* checking for file ‘survcomp/DESCRIPTION’ ... OK
* preparing ‘survcomp’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* 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 3.1415926-1.40.11 (TeX Live 2010)
\write18 enabled.
entering extended mode
(./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, ancientgreek, ibycus, arabic, armenian
, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutch, u
kenglish, usenglishmax, esperanto, estonian, farsi, finnish, french, galician,
german, ngerman, swissgerman, monogreek, greek, hungarian, icelandic, assamese,
bengali, gujarati, hindi, kannada, malayalam, marathi, oriya, panjabi, tamil,
telugu, indonesian, interlingua, irish, italian, kurmanji, lao, latin, latvian,
lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, roma
nian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish,
turkmen, ukrainian, uppersorbian, welsh, loaded.
(/usr/share/texmf/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-2.12-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texmf/tex/latex/base/ifthen.sty)
(/usr/share/texmf/tex/latex/tools/longtable.sty)
(/usr/share/texmf/tex/latex/tools/bm.sty)
(/usr/share/texmf/tex/latex/base/alltt.sty)
(/usr/share/texmf/tex/latex/tools/verbatim.sty)
(/usr/share/texmf/tex/latex/url/url.sty) NOT loading ae
(/usr/share/texmf/tex/latex/base/fontenc.sty
(/usr/share/texmf/tex/latex/base/t1enc.def))
(/usr/share/texmf/tex/latex/psnfss/times.sty) NOT loading lmodern
(/usr/share/texmf/tex/latex/inconsolata/inconsolata.sty
(/usr/share/texmf/tex/latex/base/textcomp.sty
(/usr/share/texmf/tex/latex/base/ts1enc.def))
(/usr/share/texmf/tex/latex/graphics/keyval.sty))
(/usr/share/texmf/tex/latex/graphics/color.sty
(/usr/share/texmf/tex/latex/latexconfig/color.cfg)
(/usr/share/texmf/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texmf/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texmf/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texmf/tex/generic/oberdiek/etexcmds.sty))
(/usr/share/texmf/tex/generic/oberdiek/pdfescape.sty
(/usr/share/texmf/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf/tex/generic/oberdiek/ifluatex.sty)))
(/usr/share/texmf/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf/tex/latex/oberdiek/letltxmacro.sty)
(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf/tex/generic/oberdiek/bigintcalc.sty))
(/usr/share/texmf/tex/generic/oberdiek/atbegshi.sty))
* hyperref using default driver hpdftex *
(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
(/usr/share/texmf/tex/latex/oberdiek/atveryend.sty)
(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty
(/usr/share/texmf/tex/generic/oberdiek/uniquecounter.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/share/texmf/tex/latex/base/makeidx.sty)
(/usr/share/texmf/tex/latex/base/inputenc.sty
(/usr/share/texmf/tex/latex/base/utf8.def
(/usr/share/texmf/tex/latex/base/t1enc.dfu)
(/usr/share/texmf/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf/tex/latex/base/omsenc.dfu)
(/usr/share/texmf/tex/latex/base/ts1enc.dfu))
(/usr/share/texmf/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/share/texmf/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf/tex/latex/hyperref/nameref.sty
(/usr/share/texmf/tex/latex/oberdiek/refcount.sty)
(/usr/share/texmf/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texmf/tex/latex/inconsolata/t1fi4.fd)
Overfull \hbox (27.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <bhaibeka@jimmy.harvard.edu>\T1/ptm/m/n/10
, Markus Schroeder \T1/fi4/m/n/10 <mschroed@jimmy.harvard.edu>\T1/ptm/m/n/10 ,
Catha-
(/usr/share/texmf/tex/latex/psnfss/t1phv.fd)
(/usr/share/texmf/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts/map/pdftex/u
pdmap/pdftex.map}]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 54--55
[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
Overfull \hbox (7.89719pt too wide) in paragraph at lines 74--75
[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
(/usr/share/texmf/tex/latex/base/utf8.def) [2]
(/usr/share/texmf/tex/latex/psnfss/ts1ptm.fd) [3] [4]
(/usr/share/texmf/tex/latex/base/utf8.def)
(/usr/share/texmf/tex/latex/base/utf8.def) [5] [6]
(/usr/share/texmf/tex/latex/base/utf8.def) [7]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 384--385
[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
lytical for-mula to com-pute a meta-estimate.
