BioC 2.13: CHECK report for ReportingTools on zin1

Package: ReportingTools

Version: 2.2.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ReportingTools_2.2.0.tar.gz

StartedAt: 2014-04-05 03:28:25 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:36:15 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 469.8 seconds

RetCode: 0

Status:  OK

CheckDir: ReportingTools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ReportingTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [40s/40s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [125s/126s]
 [126s/127s] 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
  ‘/home/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	0.004	0.004	0.009
CSVFile-class	0.384	0.004	0.392
CSVFile	0.012	0.000	0.012
DataPackage-class	0.012	0.004	0.014
DataPackage	0.004	0.000	0.006
HTMLReport	0.040	0.008	0.048
HTMLReportRef-class	0.000	0.000	0.002
Link	0.012	0.000	0.014
ReportHandlers-class	0.004	0.000	0.004
finish-methods	0.004	0.000	0.003
makeDESeqDF	0.000	0.000	0.004
mockRnaSeqData	0.028	0.000	0.024
publish-methods	0.012	0.000	0.013
reporting.theme	0.032	0.000	0.031
reporting.theme.alternate	0.032	0.004	0.035
validConnection	0.068	0.008	0.074