Package: affyPara

Version: 1.11.2

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings affyPara_1.11.2.tar.gz

StartedAt: 2011-02-24 17:10:57 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:11:56 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 58.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affyPara.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/affyPara.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.11.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘affyPara’ can be installed ... 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 ... WARNING
Codoc mismatches from documentation object 'preproPara':
preproPara
  Code: function(object, bgcorrect = TRUE, bgcorrect.method = NULL,
                 bgcorrect.param = list(), normalize = TRUE,
                 normalize.method = NULL, normalize.param = list(),
                 pmcorrect.method = NULL, pmcorrect.param = list(),
                 summary.method = NULL, summary.param = list(), ids =
                 NULL, phenoData = new("AnnotatedDataFrame"), cdfname =
                 NULL, cluster, verbose = getOption("verbose"), ...)
  Docs: function(object, bgcorrect = TRUE, bgcorrect.method = NULL,
                 bgcorrect.param = list(), normalize = TRUE,
                 normalize.method = NULL, normalize.param = list(),
                 pmcorrect.method = NULL, pmcorrect.param = list(),
                 summary.method = NULL, summary.param = list(), ids =
                 NULL, phenoData = new("AnnotatedDataFrame"), cdfname =
                 NULL, cluster, verbose = getOption("verbose"))
  Argument names in code not in docs:
    ...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/affyPara.Rcheck/00check.log’
for details

* installing *source* package ‘affyPara’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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


Attaching package: 'snow'

The following object(s) are masked from 'package:base':

    enquote

Loading required package: tcltk
Loading Tcl/Tk interface ... done
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (affyPara)

name	user	system	elapsed
MAplotPara	0.000	0.000	0.001
bgcPara	0	0	0
boxplotPara	0	0	0
computeExprSetPara	0.004	0.000	0.000
distributeFiles	0	0	0
mergeSplitObjects	5.124	0.188	5.397
normalizeAffyBatchConstantPara	0	0	0
normalizeAffyBatchInvariantsetPara	0	0	0
normalizeAffyBatchLoessPara	0	0	0
normalizeAffyBatchLoessParaIter	0	0	0
normalizeAffyBatchQuantilesPara	0	0	0
preproPara	0	0	0
qa	0	0	0
readAffybatchPara	0.000	0.000	0.001
removeDistributedFiles	0.000	0.000	0.001
rmaPara	0	0	0
snowReplace	0	0	0
split	1.796	0.032	1.826
vsnPara	0.000	0.004	0.000