Package: ReportingTools

Version: 1.2.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ReportingTools_1.2.3.tar.gz

StartedAt: 2013-01-16 05:48:55 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:53:24 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 268.3 seconds

RetCode: 0

Status:  OK

CheckDir: ReportingTools.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ReportingTools.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.2.3’
* 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 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 for unstated 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 ... OK
* 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 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘ReportingTools’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘publish’ with signature ‘object="trellis",publicationType="HTMLReport"’: no definition for class “trellis”
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘basicReportingTools.Rnw’ 
   ‘microarrayAnalysis.Rnw’ 
   ‘rnaseqAnalysis.Rnw’ 
** testing if installed package can be loaded

* DONE (ReportingTools)

name	user	system	elapsed
BaseReportType-class	0.016	0.000	0.014
CSVFile-class	0.012	0.000	0.012
CSVFile	0.352	0.004	0.355
DataPackage-class	0.024	0.004	0.028
DataPackage	0.012	0.004	0.016
HTMLReport-class	0.112	0.012	0.127
HTMLReport	0.036	0.008	0.045
finish-methods	0.012	0.000	0.013
makeDESeqDf	0.020	0.000	0.018
mockRnaSeqData	0.036	0.000	0.037
publish-methods	0.040	0.000	0.039
reporting.theme	0.048	0.000	0.048
reporting.theme.alternate	0.028	0.012	0.039
validConnection	0.068	0.004	0.074