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 3.1: BUILD report for RamiGO on zin2

This page was generated on 2015-10-09 09:24:24 -0700 (Fri, 09 Oct 2015).

Package 778/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RamiGO 1.14.0
Markus Schroeder
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/RamiGO
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded [ OK ] OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RamiGO
Version: 1.14.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RamiGO
StartedAt: 2015-10-08 19:44:29 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 19:44:44 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 15.0 seconds
RetCode: 0
Status:  OK 
PackageFile: RamiGO_1.14.0.tar.gz
PackageFileSize: 431.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-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 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
 \write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9h> and hyphenation patterns for 26 languages loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.1-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
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/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))

Package hyperref Message: Driver (autodetected): hpdftex.

(/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 366.


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

) (/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/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 295--298
[]\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 432--433
[]\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) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.60664pt too wide) in paragraph at lines 553--554
[]\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
[9]
Overfull \hbox (21.4809pt too wide) in paragraph at lines 576--576
 []\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[] 

Overfull \hbox (21.4809pt too wide) in paragraph at lines 577--577
 []\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[] 

Overfull \hbox (66.4809pt too wide) in paragraph at lines 581--581
 []\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] (./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, 120519 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (57 entries accepted, 0 rejected).
Sorting entries....done (339 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 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
 \write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9h> and hyphenation patterns for 26 languages loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.1-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
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/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))

Package hyperref Message: Driver (autodetected): hpdftex.

(/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 366.


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

) (/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
(./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/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))
(./Rd2.out) (./Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
(/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 295--298
[]\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 .
[5] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
Overfull \hbox (3.19798pt too wide) in paragraph at lines 432--433
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.60664pt too wide) in paragraph at lines 553--554
[]\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
[9]
Overfull \hbox (21.4809pt too wide) in paragraph at lines 576--576
 []\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[] 

Overfull \hbox (21.4809pt too wide) in paragraph at lines 577--577
 []\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[] 

Overfull \hbox (66.4809pt too wide) in paragraph at lines 581--581
 []\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) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11] (./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]) (./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, 145715 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2013] (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 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
 \write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9h> and hyphenation patterns for 26 languages loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.1-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
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/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))

Package hyperref Message: Driver (autodetected): hpdftex.

(/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 366.


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

) (/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
(./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/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))
(./Rd2.out) (./Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/li
b/texmf/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 295--298
[]\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 .
[5] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
Overfull \hbox (3.19798pt too wide) in paragraph at lines 432--433
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.60664pt too wide) in paragraph at lines 553--554
[]\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
[9]
Overfull \hbox (21.4809pt too wide) in paragraph at lines 576--576
 []\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[] 

Overfull \hbox (21.4809pt too wide) in paragraph at lines 577--577
 []\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[] 

Overfull \hbox (66.4809pt too wide) in paragraph at lines 581--581
 []\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) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11] (./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]) (./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, 146434 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
 \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2011/06/27>
Babel <3.9h> and hyphenation patterns for 26 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.1-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
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/etc/texmf/tex/latex/config/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/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))

Package hyperref Message: Driver (autodetected): hpdftex.

(/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 366.


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

) (/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
(./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/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))
(./Rd2.out) (./Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/li
b/texmf/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 295--298
[]\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 .
[5] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
Overfull \hbox (3.19798pt too wide) in paragraph at lines 432--433
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.60664pt too wide) in paragraph at lines 553--554
[]\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
[9]
Overfull \hbox (21.4809pt too wide) in paragraph at lines 576--576
 []\T1/zi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[] 

Overfull \hbox (21.4809pt too wide) in paragraph at lines 577--577
 []\T1/zi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[] 

Overfull \hbox (66.4809pt too wide) in paragraph at lines 581--581
 []\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) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11] (./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]) (./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, 146434 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/Rtmp8TfGwc/Rbuild338d78221896/RamiGO/build/RamiGO.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 ‘RamiGO_1.14.0.tar.gz’