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BioC 2.13: BUILD report for rTRM on perceval

This page was generated on 2014-04-05 09:53:09 -0700 (Sat, 05 Apr 2014).

Package 636/750HostnameOS / ArchBUILDCHECKBUILD BIN
rTRM 1.0.5
Diego Diez
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/rTRM
Last Changed Rev: 86449 / Revision: 88450
Last Changed Date: 2014-02-13 20:31:47 -0800 (Thu, 13 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK 

Summary

Package: rTRM
Version: 1.0.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rTRM
StartedAt: 2014-04-04 22:30:06 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 22:32:16 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 130.5 seconds
RetCode: 0
Status:  OK 
PackageFile: rTRM_1.0.5.tar.gz
PackageFileSize: 2.268 MiB

Command output

* 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 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpQmCklP/Rbuild24de62c80c0b/rTRM/.Rd2pdf9438/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/bk10.clo))
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Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2012/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 361.


Package hyperref Warning: Option `pagebackref' has already been used,
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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).]
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(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
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ive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
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ended = FALSE, strict = FALSE, type = "igraph")[] 
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Overfull \hbox (999.78088pt too wide) in paragraph at lines 861--861
 []\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/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (849.78088pt too wide) in paragraph at lines 905--905
 []\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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 []\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
 "physical", mimic.old = FALSE)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [18]
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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'.

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(see the transcript file for additional information){/usr/local/texlive/2012/te
xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2012/texmf-dist/fonts/
enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive/2012/texmf-dist/fonts/type
1/public/inconsolata/Inconsolata.pfb></usr/local/texlive/2012/texmf-dist/fonts/
type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/u
rw/times/utmb8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/times/u
tmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/times/utmr8a.pfb>
</usr/local/texlive/2012/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (19 pages, 96745 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2012] (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.
Transcript written in ./Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpQmCklP/Rbuild24de62c80c0b/rTRM/.Rd2pdf9438/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
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(./Rd2.out) (./Rd2.out)
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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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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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