* checking for file 'aCGH/DESCRIPTION' ... OK
* preparing 'aCGH':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'aCGH' ...
** libs
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -g3 -I/usr/local/include -fpic -g -O2 -Wall -c hmm.cpp -o hmm.o
g++ -shared -L/usr/local/lib -o aCGH.so hmm.o -lm
** R
** data
** demo
** inst
** save image
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: multtest
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: sma
** help
>>> Building/Updating help pages for package 'aCGH'
Formats: text html latex example
aCGH text html latex example
aCGH.process text html latex example
aCGH.read.Sprocs text html latex example
aCGH.test text html latex example
clusterGenome text html latex example
colorectal text html latex example
computeSD.func text html latex
fga.func text html latex example
find.genomic.events text html latex
find.hmm.states text html latex example
findAber.func text html latex
findAmplif.func text html latex
findOutliers.func text html latex
findTrans.func text html latex
gainLoss text html latex example
heatmap text html latex example
human.chrom.info.Jul03 text html latex
human.chrom.info.May04 text html latex
impute.HMM text html latex example
impute.lowess text html latex example
mergeFunc text html latex
mergeLevels text html latex example
plotFreqStat text html latex example
plotGenome text html latex example
plotHmmStates text html latex example
plotSummaryProfile text html latex example
states.hmm.func text html latex
summarize.clones text html latex example
threshold.func text html latex example
** building package indices ...
* DONE (aCGH)
* creating vignettes ... ERROR
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: multtest
Loading required package: Biobase
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: sma
Attaching package: 'aCGH'
The following object(s) are masked from package:stats :
heatmap
the part of the args list of 'list' being evaluated was:
(pal = c("red", "blue", "green", "orange")[1:length(p.thres)], gain.low = "white", gain.high = "green", loss.low = "red", loss.high = "white", abline1 = "blue", abline2 = "grey50", mtext = "red", kb.loc = "blue", abline3 = "black", abline4 = "grey50", )
There were 36 warnings (use warnings() to see them)
Error: chunk 5
Error in plotFreqStat(x) : element 12 is empty
Error in buildVignettes(dir = ".") : Error: chunk 5
Error in plotFreqStat(x) : element 12 is empty
Execution halted