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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rTRM
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* checking for file ‘rTRM/DESCRIPTION’ ... OK
* preparing ‘rTRM’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX Loading required package: igraph
...
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
\write18 enabled.
entering extended mode
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
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*hyperref using default driver hpdftex*
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\T1/ptm/m/n/10 rich, biomaRt,knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.mas
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[]\T1/fi4/m/n/10 plotGraph(g, layout = layout.fruchterman.reingold, mar = .5,
vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge.
lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offs
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abel.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = F
ALSE, normalize.layout = TRUE)[]
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[]\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
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(see the transcript file for additional information){/usr/share/texmf-texlive/f
onts/enc/dvips/base/8r.enc}{/usr/share/texmf-texlive/fonts/enc/dvips/inconsolat
a/fi4-ec.enc}</usr/share/texmf-texlive/fonts/type1/public/inconsolata/Inconsola
ta.pfb></usr/share/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/shar
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s/type1/urw/times/utmr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/ut
mr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (21 pages, 132143 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2009] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (37 entries accepted, 0 rejected).
Sorting entries....done (228 comparisons).
Generating output file Rd2.ind....done (71 lines written, 0 warnings).
Output written in Rd2.ind.
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This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
\write18 enabled.
entering extended mode
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(./Rd2.tex (/usr/share/texmf-texlive/tex/latex/base/book.cls
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[]\T1/fi4/m/n/10 plotGraph(g, layout = layout.fruchterman.reingold, mar = .5,
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lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offs
et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE)[]
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ALSE, normalize.layout = TRUE)[]
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onts/enc/dvips/base/8r.enc}{/usr/share/texmf-texlive/fonts/enc/dvips/inconsolat
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Output written on Rd2.pdf (23 pages, 164924 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2009] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (37 entries accepted, 0 rejected).
Sorting entries....done (228 comparisons).
Generating output file Rd2.ind....done (71 lines written, 0 warnings).
Output written in Rd2.ind.
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This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
\write18 enabled.
entering extended mode
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
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