Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 2.13: BUILD report for rTRM on zin1

This page was generated on 2014-04-05 09:48:41 -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: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rTRM
StartedAt: 2014-04-04 22:49:04 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 22:49:58 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 53.7 seconds
RetCode: 0
Status:  OK 
PackageFile: rTRM_1.0.5.tar.gz
PackageFileSize: 2.274 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 3.1415926-1.40.10 (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
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-2.13-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def))
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty)
(/usr/share/texmf-texlive/tex/latex/inconsolata/inconsolata.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty))
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))
(/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty))
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def)

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,
(hyperref)                setting the option has no effect on input line 361.

) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
(/usr/share/texmf-texlive/tex/latex/base/utf8.def
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu))
(/usr/share/texmf-texlive/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty))
(/usr/share/texmf-texlive/tex/latex/inconsolata/t1fi4.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts/map/
pdftex/updmap/pdftex.map}] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
[2] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [3]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [4]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (116.44772pt too wide) in paragraph at lines 207--207
 []\T1/fi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[] 
[5] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [6]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [7]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [8]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [9]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [10]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [11]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [12]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [13]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [14]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [15]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [16]
Overfull \hbox (944.78122pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [17]
Overfull \hbox (801.44785pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [18]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (44.781pt too wide) in paragraph at lines 969--969
 []\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
 "physical", mimic.old = FALSE)[] 
[19] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [20]
No file Rd2.ind.
[21] (./Rd2.aux) )
(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
e/texmf-texlive/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/font
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, 132128 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.
Transcript written in Rd2.ilg.
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
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-2.13-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def))
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty)
(/usr/share/texmf-texlive/tex/latex/inconsolata/inconsolata.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty))
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))
(/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty))
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def)

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,
(hyperref)                setting the option has no effect on input line 361.

) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
(/usr/share/texmf-texlive/tex/latex/base/utf8.def
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu))
(/usr/share/texmf-texlive/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./Rd2.out)
(./Rd2.out) (/usr/share/texmf-texlive/tex/latex/inconsolata/t1fi4.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Underfull \vbox (badness 5533) has occurred while \output is active [2]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [3]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [4]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (116.44772pt too wide) in paragraph at lines 207--207
 []\T1/fi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[] 
[5] [6] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [7]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [8]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [9]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [10]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [11]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [12]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [13]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [14]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [15]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [16]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [17]
Overfull \hbox (944.78122pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [18]
Overfull \hbox (801.44785pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [19]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (44.781pt too wide) in paragraph at lines 969--969
 []\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
 "physical", mimic.old = FALSE)[] 
[20] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [21] (./Rd2.ind [22]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/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/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/public/amsfonts/cm/cmsy10.pfb></us
r/share/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texmf-tex
live/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw
/times/utmr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></
usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 164899 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.
Transcript written in Rd2.ilg.
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
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-2.13-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def))
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty)
(/usr/share/texmf-texlive/tex/latex/inconsolata/inconsolata.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty))
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))
(/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty))
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def)

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,
(hyperref)                setting the option has no effect on input line 361.

) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
(/usr/share/texmf-texlive/tex/latex/base/utf8.def
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu))
(/usr/share/texmf-texlive/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./Rd2.out)
(./Rd2.out) (/usr/share/texmf-texlive/tex/latex/inconsolata/t1fi4.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [2]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [3]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [4]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (116.44772pt too wide) in paragraph at lines 207--207
 []\T1/fi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[] 
[5] [6] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [7]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [8]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [9]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [10]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [11]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [12]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [13]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [14]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [15]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [16]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [17]
Overfull \hbox (944.78122pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [18]
Overfull \hbox (801.44785pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [19]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (44.781pt too wide) in paragraph at lines 969--969
 []\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
 "physical", mimic.old = FALSE)[] 
[20] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [21] (./Rd2.ind [22]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/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/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/public/amsfonts/cm/cmsy10.pfb></us
r/share/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texmf-tex
live/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw
/times/utmr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></
usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 166021 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
 \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(/usr/share/texmf-texlive/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-2.13-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/tools/longtable.sty)
(/usr/share/texmf-texlive/tex/latex/tools/bm.sty)
(/usr/share/texmf-texlive/tex/latex/base/alltt.sty)
(/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty)
(/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty)
(/usr/share/texmf-texlive/tex/latex/base/textcomp.sty
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))
(/usr/share/texmf-texlive/tex/latex/base/fontenc.sty
(/usr/share/texmf-texlive/tex/latex/base/t1enc.def))
(/usr/share/texmf-texlive/tex/latex/psnfss/times.sty)
(/usr/share/texmf-texlive/tex/latex/inconsolata/inconsolata.sty
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty))
(/usr/share/texmf-texlive/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty))
(/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty))
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty)
(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
(/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def)

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,
(hyperref)                setting the option has no effect on input line 361.

) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty)
(/usr/share/texmf-texlive/tex/latex/base/inputenc.sty
(/usr/share/texmf-texlive/tex/latex/base/utf8.def
(/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu)
(/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu))
(/usr/share/texmf-texlive/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty
(/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) (./Rd2.out)
(./Rd2.out) (/usr/share/texmf-texlive/tex/latex/inconsolata/t1fi4.fd)
(/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [2]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [3]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [4]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (116.44772pt too wide) in paragraph at lines 207--207
 []\T1/fi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[] 
[5] [6] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [7]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [8]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [9]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [10]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [11]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [12]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [13]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [14]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [15]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [16]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [17]
Overfull \hbox (944.78122pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [18]
Overfull \hbox (801.44785pt 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)[] 
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [19]
(/usr/share/texmf-texlive/tex/latex/base/utf8.def)
Overfull \hbox (44.781pt too wide) in paragraph at lines 969--969
 []\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
 "physical", mimic.old = FALSE)[] 
[20] (/usr/share/texmf-texlive/tex/latex/base/utf8.def)
(/usr/share/texmf-texlive/tex/latex/base/utf8.def) [21] (./Rd2.ind [22]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/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/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/public/amsfonts/cm/cmsy10.pfb></us
r/share/texmf-texlive/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texmf-tex
live/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf-texlive/fonts/type1/urw
/times/utmr8a.pfb></usr/share/texmf-texlive/fonts/type1/urw/times/utmr8a.pfb></
usr/share/texmf-texlive/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 166021 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/Rtmp0iM54g/Rbuild684c6690fac2/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_1.0.5.tar.gz’