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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data ADaCGH2
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* checking for file ‘ADaCGH2/DESCRIPTION’ ... OK
* preparing ‘ADaCGH2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ADaCGH2.Rnw’ using Sweave
Loading required package: parallel
Loading required package: ff
Loading required package: bit
Attaching package: ‘bit’
The following object is masked from ‘package:base’:
xor
Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpMkISFQ/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package: ‘ff’
The following objects are masked from ‘package:utils’:
write.csv, write.csv2
The following objects are masked from ‘package:base’:
is.factor, is.ordered
Loading required package: GLAD
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Have fun with GLAD
For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008,
If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,
If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,
For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg
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New options are available in daglad: see help for details.
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Warning in cutFile(fnametxt, 1, 2, 3, sep = "\t", mc.cores = 2) :
Number of columns not specified. We guess they are 9
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Loading required package: limma
Loading required package: snapCGH
Loading required package: CGHregions
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object is masked from ‘package:limma’:
plotMA
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: CGHbase
Loading required package: marray
Error: processing vignette 'ADaCGH2.Rnw' failed with diagnostics:
unable to run pdflatex on 'ADaCGH2.tex'
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.12 \usepackage
{array}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ADaCGH2.Rnw’
SUMMARY: processing the following file failed:
‘ADaCGH2.Rnw’
Error: Vignette re-building failed.
Execution halted