Package: arrayQuality

Version: 1.14.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check arrayQuality_1.14.0.tar.gz

RetCode: 0

Time: 134.8 seconds

Status: OK

CheckDir: arrayQuality.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/arrayQuality.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.14.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'arrayQuality' 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 name space can be loaded with stated dependencies ... 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
arrayScal: no visible binding for global variable 'MmReferenceDB'
getSpikeIds: no visible binding for global variable 'MEEBOset'
getSpikeIndex: no visible binding for global variable 'MEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOset'
heeboQuality: no visible binding for global variable 'HEEBOctrl'
heeboQuality: no visible binding for global variable 'HEEBOtilingres'
heeboQualityPlots: no visible binding for global variable 'HEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOset'
meeboQuality: no visible binding for global variable 'MEEBOctrl'
meeboQuality: no visible binding for global variable 'MEEBOtilingres'
meeboQualityPlots: no visible binding for global variable 'MEEBOset'
PRvQCHyb: no visible binding for global variable 'MmDEGenes'
qpBEplot.linear: no visible binding for global variable 'MEEBOctrl'
qpBoxplotMeebo: no visible binding for global variable 'MEEBOset'
qpDotPlotsEEBO: no visible binding for global variable 'MEEBOset'
qpDotPlotsMeebo: no visible binding for global variable 'MEEBOset'
qpMisMatchPlot: no visible binding for global variable 'HEEBOctrl'
qpTiling: no visible binding for global variable 'MEEBOtilingres'
qualBoxplot: no visible binding for global variable 'MmReferenceDB'
qualBoxplot: no visible binding for global variable 'HsReferenceDB'
qualityScore: no visible binding for global variable 'MmReferenceDB'
readAllSpikes: no visible binding for global variable 'MEEBOset'
scaleRefTable: no visible binding for global variable 'MmReferenceDB'
Spike.Cy5vsCy3: no visible binding for global variable 'MEEBOset'
Spike.Cy5vsCy3: no visible binding for global variable 'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
  'RG'
Spike.Individual.Sensitivity: no visible binding for global variable
  'MEEBOset'
Spike.Individual.Sensitivity: no visible binding for global variable
  'MEEBOctrl'
Spike.MMplot: no visible binding for global variable 'RG'
Spike.MMplot: no visible binding for global variable 'MEEBOset'
Spike.MM.Scatter: no visible binding for global variable 'RG'
Spike.MM.Scatter: no visible binding for global variable 'MEEBOset'
Spike.Sensitivity: no visible binding for global variable 'RG'
Spike.Sensitivity: no visible binding for global variable 'MEEBOset'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating arrayQuality-Ex.R ... OK
* checking examples ... OK
* creating arrayQuality-manual.tex ... OK
* checking arrayQuality-manual.tex ... OK

* Installing *source* package 'arrayQuality' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: marray
Loading required package: limma
Loading required package: convert
Loading required package: Biobase
Loading required package: tools

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: hexbin
Loading required package: grid
Loading required package: lattice
Loading required package: gridBase
Loading required package: RColorBrewer
Warning in namespaceImportFrom(self, asNamespace(ns)) :
  replacing previous import: summary
** help
Note: unmatched right brace in 'PRv9mers' on or after line 36
Note: unmatched right brace in 'scaleRefTable' on or after line 11
Note: unmatched right brace in 'scaleRefTable' on or after line 32
 >>> Building/Updating help pages for package 'arrayQuality'
     Formats: text html latex example 
  MmDEGenes                         text    html    latex
  PRv9mers                          text    html    latex   example
  PRvQCHyb                          text    html    latex   example
  agQuality                         text    html    latex   example
  arrayQuality-internal             text    html    latex
  globalQuality                     text    html    latex   example
  gpQuality                         text    html    latex   example
  gprDB                             text    html    latex
  heeboQuality                      text    html    latex   example
  heeboQualityPlots                 text    html    latex   example
  maQualityPlots                    text    html    latex   example
  meeboQuality                      text    html    latex   example
  meeboQualityPlots                 text    html    latex   example
  prdata                            text    html    latex
  qualBoxplot                       text    html    latex   example
  qualityScore                      text    html    latex
  readAgilent                       text    html    latex   example
  readGPR                           text    html    latex   example
  readSpikeTypes                    text    html    latex   example
  readSpot                          text    html    latex   example
  readcontrolCode                   text    html    latex
  scaleRefTable                     text    html    latex
  slideQuality                      text    html    latex   example
  spotQuality                       text    html    latex   example
** building package indices ...
* DONE (arrayQuality)