[8] (/usr/share/texmf/tex/latex/base/utf8.def) [9]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (674.78088pt too wide) in paragraph at lines 504--504
[]\T1/fi4/m/n/10 concordance.index(x, surv.time, surv.event, cl, weights, comp
pairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether
", "nam"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
[10]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 520--521
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
[11] (/usr/share/texmf/tex/latex/base/utf8.def) [12]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (299.78088pt too wide) in paragraph at lines 652--652
[]\T1/fi4/m/n/10 D.index(x, surv.time, surv.event, weights, strat, alpha = 0.0
5, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE, ...)[
]
[13] (/usr/share/texmf/tex/latex/base/utf8.def) [14] [15]
(/usr/share/texmf/tex/latex/base/utf8.def) [16]
(/usr/share/texmf/tex/latex/base/utf8.def) [17]
(/usr/share/texmf/tex/latex/base/utf8.def) [18]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 960--961
\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons
and cu-mu-la-tive meta-analyses. Draws
[19]
Overfull \hbox (5.28088pt too wide) in paragraph at lines 977--977
[]\T1/fi4/m/n/9 forestplot.surv(labeltext=labeltext, mean=r.mean, lower=r.lowe
r, upper=r.upper, zero=0.5,[]
Overfull \hbox (167.28088pt too wide) in paragraph at lines 978--978
[] \T1/fi4/m/n/9 align=c("l"), graphwidth=unit(2, "inches"), x.ticks=seq(0.
3,0.8,0.1), xlab=paste( "Forestplot Example", myspace, sep=""),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 979--979
[] \T1/fi4/m/n/9 col=meta.colors(box="royalblue", line="darkblue", zero="da
rkred"), box.size=bs, clip=c(0.3,0.8))[]
(/usr/share/texmf/tex/latex/base/utf8.def) [20]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (324.78088pt too wide) in paragraph at lines 1044--1044
[]\T1/fi4/m/n/10 hazard.ratio(x, surv.time, surv.event, weights, strat, alpha
= 0.05, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE,
...)[]
[21] (/usr/share/texmf/tex/latex/base/utf8.def) [22]
(/usr/share/texmf/tex/latex/base/utf8.def) [23]
(/usr/share/texmf/tex/latex/base/utf8.def) [24] [25]
(/usr/share/texmf/tex/latex/base/utf8.def) [26]
(/usr/share/texmf/tex/latex/base/utf8.def) [27]
(/usr/share/texmf/tex/latex/base/utf8.def) [28]
Overfull \hbox (1034.78088pt too wide) in paragraph at lines 1473--1473
[]\T1/fi4/m/n/10 km.coxph.plot(formula.s, data.s, sub.s = "all", x.label, y.la
bel, main.title, sub.title, leg.text, leg.pos = "bottomright", leg.bty = "o", l
eg.inset = 0.05, o.text, v.line, h.line, .col = 1:4, .lty = 1, .lwd = 1, show.n
.risk = FALSE, n.risk.step, n.risk.cex = 0.85, verbose = TRUE, ...)[]
[29] (/usr/share/texmf/tex/latex/base/utf8.def) [30]
(/usr/share/texmf/tex/latex/base/utf8.def) [31]
(/usr/share/texmf/tex/latex/base/utf8.def) [32]
Overfull \hbox (581.28088pt too wide) in paragraph at lines 1714--1714
[]\T1/fi4/m/n/9 metaplot.surv(mn=c(0.4,0.5,0.6), lower=c(0.35,0.4,0.57), upper
=c(0.45,0.6,0.63), labels=c("A","B","C"), xlim=c(0.2,0.8), boxsize=0.5, zero=0.
