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BioC 3.5: CHECK report for CompGO on oaxaca

This page was generated on 2017-03-04 16:47:13 -0500 (Sat, 04 Mar 2017).

Package 255/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CompGO 1.11.0
Ashley J. Waardenberg
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CompGO
Last Changed Rev: 123151 / Revision: 127142
Last Changed Date: 2016-10-28 13:43:39 -0400 (Fri, 28 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  TIMEOUT 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: CompGO
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CompGO_1.11.0.tar.gz
StartedAt: 2017-03-04 01:03:54 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 01:08:55 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 301.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CompGO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CompGO_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CompGO.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CompGO/DESCRIPTION’ ... OK
* this is package ‘CompGO’ version ‘1.11.0’
* 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 ‘CompGO’ 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 loading without being on the library search path ... 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
PCAplot: no visible global function definition for ‘par’
PCAplot: no visible global function definition for ‘text’
compareZscores: no visible global function definition for ‘pnorm’
compareZscores: no visible global function definition for ‘p.adjust’
compareZscores: no visible global function definition for ‘setNames’
doZtrans.single: no visible binding for global variable ‘Term’
doZtrans.single: no visible binding for global variable ‘Z’
plotDendrogram: no visible global function definition for ‘cor’
plotDendrogram: no visible global function definition for ‘hclust’
plotDendrogram: no visible global function definition for ‘dist’
plotInteractive: no visible global function definition for ‘cor’
plotInteractive: no visible global function definition for ‘hclust’
plotInteractive: no visible global function definition for ‘dist’
plotInteractive: no visible global function definition for ‘png’
plotInteractive: no visible global function definition for ‘par’
plotInteractive: no visible global function definition for ‘dev.off’
plotInteractive: no visible global function definition for ‘text’
plotInteractive: no visible binding for global variable ‘Var1’
plotInteractive: no visible binding for global variable ‘Var2’
plotInteractive: no visible binding for global variable ‘value’
plotPairwise: no visible global function definition for
  ‘complete.cases’
plotPairwise: no visible global function definition for ‘setNames’
plotPairwise: no visible global function definition for ‘cor’
plotTwoGODags: no visible global function definition for ‘goDag’
plotTwoGODags: no visible global function definition for ‘nodes’
plotTwoGODags: no visible global function definition for
  ‘nodeRenderInfo<-’
plotZRankedDAG: no visible global function definition for ‘goDag’
plotZRankedDAG: no visible global function definition for ‘nodes’
plotZRankedDAG: no visible global function definition for
  ‘nodeRenderInfo<-’
plotZScores: no visible global function definition for ‘complete.cases’
plotZScores: no visible global function definition for ‘setNames’
plotZScores: no visible global function definition for ‘cor’
slidingJaccard: no visible binding for global variable ‘useRawPvals’
zTransformDirectory: no visible global function definition for
  ‘read.table’
zTransformDirectory: no visible global function definition for
  ‘complete.cases’
zTransformDirectory: no visible binding for global variable ‘var’
Undefined global functions or variables:
  Term Var1 Var2 Z complete.cases cor dev.off dist goDag hclust
  nodeRenderInfo<- nodes p.adjust par png pnorm read.table setNames
  text useRawPvals value var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "complete.cases", "cor", "dist", "hclust",
             "p.adjust", "pnorm", "setNames", "var")
  importFrom("utils", "read.table")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plotTwoGODags 7.371  0.135    7.64
* 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-3.5-bioc/meat/CompGO.Rcheck/00check.log’
for details.


CompGO.Rcheck/00install.out:

* installing *source* package ‘CompGO’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CompGO)

CompGO.Rcheck/CompGO-Ex.timings:

nameusersystemelapsed
annotateBedFromDb2.0290.0962.237
compareZscores0.1930.0090.235
doZtrans.single0.0060.0020.008
getFnAnot_genome000
plotPairwise1.5420.0141.557
plotTwoGODags7.3710.1357.640
plotZRankedDAG0.0010.0000.001
plotZScores2.4010.0092.413
slidingJaccard0.0810.0050.085
viewKegg000
zTransformDirectory0.0000.0000.001