BioC 2.13: CHECK report for ReportingTools on perceval

Package: ReportingTools

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ReportingTools_2.2.0.tar.gz

StartedAt: 2014-04-05 03:49:28 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:04:04 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 876.7 seconds

RetCode: 0

Status:  OK

CheckDir: ReportingTools.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ReportingTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.2.0’
* 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 ... [71s/77s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’ ‘ggbio’ ‘knitr’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘ggbio’ ‘ggplot2’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘knitr’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... [31s/32s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [219s/234s]
 [220s/234s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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="trellis"’: no definition for class “trellis”
in method for ‘objectToHTML’ with signature ‘object="ggplot"’: no definition for class “ggplot”
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	0.040	0.008	0.048
CSVFile-class	0.004	0.004	0.007
CSVFile	0.023	0.007	0.030
DataPackage-class	0.036	0.012	0.051
DataPackage	0.017	0.007	0.028
HTMLReport	0.061	0.025	0.089
HTMLReportRef-class	0.013	0.005	0.019
Link	0.029	0.004	0.035
ReportHandlers-class	0.017	0.006	0.035
finish-methods	0.013	0.005	0.018
makeDESeqDF	0.010	0.006	0.017
mockRnaSeqData	0.032	0.005	0.037
publish-methods	0.026	0.012	0.038
reporting.theme	0.072	0.006	0.080
reporting.theme.alternate	0.088	0.007	0.096
validConnection	0.090	0.023	0.120