5, col=rmeta::meta.colors(box="royalblue",line="darkblue",zero="firebrick"))[]
(/usr/share/texmf/tex/latex/base/utf8.def) [33]
Overfull \hbox (644.78088pt too wide) in paragraph at lines 1728--1728
[]\T1/fi4/m/n/10 mrmr.cindex(x, surv.time, surv.event, cl, weights, comppairs=
10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether", "na
m"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1744--1745
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
[34]
Overfull \hbox (149.28088pt too wide) in paragraph at lines 1786--1786
[]\T1/fi4/m/n/9 mrmr.cindex(x=xx, surv.time=stime, surv.event=sevent, strat=st
rat, weights=weight, method="noether", comppairs=comppairs)[]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (859.78088pt too wide) in paragraph at lines 1800--1800
[]\T1/fi4/m/n/10 mrmr.cindex.ensemble(x, surv.time, surv.event, cl, weights, c
omppairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noet
her", "nam"), alternative = c("two.sided", "less", "greater"), maxparents, maxn
sol, nboot = 200, na.rm = FALSE)[]
[35]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1816--1817
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
(/usr/share/texmf/tex/latex/base/utf8.def) [36] [37]
(/usr/share/texmf/tex/latex/base/utf8.def) [38]
(/usr/share/texmf/tex/latex/base/utf8.def) [39]
(/usr/share/texmf/tex/latex/base/utf8.def) [40]
(/usr/share/texmf/tex/latex/base/utf8.def) [41]
(/usr/share/texmf/tex/latex/base/utf8.def) [42] [43]
(/usr/share/texmf/tex/latex/base/utf8.def) [44]
(/usr/share/texmf/tex/latex/base/utf8.def) [45]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2344--2345
[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-
Overfull \hbox (3.21828pt too wide) in paragraph at lines 2351--2352
[]\T1/fi4/m/n/10 exprs(transbig7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex
-pres-sions as mea-sured by Affymetrix hgu133a
[46] (/usr/share/texmf/tex/latex/base/utf8.def) [47]
(/usr/share/texmf/tex/latex/base/utf8.def) [48]
(/usr/share/texmf/tex/latex/base/utf8.def) [49] [50]
No file Rd2.ind.
[51] (./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.jackknife} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survivalROC} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survivalROC.C} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.prodlim} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.plot} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.sbrier} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.wilcox.test} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survfit} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.metaplot} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.meta.colors} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one
pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.normOrder} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxph.object} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.summary.coxph} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxphCPE} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.phcpe} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one
{/usr/share/texmf/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips
/inconsolata/fi4-ec.enc}</usr/share/texmf/fonts/type1/public/inconsolata/Incons
olata.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/sha
re/texmf/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texmf/fonts/type1/urw/
times/utmb8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmr8a.pfb></usr/share
/texmf/fonts/type1/urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/urw/times
/utmri8a.pfb>
Output written on Rd2.pdf (51 pages, 199851 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2010] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (168 entries accepted, 0 rejected).
Sorting entries....done (1390 comparisons).
Generating output file Rd2.ind....done (207 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010)
\write18 enabled.
entering extended mode
(./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, ancientgreek, ibycus, arabic, armenian
, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutch, u
kenglish, usenglishmax, esperanto, estonian, farsi, finnish, french, galician,
german, ngerman, swissgerman, monogreek, greek, hungarian, icelandic, assamese,
bengali, gujarati, hindi, kannada, malayalam, marathi, oriya, panjabi, tamil,
telugu, indonesian, interlingua, irish, italian, kurmanji, lao, latin, latvian,
lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, roma
nian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish,
turkmen, ukrainian, uppersorbian, welsh, loaded.
(/usr/share/texmf/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-2.12-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texmf/tex/latex/base/ifthen.sty)
