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BioC 3.2: BUILD report for rTRM on oaxaca

This page was generated on 2016-04-23 10:26:51 -0700 (Sat, 23 Apr 2016).

Package 929/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTRM 1.8.1
Diego Diez
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/rTRM
Last Changed Rev: 111921 / Revision: 116712
Last Changed Date: 2015-12-25 05:33:59 -0800 (Fri, 25 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK [ OK ] OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rTRM
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rTRM
StartedAt: 2016-04-22 19:37:56 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 19:39:06 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 69.9 seconds
RetCode: 0
Status:  OK 
PackageFile: rTRM_1.8.1.tar.gz
PackageFileSize: 3.144 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

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

...
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
 \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(/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
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2013/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2013/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/local/texlive/2013/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2013/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (144.78088pt too wide) in paragraph at lines 213--213
 []\T1/fi4/m/n/10 findTRM(g, target, query, method = "nsa", max.bridge = 1, ext
ended = FALSE, strict = FALSE, type = "igraph")[] 
[4] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (999.78088pt too wide) in paragraph at lines 867--867
 []\T1/fi4/m/n/10 plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, 
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)[] 
[15] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (849.78088pt too wide) in paragraph at lines 911--911
 []\T1/fi4/m/n/10 plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, ve
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)[] 
[16] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (64.78088pt too wide) in paragraph at lines 975--975
 []\T1/fi4/m/n/10 processBiogrid(dblist, org = "human", simplify = TRUE, type =
 "physical", mimic.old = FALSE)[] 
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
No file Rd2.ind.
[19] (./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){/usr/local/texlive/2013/te
xmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive/2013/texmf-dist/fonts/
enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive/2013/texmf-dist/fonts/type
1/public/inconsolata/Inconsolata.pfb></usr/local/texlive/2013/texmf-dist/fonts/
type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/u
rw/times/utmb8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/urw/times/u
tmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/urw/times/utmr8a.pfb>
</usr/local/texlive/2013/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (19 pages, 97066 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmpx3frhq/Rbuild1511b39117a11/rTRM/build/rTRM.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 ‘rTRM_1.8.1.tar.gz’