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Package 29/319HostnameOS / ArchBUILDCHECKBUILD BIN
arrayQuality 1.22.0
Agnes Paquet
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/arrayQuality
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: arrayQuality
Version: 1.22.0
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes arrayQuality_1.22.0.tar.gz
StartedAt: 2009-10-20 15:28:53 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 15:29:34 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 41.5 seconds
RetCode: 0
Status: OK
CheckDir: arrayQuality.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/arrayQuality.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'arrayQuality/DESCRIPTION' ... OK
* this is package 'arrayQuality' version '1.22.0'
* 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.MM.Scatter: no visible binding for global variable 'RG'
Spike.MM.Scatter: no visible binding for global variable 'MEEBOset'
Spike.MMplot: no visible binding for global variable 'RG'
Spike.MMplot: 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 files against version 2 parser ... 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
* checking examples ... OK
* checking PDF version of manual ... OK

arrayQuality.Rcheck/00install.out:

* Installing *source* package 'arrayQuality' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
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: grid
Loading required package: lattice
Warning in namespaceImportFrom(self, asNamespace(ns)) :
  replacing previous import: summary
** help
*** installing help indices
 >>> 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
  qcScore                           text    html    latex
  qualBoxplot                       text    html    latex   example
  qualityScore                      text    html    latex
  readAgilent                       text    html    latex
  readGPR                           text    html    latex   example
  readSpikeTypes                    text    html    latex   example
  readSpot                          text    html    latex
  readcontrolCode                   text    html    latex
  scaleRefTable                     text    html    latex
  slideQuality                      text    html    latex   example
Note: removing empty section \examples in file 'spotQuality.Rd'
  spotQuality                       text    html    latex
** building package indices ...
* DONE (arrayQuality)