(/usr/share/texmf/tex/latex/tools/longtable.sty)
(/usr/share/texmf/tex/latex/tools/bm.sty)
(/usr/share/texmf/tex/latex/base/alltt.sty)
(/usr/share/texmf/tex/latex/tools/verbatim.sty)
(/usr/share/texmf/tex/latex/url/url.sty) NOT loading ae
(/usr/share/texmf/tex/latex/base/fontenc.sty
(/usr/share/texmf/tex/latex/base/t1enc.def))
(/usr/share/texmf/tex/latex/psnfss/times.sty) NOT loading lmodern
(/usr/share/texmf/tex/latex/inconsolata/inconsolata.sty
(/usr/share/texmf/tex/latex/base/textcomp.sty
(/usr/share/texmf/tex/latex/base/ts1enc.def))
(/usr/share/texmf/tex/latex/graphics/keyval.sty))
(/usr/share/texmf/tex/latex/graphics/color.sty
(/usr/share/texmf/tex/latex/latexconfig/color.cfg)
(/usr/share/texmf/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texmf/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texmf/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texmf/tex/generic/oberdiek/etexcmds.sty))
(/usr/share/texmf/tex/generic/oberdiek/pdfescape.sty
(/usr/share/texmf/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf/tex/generic/oberdiek/ifluatex.sty)))
(/usr/share/texmf/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf/tex/latex/oberdiek/letltxmacro.sty)
(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf/tex/generic/oberdiek/bigintcalc.sty))
(/usr/share/texmf/tex/generic/oberdiek/atbegshi.sty))
* hyperref using default driver hpdftex *
(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
(/usr/share/texmf/tex/latex/oberdiek/atveryend.sty)
(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty
(/usr/share/texmf/tex/generic/oberdiek/uniquecounter.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/share/texmf/tex/latex/base/makeidx.sty)
(/usr/share/texmf/tex/latex/base/inputenc.sty
(/usr/share/texmf/tex/latex/base/utf8.def
(/usr/share/texmf/tex/latex/base/t1enc.dfu)
(/usr/share/texmf/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf/tex/latex/base/omsenc.dfu)
(/usr/share/texmf/tex/latex/base/ts1enc.dfu))
(/usr/share/texmf/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/share/texmf/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf/tex/latex/hyperref/nameref.sty
(/usr/share/texmf/tex/latex/oberdiek/refcount.sty)
(/usr/share/texmf/tex/generic/oberdiek/gettitlestring.sty)) (./Rd2.out)
(./Rd2.out) (/usr/share/texmf/tex/latex/inconsolata/t1fi4.fd)
Overfull \hbox (27.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <bhaibeka@jimmy.harvard.edu>\T1/ptm/m/n/10
, Markus Schroeder \T1/fi4/m/n/10 <mschroed@jimmy.harvard.edu>\T1/ptm/m/n/10 ,
Catha-
(/usr/share/texmf/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]) (/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (7.89719pt too wide) in paragraph at lines 54--55
[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
[2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 74--75
[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
(/usr/share/texmf/tex/latex/base/utf8.def)
(/usr/share/texmf/tex/latex/psnfss/ts1ptm.fd) [3] [4]
(/usr/share/texmf/tex/latex/base/utf8.def) [5]
(/usr/share/texmf/tex/latex/base/utf8.def) [6]
(/usr/share/texmf/tex/latex/base/utf8.def) [7] [8]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 384--385
[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
lytical for-mula to com-pute a meta-estimate.
[9] (/usr/share/texmf/tex/latex/base/utf8.def) [10]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (674.78088pt too wide) in paragraph at lines 504--504
[]\T1/fi4/m/n/10 concordance.index(x, surv.time, surv.event, cl, weights, comp
pairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether
", "nam"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
[11]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 520--521
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
[12] (/usr/share/texmf/tex/latex/base/utf8.def) [13]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (299.78088pt too wide) in paragraph at lines 652--652
[]\T1/fi4/m/n/10 D.index(x, surv.time, surv.event, weights, strat, alpha = 0.0
5, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE, ...)[
]
[14] (/usr/share/texmf/tex/latex/base/utf8.def) [15]
(/usr/share/texmf/tex/latex/base/utf8.def) [16] [17]
(/usr/share/texmf/tex/latex/base/utf8.def) [18]
(/usr/share/texmf/tex/latex/base/utf8.def) [19]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 960--961
\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons
and cu-mu-la-tive meta-analyses. Draws
Overfull \hbox (5.28088pt too wide) in paragraph at lines 977--977
[]\T1/fi4/m/n/9 forestplot.surv(labeltext=labeltext, mean=r.mean, lower=r.lowe
r, upper=r.upper, zero=0.5,[]
Overfull \hbox (167.28088pt too wide) in paragraph at lines 978--978
[] \T1/fi4/m/n/9 align=c("l"), graphwidth=unit(2, "inches"), x.ticks=seq(0.
