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Package 226/251HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.7.0
John Marioni
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snapCGH
Last Changed Rev: 27716 / Revision: 29143
Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 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: snapCGH
Version: 1.7.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD build snapCGH
StartedAt: 2007-12-11 03:57:47 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:58:35 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 47.6 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'snapCGH/DESCRIPTION' ... OK
* preparing 'snapCGH':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
/tmp/Rinst2887602917
* Installing *source* package 'snapCGH' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c optimizer.c -o optimizer.o
gcc -std=gnu99 -shared -L/usr/local/lib -o snapCGH.so optimizer.o   -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
Loading required package: tilingArray
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: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo
Loading required package: sandwich
Loading required package: vsn
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: pixmap
Loading required package: DNAcopy

Attaching package: 'DNAcopy'


	The following object(s) are masked from package:tilingArray :

	 segment 

Loading required package: GLAD
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
[1] "Have fun with GLAD"
Loading required package: cluster
Loading required package: aCGH
Loading required package: multtest
Loading required package: sma

Attaching package: 'aCGH'


	The following object(s) are masked from package:stats :

	 heatmap 

** help
Note: unmatched right brace in 'SegList' on or after line 30
Note: unmatched right brace in 'find.param.one' on or after line 18
Note: removing empty section \examples
Note: removing empty section \examples
Note: unmatched right brace in 'non.zero.length.distr.non.tiled' on or after line 9
Note: removing empty section \examples
Note: unmatched right brace in 'processCGH' on or after line 44
Note: removing empty section \examples
 >>> Building/Updating help pages for package 'snapCGH'
     Formats: text html latex example 
  IDProbes                          text    html    latex
  LargeDataObject                   text    html    latex   example
  SegList                           text    html    latex
  Viterbi.five                      text    html    latex
  Viterbi.four                      text    html    latex
  Viterbi.three                     text    html    latex
  Viterbi.two                       text    html    latex
  cbind                             text    html    latex
  chrominfo.Mb                      text    html    latex
  compareSegmentations              text    html    latex
  convert.output                    text    html    latex   example
  dim                               text    html    latex   example
  dimnames                          text    html    latex
  filter                            text    html    latex
  find.param.five                   text    html    latex
  find.param.four                   text    html    latex
  find.param.one                    text    html    latex
  find.param.three                  text    html    latex
  find.param.two                    text    html    latex
  findBreakPoints                   text    html    latex
  fit.model                         text    html    latex
  genomePlot                        text    html    latex
  heatmapGenome                     text    html    latex
  imputeMissingValues               text    html    latex
  log2ratios                        text    html    latex
  mergeStates                       text    html    latex
  non.zero.length.distr.non.tiled   text    html    latex
  non.zero.length.distr.tiled       text    html    latex
  nudSegmentation                   text    html    latex
  plotSegmentedGenome               text    html    latex
  processCGH                        text    html    latex
  read.clonesinfo                   text    html    latex
  readPositionalInfo                text    html    latex
  removeByWeights                   text    html    latex
  runBioHMM                         text    html    latex
  runDNAcopy                        text    html    latex
  runGLAD                           text    html    latex
  runHMM                            text    html    latex
  runPicard                         text    html    latex
  sim.structure                     text    html    latex
  zero.length.distr.non.tiled       text    html    latex
  zero.length.distr.tiled           text    html    latex
  zoomChromosome                    text    html    latex
  zoomGenome                        text    html    latex
** building package indices ...
* DONE (snapCGH)
* creating vignettes ... ERROR
Loading required package: limma
Loading required package: tilingArray
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: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo
Loading required package: sandwich
Loading required package: vsn
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: pixmap
Loading required package: DNAcopy

Attaching package: 'DNAcopy'


	The following object(s) are masked from package:tilingArray :

	 segment 

Loading required package: GLAD
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: cluster
Loading required package: aCGH
Loading required package: multtest
Loading required package: sma

Attaching package: 'aCGH'


	The following object(s) are masked from package:stats :

	 heatmap 


Attaching package: 'snapCGH'


	The following object(s) are masked from package:aCGH :

	 prop.na 


Error: processing vignette 'snapCGHguide.Rnw' failed with diagnostics:
 chunk 18 (label=15) 
Error in segment(cna, alpha = alpha, p.method = p.method, kmax = kmax,  : 
  unused argument(s) (window.size = NULL, overlap = 0.25)
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted