* checking for file 'snapCGH/DESCRIPTION' ... OK
* preparing 'snapCGH':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'snapCGH' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c optimizer.c -o optimizer.o
gcc -shared -L/usr/local/lib64 -o snapCGH.so optimizer.o
** 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()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: affy
Loading required package: affyio
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo
Attaching package: 'zoo'
The following object(s) are masked from package:base :
rapply
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
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: aCGH
Loading required package: cluster
Loading required package: multtest
Loading required package: sma
Attaching package: 'aCGH'
The following object(s) are masked from package:stats :
heatmap
Loading required package: GLAD
[1] "Have fun with GLAD"
Attaching package: 'GLAD'
The following object(s) are masked from package:survival :
cluster
** help
>>> 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 example
heatmapGenome text html latex example
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 example
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 example
subsetting text html latex example
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 ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'snapCGH_1.2.0.tar.gz'