3,0.8,0.1), xlab=paste( "Forestplot Example", myspace, sep=""),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 979--979
[] \T1/fi4/m/n/9 col=meta.colors(box="royalblue", line="darkblue", zero="da
rkred"), box.size=bs, clip=c(0.3,0.8))[]
(/usr/share/texmf/tex/latex/base/utf8.def) [20]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (324.78088pt too wide) in paragraph at lines 1044--1044
[]\T1/fi4/m/n/10 hazard.ratio(x, surv.time, surv.event, weights, strat, alpha
= 0.05, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE,
...)[]
[21] [22] (/usr/share/texmf/tex/latex/base/utf8.def) [23]
(/usr/share/texmf/tex/latex/base/utf8.def) [24]
(/usr/share/texmf/tex/latex/base/utf8.def) [25] [26]
(/usr/share/texmf/tex/latex/base/utf8.def) [27]
(/usr/share/texmf/tex/latex/base/utf8.def) [28]
(/usr/share/texmf/tex/latex/base/utf8.def) [29]
Overfull \hbox (1034.78088pt too wide) in paragraph at lines 1473--1473
[]\T1/fi4/m/n/10 km.coxph.plot(formula.s, data.s, sub.s = "all", x.label, y.la
bel, main.title, sub.title, leg.text, leg.pos = "bottomright", leg.bty = "o", l
eg.inset = 0.05, o.text, v.line, h.line, .col = 1:4, .lty = 1, .lwd = 1, show.n
.risk = FALSE, n.risk.step, n.risk.cex = 0.85, verbose = TRUE, ...)[]
[30] (/usr/share/texmf/tex/latex/base/utf8.def) [31]
(/usr/share/texmf/tex/latex/base/utf8.def) [32]
(/usr/share/texmf/tex/latex/base/utf8.def) [33]
Overfull \hbox (581.28088pt too wide) in paragraph at lines 1714--1714
[]\T1/fi4/m/n/9 metaplot.surv(mn=c(0.4,0.5,0.6), lower=c(0.35,0.4,0.57), upper
=c(0.45,0.6,0.63), labels=c("A","B","C"), xlim=c(0.2,0.8), boxsize=0.5, zero=0.
5, col=rmeta::meta.colors(box="royalblue",line="darkblue",zero="firebrick"))[]
(/usr/share/texmf/tex/latex/base/utf8.def) [34]
Overfull \hbox (644.78088pt too wide) in paragraph at lines 1728--1728
[]\T1/fi4/m/n/10 mrmr.cindex(x, surv.time, surv.event, cl, weights, comppairs=
10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether", "na
m"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1744--1745
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
[35]
Overfull \hbox (149.28088pt too wide) in paragraph at lines 1786--1786
[]\T1/fi4/m/n/9 mrmr.cindex(x=xx, surv.time=stime, surv.event=sevent, strat=st
rat, weights=weight, method="noether", comppairs=comppairs)[]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (859.78088pt too wide) in paragraph at lines 1800--1800
[]\T1/fi4/m/n/10 mrmr.cindex.ensemble(x, surv.time, surv.event, cl, weights, c
omppairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noet
her", "nam"), alternative = c("two.sided", "less", "greater"), maxparents, maxn
sol, nboot = 200, na.rm = FALSE)[]
[36]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1816--1817
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
(/usr/share/texmf/tex/latex/base/utf8.def) [37] [38]
(/usr/share/texmf/tex/latex/base/utf8.def) [39]
(/usr/share/texmf/tex/latex/base/utf8.def) [40]
(/usr/share/texmf/tex/latex/base/utf8.def) [41]
(/usr/share/texmf/tex/latex/base/utf8.def) [42]
(/usr/share/texmf/tex/latex/base/utf8.def) [43] [44]
(/usr/share/texmf/tex/latex/base/utf8.def) [45]
(/usr/share/texmf/tex/latex/base/utf8.def) [46]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2344--2345
[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-
Overfull \hbox (3.21828pt too wide) in paragraph at lines 2351--2352
[]\T1/fi4/m/n/10 exprs(transbig7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex
-pres-sions as mea-sured by Affymetrix hgu133a
[47] (/usr/share/texmf/tex/latex/base/utf8.def) [48]
(/usr/share/texmf/tex/latex/base/utf8.def) [49]
(/usr/share/texmf/tex/latex/base/utf8.def) [50] [51] (./Rd2.ind [52] [53]
LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font) using `T1/fi4/m/n' instead on input line 173.
[54]) (./Rd2.aux)
Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.jackknife} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survivalROC} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survivalROC.C} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.prodlim} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.plot} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.sbrier} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.wilcox.test} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survfit} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.metaplot} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.meta.colors} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one
pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.normOrder} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxph.object} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.summary.coxph} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxphCPE} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.phcpe} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one
{/usr/share/texmf/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips
/inconsolata/fi4-ec.enc}</usr/share/texmf/fonts/type1/public/inconsolata/Incons
olata.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/sha
re/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texmf/fonts/type
1/urw/helvetic/uhvr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texmf/fonts/type1/urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/
urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (54 pages, 221382 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2010] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (168 entries accepted, 0 rejected).
