ex.timings

nameusersystemelapsed
cTarget0.0000.0000.001
dTarget0.0000.0000.001
eGSEA000
eTarget000
pNode0.0010.0000.000
pPerf000
sGS000
sTarget000
xContour0.0310.0010.032
xGSEAbarplot0.0010.0000.001
xGSEAconciser000
xGSEAdotplot0.0000.0000.001
xGSsimulator0.0000.0000.001
xMLcaret000
xMLcompare000
xMLdensity0.0000.0000.001
xMLdotplot000
xMLfeatureplot0.0000.0000.001
xMLglmnet0.0010.0000.000
xMLparameters0.0000.0010.001
xMLrandomforest000
xMLrename000
xMLzoom0.0000.0010.001
xPieplot000
xPier0.0000.0000.001
xPierAnno0.0010.0000.001
xPierCor0.0010.0000.000
xPierCross000
xPierEvidence000
xPierGRs000
xPierGSEA0.0010.0000.000
xPierGenes0.0000.0010.000
xPierKEGG000
xPierManhattan0.0000.0000.001
xPierMatrix000
xPierPathways0.0000.0000.001
xPierROCR0.0010.0000.001
xPierSNPs0.0010.0000.000
xPierSNPsAdv0.0010.0010.001
xPierSNPsConsensus0.0000.0000.001
xPierSubnet0.0010.0000.001
xPierTrack0.0000.0010.001
xPierTrackAdv0.0010.0000.000
xPredictCompare000
xPredictROCR0.0000.0000.001
xRWR0.0020.0010.002
xSNP2cGenes000
xSNP2eGenes000
xVisEvidence000
xVisEvidenceAdv000