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Package 132/264HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 1.5.18
Pan Du
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi
Last Changed Rev: 30847 / Revision: 30951
Last Changed Date: 2008-04-04 11:52:53 -0700 (Fri, 04 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  ERROR  skipped 
wilson2 Linux (openSUSE 10.3) / x86_64  ERROR  skipped 
wellington Linux (openSUSE 10.3) / i686  ERROR  skipped 
liverpool Windows Server 2003 R2 (32-bit) / x64 [ ERROR ] skipped  skipped 
pelham Mac OS X Leopard (10.5.1) / i386  ERROR  skipped  skipped 
Package: lumi
Version: 1.5.18
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD build lumi
StartedAt: 2008-04-09 03:56:20 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 03:57:14 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 53.8 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'lumi/DESCRIPTION' ... OK
* preparing 'lumi':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst503660086


---------- Making package lumi ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  preparing package lumi 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
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Creating a new generic function for "pairs" in "lumi"
Creating a new generic function for "plot" in "lumi"
  installing man source files
  installing indices
  not zipping data
  installing help
Note: removing empty section \references
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 >>> Building/Updating help pages for package 'lumi'
     Formats: text html latex example chm 
  LumiBatch-class                   text    html    latex   example chm
  MAplot-methods                    text    html    latex   example chm
  addControlData2lumi               text    html    latex   example chm
  addNuId2lumi                      text    html    latex   example chm
  affyExpresso                      text    html    latex           chm
  affyVstRma                        text    html    latex           chm
  bgAdjust                          text    html    latex   example chm
  boxplot-methods                   text    html    latex   example chm
  density-methods                   text    html    latex   example chm
  detectOutlier                     text    html    latex   example chm
  detectionCall                     text    html    latex   example chm
  estimateLumiCV                    text    html    latex   example chm
  example.lumi                      text    html    latex   example chm
  getControlData                    text    html    latex   example chm
  getControlProbe                   text    html    latex   example chm
  getControlType                    text    html    latex   example chm
  hist-methods                      text    html    latex   example chm
  id2seq                            text    html    latex   example chm
  inverseVST                        text    html    latex   example chm
  is.nuID                           text    html    latex   example chm
  lumi.package                      text    html    latex           chm
  lumiB                             text    html    latex   example chm
  lumiExpresso                      text    html    latex   example chm
  lumiN                             text    html    latex   example chm
  lumiQ                             text    html    latex   example chm
  lumiR                             text    html    latex   example chm
  lumiR.batch                       text    html    latex   example chm
  lumiT                             text    html    latex   example chm
  monoSmu                           text    html    latex   example chm
  monoSpline                        text    html    latex   example chm
  nuID2probeID                      text    html    latex   example chm
  nuID2targetID                     text    html    latex   example chm
  pairs-methods                     text    html    latex   example chm
  plot-methods                      text    html    latex   example chm
  plotControlData                   text    html    latex   example chm
  plotHousekeepingGene              text    html    latex   example chm
  plotSampleRelation                text    html    latex   example chm
  plotStringencyGene                text    html    latex   example chm
  plotVST                           text    html    latex   example chm
  probeID2nuID                      text    html    latex   example chm
  rsn                               text    html    latex           chm
  seq2id                            text    html    latex   example chm
  ssn                               text    html    latex           chm
  targetID2nuID                     text    html    latex   example chm
  vst                               text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.2-bioc\meat\lumi\chm\lumi.chm





Compile time: 0 minutes, 1 second

46	Topics

230	Local links

0	Internet links

1	Graphic





Created e:\biocbld\bbs-2.2-bioc\meat\lumi\chm\lumi.chm, 67,599 bytes

Compression decreased file by 98,006 bytes.

  adding MD5 sums

* 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: xtable
Loading required package: GO
Loading required package: lumiHumanV1
Loading required package: limma

Error: processing vignette 'lumi.Rnw' failed with diagnostics:
 chunk 37 
Error in lookUp(x, data, "SYMBOL") : No keys provided
In addition: Warning messages:
1: In any(G$offset) : coercing argument of type 'double' to logical
2: In any(G$offset) : coercing argument of type 'double' to logical
3: In any(G$offset) : coercing argument of type 'double' to logical
Execution halted