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Package 431/553HostnameOS / ArchBUILDCHECKBUILD BIN
RamiGO 1.2.0
Markus Schroeder
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/RamiGO
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386 [ OK ] OK  OK 

Summary

Package: RamiGO
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RamiGO
StartedAt: 2012-09-23 22:29:52 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 22:30:13 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 20.9 seconds
RetCode: 0
Status:  OK 
PackageFile: RamiGO_1.2.0.tar.gz
PackageFileSize: 537.2 KiB

Command output

* 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 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpM8eEnJ/Rbuild94ce8e8d593/RamiGO/.Rd2pdf38094/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
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(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2011/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 356.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 356.

) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
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(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
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Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
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ive/2011/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (4.67784pt too wide) in paragraph at lines 168--170
[]\T1/fi4/m/n/10 leaves(object) <- value\T1/ptm/m/n/10 Sets the the data.frame 
con-tain-ing the leaves of the tree with the columns
[3] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
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Overfull \hbox (29.36072pt too wide) in paragraph at lines 290--293
[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
 . net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/fi4/m/n/10 http :
 / / www . bioconductor .
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
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Overfull \hbox (3.19798pt too wide) in paragraph at lines 427--428
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 538--539
[]\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
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [10]
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No file Rd2.ind.
[11] (./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/local/texlive/2011/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2011/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2011/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2011/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
11/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2011/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (11 pages, 88949 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (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 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpM8eEnJ/Rbuild94ce8e8d593/RamiGO/.Rd2pdf38094/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
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(/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
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Package hyperref Message: Driver (autodetected): hpdftex.

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) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
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(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
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Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
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(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (4.67784pt too wide) in paragraph at lines 168--170
[]\T1/fi4/m/n/10 leaves(object) <- value\T1/ptm/m/n/10 Sets the the data.frame 
con-tain-ing the leaves of the tree with the columns
[3] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
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[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
 . net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/fi4/m/n/10 http :
 / / www . bioconductor .
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [5]
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Overfull \hbox (3.19798pt too wide) in paragraph at lines 427--428
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
[7] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [8]
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[]\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] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
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Package rerunfilecheck Warning: File `Rd2.out' has changed.
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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

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Output written on Rd2.pdf (13 pages, 102339 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (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 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpM8eEnJ/Rbuild94ce8e8d593/RamiGO/.Rd2pdf38094/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
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[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
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[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
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Saving output to '/private/tmp/RtmpM8eEnJ/Rbuild94ce8e8d593/RamiGO/build/RamiGO.pdf' ...
Done
* creating vignettes ... OK
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* building 'RamiGO_1.2.0.tar.gz'