Sorting entries....done (1391 comparisons).
Generating output file Rd2.ind....done (206 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010)
\write18 enabled.
entering extended mode
(./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, ancientgreek, ibycus, arabic, armenian
, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutch, u
kenglish, usenglishmax, esperanto, estonian, farsi, finnish, french, galician,
german, ngerman, swissgerman, monogreek, greek, hungarian, icelandic, assamese,
bengali, gujarati, hindi, kannada, malayalam, marathi, oriya, panjabi, tamil,
telugu, indonesian, interlingua, irish, italian, kurmanji, lao, latin, latvian,
lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, roma
nian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish,
turkmen, ukrainian, uppersorbian, welsh, loaded.
(/usr/share/texmf/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-2.12-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texmf/tex/latex/base/ifthen.sty)
(/usr/share/texmf/tex/latex/tools/longtable.sty)
(/usr/share/texmf/tex/latex/tools/bm.sty)
(/usr/share/texmf/tex/latex/base/alltt.sty)
(/usr/share/texmf/tex/latex/tools/verbatim.sty)
(/usr/share/texmf/tex/latex/url/url.sty) NOT loading ae
(/usr/share/texmf/tex/latex/base/fontenc.sty
(/usr/share/texmf/tex/latex/base/t1enc.def))
(/usr/share/texmf/tex/latex/psnfss/times.sty) NOT loading lmodern
(/usr/share/texmf/tex/latex/inconsolata/inconsolata.sty
(/usr/share/texmf/tex/latex/base/textcomp.sty
(/usr/share/texmf/tex/latex/base/ts1enc.def))
(/usr/share/texmf/tex/latex/graphics/keyval.sty))
(/usr/share/texmf/tex/latex/graphics/color.sty
(/usr/share/texmf/tex/latex/latexconfig/color.cfg)
(/usr/share/texmf/tex/latex/pdftex-def/pdftex.def))
(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty)
(/usr/share/texmf/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texmf/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texmf/tex/generic/oberdiek/etexcmds.sty))
(/usr/share/texmf/tex/generic/oberdiek/pdfescape.sty
(/usr/share/texmf/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texmf/tex/generic/oberdiek/ifluatex.sty)))
(/usr/share/texmf/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texmf/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf/tex/latex/oberdiek/hycolor.sty
(/usr/share/texmf/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/share/texmf/tex/latex/oberdiek/letltxmacro.sty)
(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf/tex/generic/oberdiek/intcalc.sty)
(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/share/texmf/tex/generic/oberdiek/bitset.sty
(/usr/share/texmf/tex/generic/oberdiek/bigintcalc.sty))
(/usr/share/texmf/tex/generic/oberdiek/atbegshi.sty))
* hyperref using default driver hpdftex *
(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
(/usr/share/texmf/tex/latex/oberdiek/atveryend.sty)
(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty
(/usr/share/texmf/tex/generic/oberdiek/uniquecounter.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/share/texmf/tex/latex/base/makeidx.sty)
(/usr/share/texmf/tex/latex/base/inputenc.sty
(/usr/share/texmf/tex/latex/base/utf8.def
(/usr/share/texmf/tex/latex/base/t1enc.dfu)
(/usr/share/texmf/tex/latex/base/ot1enc.dfu)
(/usr/share/texmf/tex/latex/base/omsenc.dfu)
(/usr/share/texmf/tex/latex/base/ts1enc.dfu))
(/usr/share/texmf/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/share/texmf/tex/latex/base/ts1cmr.fd)
(/usr/share/texmf/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texmf/tex/latex/hyperref/nameref.sty
(/usr/share/texmf/tex/latex/oberdiek/refcount.sty)
(/usr/share/texmf/tex/generic/oberdiek/gettitlestring.sty)) (./Rd2.out)
(./Rd2.out) (/usr/share/texmf/tex/latex/inconsolata/t1fi4.fd)
Overfull \hbox (27.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <bhaibeka@jimmy.harvard.edu>\T1/ptm/m/n/10
, Markus Schroeder \T1/fi4/m/n/10 <mschroed@jimmy.harvard.edu>\T1/ptm/m/n/10 ,
Catha-
(/usr/share/texmf/tex/latex/psnfss/t1phv.fd) (./Rd2.toc [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]) (/usr/share/texmf/tex/latex/base/utf8.def)
Underfull \vbox (badness 7116) has occurred while \output is active [2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 54--55
[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
Overfull \hbox (7.89719pt too wide) in paragraph at lines 74--75
[]\T1/ptm/m/n/10 - Com-pu-ta-tional Bi-ol-ogy and Func-tional Ge-nomics Lab-o-r
a-tory, Dana-Farber Can-cer In-sti-tute, Boston,
(/usr/share/texmf/tex/latex/base/utf8.def)
(/usr/share/texmf/tex/latex/psnfss/ts1ptm.fd) [3] [4]
(/usr/share/texmf/tex/latex/base/utf8.def) [5]
(/usr/share/texmf/tex/latex/base/utf8.def) [6]
(/usr/share/texmf/tex/latex/base/utf8.def) [7] [8]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 384--385
[]\T1/ptm/m/n/10 The func-tion com-bines sev-eral es-ti-ma-tors us-ing meta-ana
lytical for-mula to com-pute a meta-estimate.
