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BioC 3.3: CHECK report for ReportingTools on oaxaca

This page was generated on 2016-10-13 12:58:38 -0700 (Thu, 13 Oct 2016).

Package 962/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReportingTools 2.12.2
Jason A. Hackney , Gabriel Becker , Jessica L. Larson
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ReportingTools
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ReportingTools
Version: 2.12.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ReportingTools_2.12.2.tar.gz
StartedAt: 2016-10-13 05:39:19 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 05:47:38 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 498.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ReportingTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ReportingTools_2.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ReportingTools.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReportingTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReportingTools’ version ‘2.12.2’
* 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 ‘ReportingTools’ 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
.DGEExact.to.data.frame: no visible global function definition for
  'p.adjust'
.DGEExact.to.html: no visible global function definition for 'p.adjust'
.DGELRT.to.data.frame: no visible global function definition for
  'p.adjust'
.DGELRT.to.html: no visible global function definition for 'p.adjust'
.GOhyperG.to.html: no visible global function definition for 'png'
.GOhyperG.to.html: no visible global function definition for 'dev.off'
.GOhyperG.to.html: no visible global function definition for 'pdf'
.GOhyperG.to.html2: no visible global function definition for 'png'
.GOhyperG.to.html2: no visible global function definition for 'dev.off'
.GOhyperG.to.html2: no visible global function definition for 'pdf'
.GeneSetCollection.to.data.frame: no visible binding for global
  variable 'description'
.GeneSetCollection.to.html: no visible binding for global variable
  'description'
.GeneSetCollection.to.html2: no visible binding for global variable
  'description'
.PFAMhyperG.to.html: no visible global function definition for 'png'
.PFAMhyperG.to.html: no visible global function definition for
  'dev.off'
.PFAMhyperG.to.html: no visible global function definition for 'pdf'
.PFAMhyperG.to.htmlDF2: no visible global function definition for 'png'
.PFAMhyperG.to.htmlDF2: no visible global function definition for
  'dev.off'
.PFAMhyperG.to.htmlDF2: no visible global function definition for 'pdf'
.doImage: no visible global function definition for 'runif'
.doImage: no visible global function definition for 'cairo_pdf'
.doImage: no visible global function definition for 'dev.off'
.doImage: no visible global function definition for 'png'
.filter.vals: no visible global function definition for 'setNames'
.make.gene.plots: no visible global function definition for 'exprs'
.make.gene.plots: no visible global function definition for 'png'
.make.gene.plots: no visible global function definition for 'dev.off'
.make.gene.plots: no visible global function definition for 'pdf'
.makeSplash: no visible global function definition for 'sessionInfo'
.marrayLM.to.data.frame: no visible binding for global variable
  'p.adjust'
.marrayLM.to.data.frame: no visible global function definition for
  'featureNames'
.marrayLM.to.data.frame: no visible global function definition for
  'fData'
.marrayLM.to.html: no visible binding for global variable 'p.adjust'
.marrayLM.to.html: no visible global function definition for
  'featureNames'
.marrayLM.to.html: no visible global function definition for 'fData'
.save.rda.by.name: no visible global function definition for
  'promptData'
.save.rda.fn: no visible global function definition for 'promptData'
custHeaderPanel : <anonymous>: no visible binding for global variable
  'tags'
custHeaderPanel : <anonymous>: no visible global function definition
  for 'HTML'
custHeaderPanel: no visible global function definition for 'tagList'
custHeaderPanel: no visible global function definition for 'tag'
custHeaderPanel: no visible global function definition for 'div'
custHeaderPanel: no visible global function definition for 'h1'
hyperGPlot: no visible global function definition for 'plot'
hyperGPlot: no visible global function definition for 'rect'
hyperGPlot: no visible global function definition for 'text'
makeDESeqFigures: no visible global function definition for 'png'
makeDESeqFigures: no visible global function definition for 'dev.off'
makeDESeqFigures: no visible global function definition for 'pdf'
plotGOResults: no visible global function definition for 'svg'
plotGOResults: no visible global function definition for 'dev.off'
reporting.theme: no visible global function definition for
  'colorRampPalette'
reporting.theme.alternate: no visible global function definition for
  'colorRampPalette'
modifyReportDF,ANY-ANY-GOHyperGResult: no visible global function
  definition for 'png'
modifyReportDF,ANY-ANY-GOHyperGResult: no visible global function
  definition for 'dev.off'
modifyReportDF,ANY-ANY-GOHyperGResult: no visible global function
  definition for 'pdf'
publish,data.frame-CSVFile: no visible global function definition for
  'write.csv'
publish,trellis-HTMLReport: no visible binding for global variable
  'htmlRep'
publish,trellis-HTMLReport: no visible global function definition for
  'runif'
publish,trellis-HTMLReport: no visible global function definition for
  'cairo_pdf'
publish,trellis-HTMLReport: no visible global function definition for
  'dev.off'
publish,trellis-HTMLReport: no visible global function definition for
  'png'
toReportDF,DESeqDataSet: no visible global function definition for
  'mcols'
Undefined global functions or variables:
  HTML cairo_pdf colorRampPalette description dev.off div exprs fData
  featureNames h1 htmlRep mcols p.adjust pdf plot png promptData rect
  runif sessionInfo setNames svg tag tagList tags text write.csv
Consider adding
  importFrom("grDevices", "cairo_pdf", "colorRampPalette", "dev.off",
             "pdf", "png", "svg")
  importFrom("graphics", "plot", "rect", "text")
  importFrom("stats", "p.adjust", "runif", "setNames")
  importFrom("utils", "promptData", "sessionInfo", "write.csv")
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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.3-bioc/meat/ReportingTools.Rcheck/00check.log’
for details.


ReportingTools.Rcheck/00install.out:

* installing *source* package ‘ReportingTools’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
in method for 'objectToHTML' with signature 'object="ggbio"': no definition for class "ggbio"
Note: no visible binding for '<<-' assignment to '.reportDirectory' 
Note: no visible binding for '<<-' assignment to '.reportDirectory' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (ReportingTools)

ReportingTools.Rcheck/ReportingTools-Ex.timings:

nameusersystemelapsed
BaseReportType-class0.0030.0010.003
CSVFile-class0.0010.0000.001
CSVFile0.0050.0010.006
DataPackage-class0.0120.0020.013
DataPackage0.0060.0010.007
HTMLReport0.0300.0050.034
HTMLReportRef-class0.0010.0000.002
Link0.0120.0010.012
ReportHandlers-class0.0010.0000.002
finish-methods0.0010.0000.001
makeDESeqDF0.0010.0010.001
mockRnaSeqData0.0230.0010.025
publish-methods0.0010.0000.002
reporting.theme0.0170.0010.019
reporting.theme.alternate0.0260.0010.027
validConnection0.0610.0150.076