Package: HELP

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HELP_1.11.0.tar.gz

StartedAt: 2011-05-09 15:09:41 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:10:31 -0700 (Mon, 09 May 2011)

EllapsedTime: 49.9 seconds

RetCode: 0

Status:  OK

CheckDir: HELP.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/HELP.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HELP/DESCRIPTION’ ... OK
* this is package ‘HELP’ version ‘1.11.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘HELP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘HELP.pdf’ from 1395Kb to 345Kb
  consider running tools::compactPDF() on these files
* checking examples ... 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 ‘HELP’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘HELP.Rnw’ 
** testing if installed package can be loaded

* DONE (HELP)

name	user	system	elapsed
base.stacking.thermodynamics	0.026	0.005	0.031
calcGC	0.001	0.000	0.001
calcPrototype	0.123	0.004	0.128
calcTm	0.009	0.001	0.010
combineData	0.024	0.000	0.031
createWiggle	0.003	0.001	0.004
exprs2	0.001	0.000	0.000
fuzzyMatches	0.006	0.000	0.006
getFeatures	0.159	0.004	0.163
getSamples	0.112	0.003	0.126
plotBins	0.112	0.012	0.126
plotChip	0.111	0.025	0.138
plotFeature	0.070	0.006	0.077
plotPairs	1.562	0.056	1.635
quantileNormalize	0.068	0.002	0.071
readDesign	0.170	0.005	0.180
readPairs	0.190	0.003	0.194
readSampleKey	0.003	0.001	0.004