Package: lumi

Version: 1.3.26

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build lumi

RetCode: 1

Time: 116.8 seconds

Status: ERROR

PackageFile: None

* checking for file 'lumi/DESCRIPTION' ... OK
* preparing 'lumi':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* Installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
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: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: mgcv
This is mgcv 1.3-26 
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
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 
  LumiBatch-class                   text    html    latex   example
  MAplot-methods                    text    html    latex   example
  addNuId2lumi                      text    html    latex   example
  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
  hist-methods                      text    html    latex   example
  id2seq                            text    html    latex   example
  inverseVST                        text    html    latex   example
  is.nuID                           text    html    latex   example
  lumi.package                      text    html    latex   example
  lumiB                             text    html    latex   example
  lumiExpresso                      text    html    latex   example
  lumiN                             text    html    latex   example
  lumiQ                             text    html    latex   example
  lumiR                             text    html    latex   example
  lumiT                             text    html    latex   example
  monoSmu                           text    html    latex   example
  monoSpline                        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
  plotSampleRelation                text    html    latex   example
  plotVST                           text    html    latex   example
  probeID2nuID                      text    html    latex   example
  rsn                               text    html    latex   example
  seq2id                            text    html    latex   example
  targetID2nuID                     text    html    latex   example
  vst                               text    html    latex   example
** building package indices ...
* DONE (lumi)
* creating vignettes ... ERROR
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: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: mgcv
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: GO
Loading required package: lumiHumanV1
Loading required package: lumiHumanV1
Loading required package: lumiHumanV1
Loading required package: lumiHumanV1
Loading required package: lumiHumanV1
Loading required package: limma
Loading required package: lumiHumanV1
Loading required package: survival
Loading required package: splines
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997

Error: processing vignette 'lumi_VST_evaluation.Rnw' failed with diagnostics:
 chunk 1 (label=libraries) 
Error in library("lumiBarnes") : there is no package called 'lumiBarnes'
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'lumiHumanV1'
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'lumiHumanV1'
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'lumiHumanV1'
4: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'lumiHumanV1'
5: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'lumiHumanV1'
6: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'lumiHumanV1'
Execution halted