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BioC 3.0: BUILD report for RamiGO on oaxaca

This page was generated on 2015-04-10 10:05:11 -0700 (Fri, 10 Apr 2015).

Package 713/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RamiGO 1.12.1
Markus Schroeder
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/RamiGO
Last Changed Rev: 100640 / Revision: 102249
Last Changed Date: 2015-03-13 07:08:14 -0700 (Fri, 13 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded [ OK ] OK  OK 

Summary

Package: RamiGO
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RamiGO
StartedAt: 2015-04-09 18:51:22 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 18:51:49 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 27.8 seconds
RetCode: 0
Status:  OK 
PackageFile: RamiGO_1.12.1.tar.gz
PackageFileSize: 445.9 KiB

Command output

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###
### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RamiGO
###
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##############################################################################


* 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)
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entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(./Rd2.tex (/usr/local/texlive/2013/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
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(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/keyval.sty))
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) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/makeidx.sty)
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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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 / / www . bioconductor .
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llette MA, Paulovich A, Pomeroy
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e-tween two nodes. In par-tic-u-lar: green=positively

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 []\T1/fi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="svg",saveResult=FALSE)[] 

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 []\T1/fi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
picType="dot",saveResult=FALSE)[] 

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 []\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.
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Output written on Rd2.pdf (12 pages, 89444 bytes).
Transcript written on Rd2.log.
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Sorting entries....done (338 comparisons).
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Output written in Rd2.ind.
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This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(./Rd2.tex (/usr/local/texlive/2013/texmf-dist/tex/latex/base/book.cls
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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 [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
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 / / www . bioconductor .
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llette MA, Paulovich A, Pomeroy
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 []\T1/fi4/m/n/9 ss <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
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 []\T1/fi4/m/n/9 dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example",
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 []\T1/fi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[] 
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This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
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LaTeX2e <2011/06/27>
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(./Rd2.tex (/usr/local/texlive/2013/texmf-dist/tex/latex/base/book.cls
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[]\T1/fi4/m/n/10 leaves(object) <- value\T1/ptm/m/n/10 Sets the the data.frame 
con-tain-ing the leaves of the tree with the columns
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[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
 . net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/fi4/m/n/10 http :
 / / www . bioconductor .
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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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[]\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

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","GO:0003824","GO:0005783","GO:0043229")[] 
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Saving output to ‘/private/tmp/Rtmpx0WkBf/Rbuildca0a56f39150/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_1.12.1.tar.gz’