rTRM 1.21.0
Diego Diez
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rTRM |
| Branch: master |
| Last Commit: a1b91c6 |
| Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ OK ] | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rTRM
###
##############################################################################
##############################################################################
* 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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (127.78088pt too wide) in paragraph at lines 218--218
[]\T1/zi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[]
[4] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (966.78088pt too wide) in paragraph at lines 872--872
[]\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)[]
[15] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (820.78088pt too wide) in paragraph at lines 916--916
[]\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)[]
[16] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (52.78088pt too wide) in paragraph at lines 980--980
[]\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
"physical", mimic.old = FALSE)[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
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/2016/te
xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2016/texmf-dist/fonts/
enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/2016/texmf-dist/fonts/typ
e1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2016/texmf-dist/
fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/t
ype1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/t
imes/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/times/utmr8
a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (19 pages, 111595 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2016] (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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Underfull \vbox (badness 10000) has occurred while \output is active [2]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (127.78088pt too wide) in paragraph at lines 218--218
[]\T1/zi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[]
[5] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (966.78088pt too wide) in paragraph at lines 872--872
[]\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)[]
[16] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (820.78088pt too wide) in paragraph at lines 916--916
[]\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)[]
[17] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (52.78088pt too wide) in paragraph at lines 980--980
[]\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
"physical", mimic.old = FALSE)[]
[18] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) (./Rd2.ind
[19] [20]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 63.
[21]) (./Rd2.aux)
Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/local/texlive/2016/te
xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2016/texmf-dist/fonts/
enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/2016/texmf-dist/fonts/typ
e1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2016/texmf-dist/
fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2016/texmf-dist/f
onts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/ty
pe1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/ti
mes/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/times/utmr8a
.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (21 pages, 125168 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2016] (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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (127.78088pt too wide) in paragraph at lines 218--218
[]\T1/zi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[]
[5] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (966.78088pt too wide) in paragraph at lines 872--872
[]\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)[]
[16] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (820.78088pt too wide) in paragraph at lines 916--916
[]\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)[]
[17] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (52.78088pt too wide) in paragraph at lines 980--980
[]\T1/zi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
"physical", mimic.old = FALSE)[]
[18] (/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) (./Rd2.ind
[19] [20]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 63.
[21]) (./Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information){/usr/local/texlive/2016/te
xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2016/texmf-dist/fonts/
enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/2016/texmf-dist/fonts/typ
e1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/texlive/2016/texmf-dist/
fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2016/texmf-dist/f
onts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/ty
pe1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/ti
mes/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/times/utmr8a
.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (21 pages, 125493 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmpy2kNLt/Rbuild12cec697eb100/rTRM/build/rTRM.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘rTRM_1.21.0.tar.gz’