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Package 156/294HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 1.8.3
Pan Du
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/lumi
Last Changed Rev: 35146 / Revision: 38965
Last Changed Date: 2008-11-07 07:52:42 -0800 (Fri, 07 Nov 2008)
wilson2 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 (10.5.6) / i386  OK  OK  OK 
Package: lumi
Version: 1.8.3
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes lumi_1.8.3.tar.gz
StartedAt: 2009-04-18 17:15:15 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:19:33 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 257.9 seconds
RetCode: 0
Status: OK
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/lumi.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '1.8.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'lumi' 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 ... OK
* 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 lumi-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating lumi-manual.tex ... OK
* checking lumi-manual.tex using pdflatex ... OK

lumi.Rcheck/00install.out:

* Installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: annotate
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: AnnotationDbi
Loading required package: xtable
Loading required package: affy
Loading required package: mgcv
This is mgcv  1.5-2 . For overview type `help("mgcv-package")'.
Loading required package: preprocessCore
Loading required package: RSQLite
Loading required package: DBI
Creating a new generic function for "density" in "lumi"
Creating a new generic function for "pairs" in "lumi"
Creating a new generic function for "plot" in "lumi"
** help
 >>> Building/Updating help pages for package 'lumi'
     Formats: text html latex example 
Note: removing empty section \examples in file 'IlluminaID2nuID.Rd'
  IlluminaID2nuID                   text    html    latex
  LumiBatch-class                   text    html    latex   example
  MAplot-methods                    text    html    latex   example
Note: removing empty section \references in file 'addControlData2lumi.Rd'
  addControlData2lumi               text    html    latex   example
  addNuID2lumi                      text    html    latex   example
Note: removing empty section \references in file 'affyExpresso.Rd'
Note: removing empty section \examples in file 'affyExpresso.Rd'
  affyExpresso                      text    html    latex
Note: removing empty section \references in file 'affyVstRma.Rd'
Note: removing empty section \examples in file 'affyVstRma.Rd'
  affyVstRma                        text    html    latex
  bgAdjust                          text    html    latex   example
  boxplot-methods                   text    html    latex   example
  density-methods                   text    html    latex   example
  detectOutlier                     text    html    latex   example
  detectionCall                     text    html    latex   example
  estimateLumiCV                    text    html    latex   example
  example.lumi                      text    html    latex   example
Note: removing empty section \references in file 'getChipInfo.Rd'
  getChipInfo                       text    html    latex   example
Note: removing empty section \details in file 'getControlData.Rd'
Note: removing empty section \references in file 'getControlData.Rd'
  getControlData                    text    html    latex   example
Note: removing empty section \details in file 'getControlProbe.Rd'
Note: removing empty section \references in file 'getControlProbe.Rd'
  getControlProbe                   text    html    latex   example
Note: removing empty section \details in file 'getControlType.Rd'
Note: removing empty section \references in file 'getControlType.Rd'
  getControlType                    text    html    latex   example
  getNuIDMappingInfo                text    html    latex   example
  hist-methods                      text    html    latex   example
  id2seq                            text    html    latex   example
  inverseVST                        text    html    latex   example
  is.nuID                           text    html    latex   example
Note: removing empty section \seealso in file 'lumi.package.Rd'
Note: removing empty section \examples in file 'lumi.package.Rd'
  lumi.package                      text    html    latex
  lumiB                             text    html    latex   example
  lumiExpresso                      text    html    latex   example
Note: removing empty section \note in file 'lumiN.Rd'
Note: removing empty section \references in file 'lumiN.Rd'
  lumiN                             text    html    latex   example
  lumiQ                             text    html    latex   example
  lumiR                             text    html    latex   example
  lumiR.batch                       text    html    latex   example
  lumiT                             text    html    latex   example
Note: removing empty section \examples in file 'monoSmu.Rd'
  monoSmu                           text    html    latex
Note: removing empty section \references in file 'monoSpline.Rd'
Note: removing empty section \examples in file 'monoSpline.Rd'
  monoSpline                        text    html    latex
  nuID2EntrezID                     text    html    latex   example
  nuID2IlluminaID                   text    html    latex   example
  nuID2RefSeqID                     text    html    latex   example
  nuID2probeID                      text    html    latex   example
  nuID2targetID                     text    html    latex   example
  pairs-methods                     text    html    latex   example
  plot-methods                      text    html    latex   example
Note: removing empty section \references in file 'plotControlData.Rd'
  plotControlData                   text    html    latex   example
Note: removing empty section \details in file 'plotHousekeepingGene.Rd'
Note: removing empty section \references in file 'plotHousekeepingGene.Rd'
  plotHousekeepingGene              text    html    latex   example
  plotSampleRelation                text    html    latex   example
Note: removing empty section \details in file 'plotStringencyGene.Rd'
Note: removing empty section \references in file 'plotStringencyGene.Rd'
  plotStringencyGene                text    html    latex   example
Note: removing empty section \details in file 'plotVST.Rd'
  plotVST                           text    html    latex   example
  probeID2nuID                      text    html    latex   example
Note: removing empty section \examples in file 'produceGEOPlatformFile.Rd'
  produceGEOPlatformFile            text    html    latex
Note: removing empty section \examples in file 'produceGEOSampleInfoTemplate.Rd'
  produceGEOSampleInfoTemplate      text    html    latex
  produceGEOSubmissionFile          text    html    latex   example
Note: removing empty section \note in file 'rsn.Rd'
Note: removing empty section \references in file 'rsn.Rd'
Note: removing empty section \examples in file 'rsn.Rd'
  rsn                               text    html    latex
  seq2id                            text    html    latex   example
Note: removing empty section \references in file 'ssn.Rd'
Note: removing empty section \examples in file 'ssn.Rd'
  ssn                               text    html    latex
  targetID2nuID                     text    html    latex   example
  vst                               text    html    latex   example
** building package indices ...
* DONE (lumi)