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### Running command:
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### /home/biocbuild/bbs-3.1-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
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
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...
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
\write18 enabled.
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t/fonts/type1/urw/times/utmri8a.pfb>
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This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
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This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
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[]\T1/zi4/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
et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE)[]
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[]\T1/zi4/m/n/10 plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, ve
rtex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, l
abel.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = F
ALSE, normalize.layout = TRUE)[]
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[]\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
"physical", mimic.old = FALSE)[]
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(Font) using `T1/zi4/m/n' instead on input line 63.
[23]) (./Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/
inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/incon
solata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/u
hvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr
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texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 170088 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpqHW39s/Rbuild6f5542c06436/rTRM/build/rTRM.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘rTRM_1.6.0.tar.gz’
