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Package 23/251HostnameOS / ArchBUILDCHECKBUILD BIN
arrayMagic 1.17.2
Andreas Buness
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/arrayMagic
Last Changed Rev: 28902 / Revision: 29143
Last Changed Date: 2007-11-25 08:43:29 -0800 (Sun, 25 Nov 2007)
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 
lemming Windows Server 2003 (32-bit) / x64  ERROR  skipped  skipped 
Package: arrayMagic
Version: 1.17.2
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD build arrayMagic
StartedAt: 2007-12-11 03:12:09 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:13:17 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 67.5 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'arrayMagic/DESCRIPTION' ... OK
* preparing 'arrayMagic':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
installing R.css in E:/biocbld/bbs-2.2-bioc/tmpdir/Rinst456822998


---------- Making package arrayMagic ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  preparing package arrayMagic 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: vsn
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
  installing man source files
  installing indices
  installing help
Note: removing empty section \examples
Note: removing empty section \examples
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Note: removing empty section \details
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Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
Note: removing empty section \details
 >>> Building/Updating help pages for package 'arrayMagic'
     Formats: text html latex example chm 
  arrayData-class                   text    html    latex   example chm
  cbind.arrayData                   text    html    latex           chm
  cbind.exprSetRG                   text    html    latex           chm
  colCors                           text    html    latex   example chm
  controlledApply                   text    html    latex   example chm
  controlledSubsetting              text    html    latex   example chm
  detectReplicas                    text    html    latex   example chm
  exprSetRG-class                   text    html    latex   example chm
  fdc                               text    html    latex   example chm
  interweave                        text    html    latex   example chm
  normalise                         text    html    latex   example chm
  plot.imageMatrix                  text    html    latex   example chm
  plotDistributions                 text    html    latex   example chm
  processArrayData                  text    html    latex   example chm
  processArrayDataObject            text    html    latex   example chm
  qualityDiagnostics                text    html    latex           chm
  qualityParameters                 text    html    latex   example chm
  readIntensities                   text    html    latex   example chm
  readpDataSlides                   text    html    latex   example chm
  removeSpots                       text    html    latex   example chm
  simpleApply                       text    html    latex   example chm
  slideMerge                        text    html    latex   example chm
  spatialLayout                     text    html    latex   example chm
  spotMerge                         text    html    latex   example chm
  visualiseHybridisations           text    html    latex           chm
  visualiseQualityParameters        text    html    latex           chm
  write.htmltable                   text    html    latex   example chm
  writeToFile                       text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



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





Compile time: 0 minutes, 1 second

29	Topics

247	Local links

1	Internet link

1	Graphic





Created e:\biocbld\bbs-2.2-bioc\meat\arrayMagic\chm\arrayMagic.chm, 71,849 bytes

Compression decreased file by 101,476 bytes.

  adding MD5 sums

* DONE (arrayMagic)
* creating vignettes ... ERROR

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: limma
Loading required package: survival
Loading required package: splines

******      Deprecation warning                  ***
* The package 'arrayMagic' is deprecated and will  *
* not be supported after the retirement of the     *
* exprSet class from Bioconductor.                 *
* Please consider using the NchannelSet class from *
* Biobase and functions from the limma and         *
* arrayQualityMetrics packages.                    *
****************************************************

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Error: processing vignette 'arrayMagicVignette.Rnw' failed with diagnostics:
 chunk 14 (label=visualiseHybridisations) 
Error in if (!(mappingColumns[["Col"]] %in% colnames(spotAttr))) { : 
  argument is of length zero
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted