RamiGO 1.29.1
Markus Schroeder
| Snapshot Date: 2018-10-28 16:46:29 -0400 (Sun, 28 Oct 2018) |
| URL: https://git.bioconductor.org/packages/RamiGO |
| Branch: master |
| Last Commit: 564e51e |
| Last Changed Date: 2018-08-03 09:14:14 -0400 (Fri, 03 Aug 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | [ ERROR ] | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | ...NOT SUPPORTED... |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RamiGO
###
##############################################################################
##############################################################################
* checking for file ‘RamiGO/DESCRIPTION’ ... OK
* preparing ‘RamiGO’:
* 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 .
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.9-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] [3]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (29.36072pt too wide) in paragraph at lines 301--304
[]\T1/ptm/m/n/10 See [][]$\T1/zi4/m/n/10 http : / / rcytoscape . systemsbiology
. net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http :
/ / www . bioconductor .
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.19798pt too wide) in paragraph at lines 438--439
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
[7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 559--560
[]\T1/ptm/m/n/10 The edge col-ors in the tree rep-re-sent the re-la-tion-ship b
e-tween two nodes. In par-tic-u-lar: green=positively
Overfull \hbox (20.27475pt too wide) in paragraph at lines 582--582
[]\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[]
Overfull \hbox (20.27475pt too wide) in paragraph at lines 583--583
[]\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[]
[9]
Overfull \hbox (65.27475pt too wide) in paragraph at lines 587--587
[]\T1/zi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11]
No file Rd2.ind.
[12] (/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/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)pdfTeX warning (dest): name
{Rfn.oldClass.Rdash.class} has been referenced but does not exist, replaced by
a fixed one
pdfTeX warning (dest): name{Rfn.igraph} has been referenced but does not exist,
replaced by a fixed one
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.
pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share
/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (12 pages, 106257 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.9-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.out)
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] [3]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (29.36072pt too wide) in paragraph at lines 301--304
[]\T1/ptm/m/n/10 See [][]$\T1/zi4/m/n/10 http : / / rcytoscape . systemsbiology
. net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http :
/ / www . bioconductor .
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.19798pt too wide) in paragraph at lines 438--439
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
[7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 559--560
[]\T1/ptm/m/n/10 The edge col-ors in the tree rep-re-sent the re-la-tion-ship b
e-tween two nodes. In par-tic-u-lar: green=positively
Overfull \hbox (20.27475pt too wide) in paragraph at lines 582--582
[]\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[]
Overfull \hbox (20.27475pt too wide) in paragraph at lines 583--583
[]\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[]
[9]
Overfull \hbox (65.27475pt too wide) in paragraph at lines 587--587
[]\T1/zi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11]
No file Rd2.ind.
[12] (/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.aux) )
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.oldClass.Rdash.class} has been referenced but does not exist, replaced by
a fixed one
pdfTeX warning (dest): name{Rfn.igraph} has been referenced but does not exist,
replaced by a fixed one
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.
pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share
/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (12 pages, 107557 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (57 entries accepted, 0 rejected).
Sorting entries....done (338 comparisons).
Generating output file Rd2.ind....done (107 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.9-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.out)
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] [3]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (29.36072pt too wide) in paragraph at lines 301--304
[]\T1/ptm/m/n/10 See [][]$\T1/zi4/m/n/10 http : / / rcytoscape . systemsbiology
. net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http :
/ / www . bioconductor .
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.19798pt too wide) in paragraph at lines 438--439
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
[7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 559--560
[]\T1/ptm/m/n/10 The edge col-ors in the tree rep-re-sent the re-la-tion-ship b
e-tween two nodes. In par-tic-u-lar: green=positively
Overfull \hbox (20.27475pt too wide) in paragraph at lines 582--582
[]\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[]
Overfull \hbox (20.27475pt too wide) in paragraph at lines 583--583
[]\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[]
[9]
Overfull \hbox (65.27475pt too wide) in paragraph at lines 587--587
[]\T1/zi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11]
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.ind [12]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 26.
[13]) (/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/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)pdfTeX warning (dest): name
{Rfn.oldClass.Rdash.class} has been referenced but does not exist, replaced by
a fixed one
pdfTeX warning (dest): name{Rfn.igraph} has been referenced but does not exist,
replaced by a fixed one
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/time
s/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (13 pages, 118355 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (57 entries accepted, 0 rejected).
Sorting entries....done (338 comparisons).
Generating output file Rd2.ind....done (107 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.9-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.out)
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2] [3]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (29.36072pt too wide) in paragraph at lines 301--304
[]\T1/ptm/m/n/10 See [][]$\T1/zi4/m/n/10 http : / / rcytoscape . systemsbiology
. net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http :
/ / www . bioconductor .
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.19798pt too wide) in paragraph at lines 438--439
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
[7] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 559--560
[]\T1/ptm/m/n/10 The edge col-ors in the tree rep-re-sent the re-la-tion-ship b
e-tween two nodes. In par-tic-u-lar: green=positively
Overfull \hbox (20.27475pt too wide) in paragraph at lines 582--582
[]\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[]
Overfull \hbox (20.27475pt too wide) in paragraph at lines 583--583
[]\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[]
[9]
Overfull \hbox (65.27475pt too wide) in paragraph at lines 587--587
[]\T1/zi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11]
(/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.ind [12]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 26.
[13]) (/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/.Rd2pdf15928/Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.oldClass.Rdash.class} has been referenced but does not exist, replaced by
a fixed one
pdfTeX warning (dest): name{Rfn.igraph} has been referenced but does not exist,
replaced by a fixed one
{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/time
s/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (13 pages, 119082 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpFDSfKd/Rbuild3e38136f8435/RamiGO/build/RamiGO.pdf’ ...
Done
* creating vignettes ... ERROR
Loading required package: gsubfn
Loading required package: proto
Warning: Package 'RamiGO' is deprecated and will be removed
from Bioconductor version 3.9
Error: processing vignette 'RamiGO.Rnw' failed with diagnostics:
chunk 5 (label = getAmigoTreeDOT)
Error in `[<-`(`*tmp*`, relations[i, "parent"], relations[i, "child"], :
subscript out of bounds
Execution halted