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BioC 2.12: BUILD report for RamiGO on petty

This page was generated on 2013-10-09 09:40:01 -0700 (Wed, 09 Oct 2013).

Package 518/671HostnameOS / ArchBUILDCHECKBUILD BIN
RamiGO 1.6.0
Markus Schroeder
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/RamiGO
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK 

Summary

Package: RamiGO
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RamiGO
StartedAt: 2013-10-08 20:47:53 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 20:48:23 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 30.5 seconds
RetCode: 0
Status:  OK 
PackageFile: RamiGO_1.6.0.tar.gz
PackageFileSize: 539.2 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 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpKae2bk/Rbuild826a192d633/RamiGO/.Rd2pdf33386/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, 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, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
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NOT loading lmodern
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Package hyperref Message: Driver (autodetected): hpdftex.

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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,
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Writing index file Rd2.idx
No file Rd2.aux.
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
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ive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
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[]\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/2012/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 .
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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/2012/texmf-dist/tex/latex/base/utf8.def) [7]
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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

Overfull \hbox (63.78088pt too wide) in paragraph at lines 580--580
 []\T1/fi4/m/n/9 goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301"
,"GO:0003824","GO:0005783","GO:0043229")[] 
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Underfull \vbox (badness 10000) has occurred while \output is active [10]
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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'.

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(see the transcript file for additional information)pdfTeX warning (dest): name
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a fixed one

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 replaced by a fixed one

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Output written on Rd2.pdf (12 pages, 89434 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2012] (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 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpKae2bk/Rbuild826a192d633/RamiGO/.Rd2pdf33386/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, 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, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
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(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
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Package hyperref Message: Driver (autodetected): hpdftex.

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Package hyperref Warning: Option `hyperindex' has already been used,
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Package hyperref Warning: Option `pagebackref' has already been used,
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Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1ptm.fd)
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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
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(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
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[]\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/2012/texmf-dist/tex/latex/base/utf8.def) [4]
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[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
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 / / www . bioconductor .
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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/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/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]
Overfull \hbox (63.78088pt too wide) in paragraph at lines 580--580
 []\T1/fi4/m/n/9 goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301"
,"GO:0003824","GO:0005783","GO:0043229")[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
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 )
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Output written on Rd2.pdf (13 pages, 102315 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2012] (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.
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This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
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LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
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c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
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rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
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[]\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
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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
llette MA, Paulovich A, Pomeroy
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Saving output to '/private/tmp/RtmpKae2bk/Rbuild826a192d633/RamiGO/build/RamiGO.pdf' ...
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* creating vignettes ... OK
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* building 'RamiGO_1.6.0.tar.gz'