BioC 3.2: CHECK report for ReportingTools on perceval

Package: ReportingTools

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ReportingTools_2.10.0.tar.gz

StartedAt: 2015-11-10 08:48:03 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 08:57:20 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 557.2 seconds

RetCode: 0

Status:  OK

CheckDir: ReportingTools.Rcheck

Warnings: 0

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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_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ReportingTools.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.10.0’
* 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 ‘ReportingTools’ can be installed ... [45s/45s] 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
.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’
.make.gene.plots: no visible global function definition for ‘exprs’
.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 global function definition for
  ‘featureNames’
.marrayLM.to.html: no visible global function definition for ‘fData’
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’
publish,trellis-HTMLReport : .local: no visible binding for global
  variable ‘htmlRep’
toReportDF,DESeqDataSet : .local: no visible global function definition
  for ‘mcols’
* 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 ... [19s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [172s/179s]
 [172s/179s] 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-3.2-bioc/meat/ReportingTools.Rcheck/00check.log’
for details.

* installing *source* package ‘ReportingTools’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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
* DONE (ReportingTools)

name	user	system	elapsed
BaseReportType-class	0.003	0.000	0.002
CSVFile-class	0.001	0.000	0.001
CSVFile	0.010	0.001	0.011
DataPackage-class	0.012	0.002	0.014
DataPackage	0.006	0.000	0.007
HTMLReport	0.029	0.009	0.045
HTMLReportRef-class	0.001	0.000	0.002
Link	0.014	0.001	0.015
ReportHandlers-class	0.002	0.001	0.002
finish-methods	0.001	0.000	0.002
makeDESeqDF	0.001	0.001	0.002
mockRnaSeqData	0.025	0.002	0.028
publish-methods	0.001	0.001	0.002
reporting.theme	0.068	0.001	0.078
reporting.theme.alternate	0.044	0.001	0.044
validConnection	0.051	0.016	0.085