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CHECK report for PADOG on merida2

This page was generated on 2019-04-09 13:27:22 -0400 (Tue, 09 Apr 2019).

Package 1137/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PADOG 1.25.0
Adi Laurentiu Tarca
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/PADOG
Branch: master
Last Commit: 221ddd6
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: PADOG
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PADOG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PADOG_1.25.0.tar.gz
StartedAt: 2019-04-09 02:41:50 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:45:43 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 232.7 seconds
RetCode: 0
Status:  OK 
CheckDir: PADOG.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PADOG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PADOG_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PADOG.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PADOG/DESCRIPTION’ ... OK
* this is package ‘PADOG’ version ‘1.25.0’
* 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 ‘PADOG’ 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
compPADOG: no visible global function definition for ‘data’
compPADOG : padogF: no visible global function definition for
  ‘p.adjust’
compPADOG : gsaF: no visible global function definition for ‘p.adjust’
compPADOG : <anonymous>: no visible global function definition for
  ‘complete.cases’
compPADOG : wi: no visible global function definition for ‘wilcox.test’
compPADOG: no visible binding for global variable ‘median’
compPADOG: no visible global function definition for ‘colors’
compPADOG: no visible global function definition for ‘par’
compPADOG: no visible global function definition for ‘boxplot’
compPADOG: no visible global function definition for ‘abline’
filteranot: no visible global function definition for ‘model.matrix’
padog: no visible global function definition for ‘quantile’
padog: no visible global function definition for ‘sd’
padog : combFun: no visible global function definition for ‘combn’
padog : gsScoreFun: no visible global function definition for
  ‘model.matrix’
padog : gsScoreFun : <anonymous>: no visible global function definition
  for ‘na.omit’
padog: no visible global function definition for ‘par’
padog: no visible global function definition for ‘boxplot’
padog: no visible global function definition for ‘points’
padog: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline boxplot colors combn complete.cases data median model.matrix
  na.omit p.adjust par points quantile sd wilcox.test
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "boxplot", "par", "points")
  importFrom("stats", "complete.cases", "median", "model.matrix",
             "na.omit", "p.adjust", "quantile", "sd", "wilcox.test")
  importFrom("utils", "combn", "data")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
compPADOG 14.314  2.108 106.788
padog     11.611  2.275  24.385
* 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-3.9-bioc/meat/PADOG.Rcheck/00check.log’
for details.



Installation output

PADOG.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PADOG
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PADOG’ ...
** R
** 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 (PADOG)

Tests output


Example timings

PADOG.Rcheck/PADOG-Ex.timings

nameusersystemelapsed
compPADOG 14.314 2.108106.788
filteranot1.9620.2702.409
padog11.611 2.27524.385