Package: affyPara

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affyPara_1.17.0.tar.gz

StartedAt: 2012-06-20 21:32:11 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 21:34:04 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 112.6 seconds

RetCode: 0

Status:  OK

CheckDir: affyPara.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/affyPara.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affyPara/DESCRIPTION' ... OK
* this is package 'affyPara' version '1.17.0'
* 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 whether package 'affyPara' 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 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 ... NOTE
File 'affyPara/R/zzz.R':
  .onLoad calls:
    require(affy)
    require(snow)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

MAplotPara: warning in drawMAplot(object, badQCu, meanchip, type, log,
  subset, span, pch = pch, ref.title, show.statistics, family.loess,
  verbose, ...): partial argument match of 'pch' to 'pchs'
MAplotSer: warning in drawMAplot(object, badQCu, meanchip, type, log,
  subset, span, pch = pch, ref.title, show.statistics, family.loess,
  verbose, ...): partial argument match of 'pch' to 'pchs'
grad_loglikPara: warning in get("px", env = .GlobalEnv): partial
  argument match of 'env' to 'envir'
* 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'vsnAddonBoxplots_20-40-60.pdf' from 515Kb to 45Kb
     compacted 'vsnStudy.pdf' from 2095Kb to 318Kb
     compacted 'vsnSubsamplesBoxplot_25.pdf' from 213Kb to 20Kb
     compacted 'vsnSubsamplesBoxplot_50.pdf' from 529Kb to 44Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... NOTE
The following directories should probably not be installed:
  'fig'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* 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

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/affyPara.Rcheck/00check.log'
for details.

* installing *source* package 'affyPara' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'affyPara.Rnw' 
   'vsnStudy.Rnw' 
** testing if installed package can be loaded

* DONE (affyPara)

name	user	system	elapsed
MAplotPara	0.001	0.000	0.001
bgcPara	0	0	0
boxplotPara	0	0	0
computeExprSetPara	0	0	0
distributeFiles	0.000	0.000	0.001
mergeSplitObjects	4.444	0.637	5.196
normalizeAffyBatchConstantPara	0	0	0
normalizeAffyBatchInvariantsetPara	0.001	0.000	0.000
normalizeAffyBatchLoessPara	0	0	0
normalizeAffyBatchLoessParaIter	0.000	0.001	0.001
normalizeAffyBatchQuantilesPara	0	0	0
preproPara	0.001	0.001	0.000
qa	0.000	0.000	0.001
readAffybatchPara	0.000	0.001	0.002
removeDistributedFiles	0.001	0.000	0.000
rmaPara	0.000	0.001	0.000
snowReplace	0	0	0
split	1.394	0.414	1.812
vsnPara	0	0	0