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### Running command:
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### chmod a+r coRNAi -R && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data coRNAi
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* checking for file 'coRNAi/DESCRIPTION' ... OK
* preparing 'coRNAi':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"C:/Users/biocbuild/bbs-3.5-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
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: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: grid
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Warning: Package 'coRNAi' is deprecated and will be removed from Bioconductor
version 3.6
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
"add" is not a graphical parameter
Warning in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, :
Estimated rdf < 1.0; not estimating variance
Warning: running command 'neato -Tpdf -o interactionGraph1.pdf interactionGraph1.dot' had status 127
Warning: running command 'neato -Tpdf -o interactionGraph2.pdf interactionGraph2.dot' had status 127
Warning: running command 'neato -Tpdf -o correlationGraph1.pdf correlationGraph1.dot' had status 127
Warning: running command 'neato -Tpdf -o correlationGraph2.pdf correlationGraph2.dot' had status 127
Warning: Data contains negative values.
Log transformation for those values resulted in NA
Warning: running command '"C:\PROGRA˜1\MIKTEX˜1.9\miktex\bin\x64\texify.exe" --quiet --pdf "coRNAi.tex" --max-iterations=20 -I "C:/Users/biocbuild/bbs-3.5-bioc/R/share/texmf/tex/latex" -I "C:/Users/biocbuild/bbs-3.5-bioc/R/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'coRNAi.tex' failed
LaTeX errors:
nettes/coRNAi.tex:558: Package pdftex.def Error: File `interactionGraph1.pdf' n
ot found.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help
nettes/coRNAi.tex:559: Package pdftex.def Error: File `correlationGraph1.pdf' n
ot found.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help
nettes/coRNAi.tex:565: Package pdftex.def Error: File `interactionGraph2.pdf' n
ot found.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help
nettes/coRNAi.tex:566: Package pdftex.def Error: File `correlationGraph2.pdf' n
ot found.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help
Execution halted
