Package: affyPara

Version: 1.7.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes affyPara_1.7.0.tar.gz

StartedAt: 2009-12-07 15:26:14 -0800 (Mon, 07 Dec 2009)

EndedAt: 2009-12-07 15:27:07 -0800 (Mon, 07 Dec 2009)

EllapsedTime: 52.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: affyPara.Rcheck

Warnings: 1

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/affyPara.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-10 r50388)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPara/DESCRIPTION' ... OK
* this is package 'affyPara' version '1.7.0'
* 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 ... WARNING

---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'affyPara', details:
  call: library.dynam.unload("affyPara", libpath)
  error: shared library 'affyPara' was not loaded 

* 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
bgCorrectPara: possible error in gsub("^/?([^/]*/)*", "",
  unlist(object), extended = TRUE): unused argument(s) (extended =
  TRUE)
boxplotPara: possible error in gsub("^/?([^/]*/)*", "", unlist(object),
  extended = TRUE): unused argument(s) (extended = TRUE)
computeExprSetPara: possible error in gsub("^/?([^/]*/)*", "",
  unlist(object), extended = TRUE): unused argument(s) (extended =
  TRUE)
MAplotPara: possible error in gsub("^/?([^/]*/)*", "", unlist(object),
  extended = TRUE): unused argument(s) (extended = TRUE)
MAplotSer: possible error in gsub("^/?([^/]*/)*", "", unlist(object),
  extended = TRUE): unused argument(s) (extended = TRUE)
normalizeAffyBatchConstantPara: possible error in gsub("^/?([^/]*/)*",
  "", unlist(object), extended = TRUE): unused argument(s) (extended =
  TRUE)
normalizeAffyBatchInvariantsetPara: possible error in
  gsub("^/?([^/]*/)*", "", unlist(object), extended = TRUE): unused
  argument(s) (extended = TRUE)
normalizeAffyBatchLoessIterPara: possible error in gsub("^/?([^/]*/)*",
  "", unlist(object), extended = TRUE): unused argument(s) (extended =
  TRUE)
normalizeAffyBatchLoessPara: possible error in gsub("^/?([^/]*/)*", "",
  unlist(object), extended = TRUE): unused argument(s) (extended =
  TRUE)
normalizeAffyBatchQuantilesPara: possible error in gsub("^/?([^/]*/)*",
  "", unlist(object), extended = TRUE): unused argument(s) (extended =
  TRUE)
preproPara: possible error in gsub("^/?([^/]*/)*", "", unlist(object),
  extended = TRUE): unused argument(s) (extended = TRUE)
read.affybatchPara: possible error in gsub("^/?([^/]*/)*", "",
  unlist(object), extended = TRUE): unused argument(s) (extended =
  TRUE)
vsn2Para: possible error in gsub("^/?([^/]*/)*", "", unlist(object),
  extended = TRUE): unused argument(s) (extended = TRUE)
vsnrmaPara: possible error in gsub("^/?([^/]*/)*", "", unlist(object),
  extended = TRUE): unused argument(s) (extended = TRUE)
* 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 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-2.6-bioc/meat/affyPara.Rcheck/00check.log
for details

* install options are ' --no-html'

* 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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: tcltk
Loading Tcl/Tk interface ... done
** help
*** installing help indices
** building package indices ...
* DONE (affyPara)