[9] (/usr/share/texmf/tex/latex/base/utf8.def) [10]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (674.78088pt too wide) in paragraph at lines 504--504
[]\T1/fi4/m/n/10 concordance.index(x, surv.time, surv.event, cl, weights, comp
pairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether
", "nam"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
[11]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 520--521
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
[12] (/usr/share/texmf/tex/latex/base/utf8.def) [13]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (299.78088pt too wide) in paragraph at lines 652--652
[]\T1/fi4/m/n/10 D.index(x, surv.time, surv.event, weights, strat, alpha = 0.0
5, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE, ...)[
]
[14] (/usr/share/texmf/tex/latex/base/utf8.def) [15]
(/usr/share/texmf/tex/latex/base/utf8.def) [16] [17]
(/usr/share/texmf/tex/latex/base/utf8.def) [18]
(/usr/share/texmf/tex/latex/base/utf8.def) [19]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 960--961
\T1/ptm/m/n/10 and ran-dom ef-fects meta-analysis for two-sample com-par-isons
and cu-mu-la-tive meta-analyses. Draws
Overfull \hbox (5.28088pt too wide) in paragraph at lines 977--977
[]\T1/fi4/m/n/9 forestplot.surv(labeltext=labeltext, mean=r.mean, lower=r.lowe
r, upper=r.upper, zero=0.5,[]
Overfull \hbox (167.28088pt too wide) in paragraph at lines 978--978
[] \T1/fi4/m/n/9 align=c("l"), graphwidth=unit(2, "inches"), x.ticks=seq(0.
3,0.8,0.1), xlab=paste( "Forestplot Example", myspace, sep=""),[]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 979--979
[] \T1/fi4/m/n/9 col=meta.colors(box="royalblue", line="darkblue", zero="da
rkred"), box.size=bs, clip=c(0.3,0.8))[]
(/usr/share/texmf/tex/latex/base/utf8.def) [20]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (324.78088pt too wide) in paragraph at lines 1044--1044
[]\T1/fi4/m/n/10 hazard.ratio(x, surv.time, surv.event, weights, strat, alpha
= 0.05, method.test = c("logrank", "likelihood.ratio", "wald"), na.rm = FALSE,
...)[]
[21] [22] (/usr/share/texmf/tex/latex/base/utf8.def) [23]
(/usr/share/texmf/tex/latex/base/utf8.def) [24]
(/usr/share/texmf/tex/latex/base/utf8.def) [25] [26]
(/usr/share/texmf/tex/latex/base/utf8.def) [27]
(/usr/share/texmf/tex/latex/base/utf8.def) [28]
(/usr/share/texmf/tex/latex/base/utf8.def) [29]
Overfull \hbox (1034.78088pt too wide) in paragraph at lines 1473--1473
[]\T1/fi4/m/n/10 km.coxph.plot(formula.s, data.s, sub.s = "all", x.label, y.la
bel, main.title, sub.title, leg.text, leg.pos = "bottomright", leg.bty = "o", l
eg.inset = 0.05, o.text, v.line, h.line, .col = 1:4, .lty = 1, .lwd = 1, show.n
.risk = FALSE, n.risk.step, n.risk.cex = 0.85, verbose = TRUE, ...)[]
[30] (/usr/share/texmf/tex/latex/base/utf8.def) [31]
(/usr/share/texmf/tex/latex/base/utf8.def) [32]
(/usr/share/texmf/tex/latex/base/utf8.def) [33]
Overfull \hbox (581.28088pt too wide) in paragraph at lines 1714--1714
[]\T1/fi4/m/n/9 metaplot.surv(mn=c(0.4,0.5,0.6), lower=c(0.35,0.4,0.57), upper
=c(0.45,0.6,0.63), labels=c("A","B","C"), xlim=c(0.2,0.8), boxsize=0.5, zero=0.
