BioC 3.2: BUILD report for rTRM on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/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’:

    union

...
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/bk10.clo))
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(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hpdftex.def
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Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 366.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 366.

) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/makeidx.sty)
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Writing index file Rd2.idx
No file Rd2.aux.
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
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Overfull \hbox (144.78088pt too wide) in paragraph at lines 213--213
 []\T1/fi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[] 
[4] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [5]
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Overfull \hbox (999.78088pt too wide) in paragraph at lines 867--867
 []\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
et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE)[] 
[15] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (849.78088pt too wide) in paragraph at lines 911--911
 []\T1/fi4/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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Overfull \hbox (64.78088pt too wide) in paragraph at lines 975--975
 []\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
 "physical", mimic.old = FALSE)[] 
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No file Rd2.ind.
[19] (./Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )
(see the transcript file for additional information){/usr/local/texlive/2013/te
xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2013/texmf-dist/fonts/
enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive/2013/texmf-dist/fonts/type
1/public/inconsolata/Inconsolata.pfb></usr/local/texlive/2013/texmf-dist/fonts/
type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/u
rw/times/utmb8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/urw/times/u
tmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/urw/times/utmr8a.pfb>
</usr/local/texlive/2013/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (19 pages, 97066 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmpx3frhq/Rbuild1511b39117a11/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_1.8.1.tar.gz’
BioC 3.2: BUILD report for rTRM on oaxaca

Summary

Command output
