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BioC 3.0: BUILD report for rTRM on perceval

This page was generated on 2015-04-10 09:58:19 -0700 (Fri, 10 Apr 2015).

Package 788/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTRM 1.4.0
Diego Diez
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/rTRM
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: rTRM
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rTRM
StartedAt: 2015-04-09 20:33:30 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 20:35:02 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 91.5 seconds
RetCode: 0
Status:  OK 
PackageFile: rTRM_1.4.0.tar.gz
PackageFileSize: 2.96 MiB

Command output

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


* checking for file ‘rTRM/DESCRIPTION’ ... OK
* preparing ‘rTRM’:
* 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 Loading required package: igraph
...
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex)
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Babel <3.9k> and hyphenation patterns for 78 languages loaded.
(./Rd2.tex (/usr/local/texlive/2014/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
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vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge.
lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offs
et = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE)[] 
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rtex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, l
abel.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = F
ALSE, normalize.layout = TRUE)[] 
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Output written on Rd2.pdf (19 pages, 100714 bytes).
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Output written on Rd2.pdf (21 pages, 114370 bytes).
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This is makeindex, version 2.15 [TeX Live 2014] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (37 entries accepted, 0 rejected).
Sorting entries....done (228 comparisons).
Generating output file Rd2.ind....done (71 lines written, 0 warnings).
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