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 | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ReportingTools_2.12.2.tar.gz
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* 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.
* 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)