5, col=rmeta::meta.colors(box="royalblue",line="darkblue",zero="firebrick"))[]
(/usr/share/texmf/tex/latex/base/utf8.def) [34]
Overfull \hbox (644.78088pt too wide) in paragraph at lines 1728--1728
[]\T1/fi4/m/n/10 mrmr.cindex(x, surv.time, surv.event, cl, weights, comppairs=
10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noether", "na
m"), alternative = c("two.sided", "less", "greater"), na.rm = FALSE)[]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1744--1745
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
[35]
Overfull \hbox (149.28088pt too wide) in paragraph at lines 1786--1786
[]\T1/fi4/m/n/9 mrmr.cindex(x=xx, surv.time=stime, surv.event=sevent, strat=st
rat, weights=weight, method="noether", comppairs=comppairs)[]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (859.78088pt too wide) in paragraph at lines 1800--1800
[]\T1/fi4/m/n/10 mrmr.cindex.ensemble(x, surv.time, surv.event, cl, weights, c
omppairs=10, strat, alpha = 0.05, outx = TRUE, method = c("conservative", "noet
her", "nam"), alternative = c("two.sided", "less", "greater"), maxparents, maxn
sol, nboot = 200, na.rm = FALSE)[]
[36]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1816--1817
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of \T1/fi4/m/n/10 "two.sided"
(/usr/share/texmf/tex/latex/base/utf8.def) [37] [38]
(/usr/share/texmf/tex/latex/base/utf8.def) [39]
(/usr/share/texmf/tex/latex/base/utf8.def) [40]
(/usr/share/texmf/tex/latex/base/utf8.def) [41]
(/usr/share/texmf/tex/latex/base/utf8.def) [42]
(/usr/share/texmf/tex/latex/base/utf8.def) [43] [44]
(/usr/share/texmf/tex/latex/base/utf8.def) [45]
(/usr/share/texmf/tex/latex/base/utf8.def) [46]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2344--2345
[]\T1/ptm/m/n/10 This dataset con-tains a sub-set of the gene ex-pres-sion, an-
no-ta-tions and clin-i-cal data from the TRANS-
Overfull \hbox (3.21828pt too wide) in paragraph at lines 2351--2352
[]\T1/fi4/m/n/10 exprs(transbig7g)\T1/ptm/m/n/10 : Ma-trix con-tain-ing gene ex
-pres-sions as mea-sured by Affymetrix hgu133a
[47] (/usr/share/texmf/tex/latex/base/utf8.def) [48]
(/usr/share/texmf/tex/latex/base/utf8.def) [49]
(/usr/share/texmf/tex/latex/base/utf8.def) [50] [51] (./Rd2.ind [52] [53]
LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font) using `T1/fi4/m/n' instead on input line 172.
[54]) (./Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.jackknife} has been referenced but does not exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survivalROC} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survivalROC.C} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.prodlim} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.plot} has been referenced but does not exist, r
eplaced by a fixed one
pdfTeX warning (dest): name{Rfn.sbrier} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.wilcox.test} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.survfit} has been referenced but does not exist
, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.metaplot} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.meta.colors} has been referenced but does not e
xist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one
pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.normOrder} has been referenced but does not exi
st, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxph.object} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.summary.coxph} has been referenced but does not
exist, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.coxphCPE} has been referenced but does not exis
t, replaced by a fixed one
pdfTeX warning (dest): name{Rfn.phcpe} has been referenced but does not exist,
replaced by a fixed one
pdfTeX warning (dest): name{Rfn.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one
{/usr/share/texmf/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips
/inconsolata/fi4-ec.enc}</usr/share/texmf/fonts/type1/public/inconsolata/Incons
olata.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/sha
re/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texmf/fonts/type
1/urw/helvetic/uhvr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texmf/fonts/type1/urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/
urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (54 pages, 221462 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpX9Oaom/Rbuild77832ea6d61d/survcomp/build/survcomp.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
* 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 ‘survcomp_1.9.2.tar.gz’