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 |
* 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