BioC 3.0: CHECK report for ReportingTools on perceval

Package: ReportingTools

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ReportingTools_2.6.0.tar.gz

StartedAt: 2015-04-10 05:35:26 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:51:00 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 933.1 seconds

RetCode: 0

Status:  OK

CheckDir: ReportingTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ReportingTools_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ReportingTools.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.6.0’
* 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 ... [77s/81s] 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
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’
* 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 ... [33s/34s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [239s/248s]
 [239s/248s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.003
CSVFile-class	0.001	0.001	0.002
CSVFile	0.011	0.001	0.012
DataPackage-class	0.015	0.003	0.024
DataPackage	0.006	0.001	0.025
HTMLReport	0.051	0.016	0.068
HTMLReportRef-class	0.001	0.000	0.002
Link	0.019	0.001	0.019
ReportHandlers-class	0.001	0.000	0.002
finish-methods	0.001	0.000	0.001
makeDESeqDF	0.001	0.001	0.001
mockRnaSeqData	0.024	0.001	0.025
publish-methods	0.002	0.001	0.002
reporting.theme	0.072	0.002	0.074
reporting.theme.alternate	0.074	0.002	0.077
validConnection	0.103	0.030	0.139