Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

Package 570/609HostnameOS / ArchBUILDCHECKBUILD BIN
survcomp 1.8.1
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/survcomp
Last Changed Rev: 70305 / Revision: 74773
Last Changed Date: 2012-10-08 14:22:49 -0700 (Mon, 08 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64 [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: survcomp
Version: 1.8.1
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
StartedAt: 2013-03-24 21:31:49 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 21:32:06 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 17.1 seconds
RetCode: 0
Status:  OK 
PackageFile: survcomp_1.8.1.tar.gz
PackageFileSize: 888.6 KiB

Command output

* 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 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \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, 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, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, 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-2.11-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
(/home/biocbuild/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/generic/oberdiek/infwarerr.sty)
(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.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/generic/oberdiek/gettitlestring.sty))

LaTeX Font Warning: Font shape `T1/fi4/m/n' undefined
(Font)              using `T1/cmr/m/n' instead on input line 22.


Overfull \hbox (36.86043pt 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)
Overfull \hbox (11.31038pt too wide) in paragraph at lines 456--457
[]\T1/fi4/m/n/10 fisher \T1/ptm/m/n/10 for the Fisher's com-bined prob-a-bil-it
y test, \T1/fi4/m/n/10 z.transform \T1/ptm/m/n/10 for the Z-transformed
[9] (/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (544.10706pt 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 (10.1068pt 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 (196.46973pt 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 (107.40839pt 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 (11.21394pt 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 (215.27069pt 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 (764.41437pt 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 (498.82086pt 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 (519.69635pt 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 (10.1068pt 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 (128.48296pt 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 (715.67627pt 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 (10.1068pt 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-
[46] (/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (16.85718pt too wide) in paragraph at lines 2408--2409
[]\T1/fi4/m/n/10 fData(unt7g)\T1/ptm/m/n/10 : An-no-tated-DataFrame con-tain-in
g an-no-ta-tions of Affy mi-croar-ray plat-form hgu133a
[47] (/usr/share/texmf/tex/latex/base/utf8.def) [48] [49]
(/usr/share/texmf/tex/latex/base/utf8.def) [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'.


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/cm-super/cm-super-t1.enc}{/usr/share/texmf/fo
nts/enc/dvips/base/8r.enc}</usr/share/texmf/fonts/type1/public/amsfonts/cm/cmmi
10.pfb></usr/share/texmf/fonts/type1/public/cm-super/sfrm0900.pfb></usr/share/t
exmf/fonts/type1/public/cm-super/sfrm1000.pfb></usr/share/texmf/fonts/type1/urw
/helvetic/uhvr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmb8a.pfb></usr/s
hare/texmf/fonts/type1/urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/urw/t
imes/utmr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (51 pages, 231040 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (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 (207 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \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, 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, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, 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-2.11-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
(/home/biocbuild/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/generic/oberdiek/infwarerr.sty)
(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.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/generic/oberdiek/gettitlestring.sty)) (./Rd2.out)
(./Rd2.out)

LaTeX Font Warning: Font shape `T1/fi4/m/n' undefined
(Font)              using `T1/cmr/m/n' instead on input line 22.


Overfull \hbox (36.86043pt 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)
Overfull \hbox (11.31038pt too wide) in paragraph at lines 456--457
[]\T1/fi4/m/n/10 fisher \T1/ptm/m/n/10 for the Fisher's com-bined prob-a-bil-it
y test, \T1/fi4/m/n/10 z.transform \T1/ptm/m/n/10 for the Z-transformed
[10] (/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (544.10706pt 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 (10.1068pt 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 (196.46973pt 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] [16]
(/usr/share/texmf/tex/latex/base/utf8.def) [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
[20]
Overfull \hbox (107.40839pt 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 (11.21394pt 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) [21]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (215.27069pt 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, 
...)[] 
[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 (764.41437pt 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 (498.82086pt 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 (519.69635pt 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 (10.1068pt 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 (128.48296pt 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 (715.67627pt 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 (10.1068pt 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-
[47] (/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (16.85718pt too wide) in paragraph at lines 2408--2409
[]\T1/fi4/m/n/10 fData(unt7g)\T1/ptm/m/n/10 : An-no-tated-DataFrame con-tain-in
g an-no-ta-tions of Affy mi-croar-ray plat-form hgu133a
[48] (/usr/share/texmf/tex/latex/base/utf8.def) [49] [50]
(/usr/share/texmf/tex/latex/base/utf8.def) [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/cm-super/cm-super-t1.enc}{/usr/share/texmf/fo
nts/enc/dvips/base/8r.enc}</usr/share/texmf/fonts/type1/public/amsfonts/cm/cmmi
10.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/
texmf/fonts/type1/public/cm-super/sfrm0900.pfb></usr/share/texmf/fonts/type1/pu
blic/cm-super/sfrm1000.pfb></usr/share/texmf/fonts/type1/urw/helvetic/uhvr8a.pf
b></usr/share/texmf/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf/fonts/ty
pe1/urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmr8a.pfb></u
sr/share/texmf/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (54 pages, 252982 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (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 (206 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \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, 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, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, 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-2.11-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
(/home/biocbuild/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/generic/oberdiek/infwarerr.sty)
(/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texmf/tex/latex/hyperref/hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texmf/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
(/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.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/generic/oberdiek/gettitlestring.sty)) (./Rd2.out)
(./Rd2.out)

LaTeX Font Warning: Font shape `T1/fi4/m/n' undefined
(Font)              using `T1/cmr/m/n' instead on input line 22.


Overfull \hbox (36.86043pt 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 7030) 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)
Overfull \hbox (11.31038pt too wide) in paragraph at lines 456--457
[]\T1/fi4/m/n/10 fisher \T1/ptm/m/n/10 for the Fisher's com-bined prob-a-bil-it
y test, \T1/fi4/m/n/10 z.transform \T1/ptm/m/n/10 for the Z-transformed
[10] (/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (544.10706pt 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 (10.1068pt 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 (196.46973pt 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] [16]
(/usr/share/texmf/tex/latex/base/utf8.def) [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
[20]
Overfull \hbox (107.40839pt 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 (11.21394pt 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) [21]
(/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (215.27069pt 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, 
...)[] 
[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 (764.41437pt 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 (498.82086pt 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 (519.69635pt 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 (10.1068pt 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 (128.48296pt 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 (715.67627pt 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 (10.1068pt 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-
[47] (/usr/share/texmf/tex/latex/base/utf8.def)
Overfull \hbox (16.85718pt too wide) in paragraph at lines 2408--2409
[]\T1/fi4/m/n/10 fData(unt7g)\T1/ptm/m/n/10 : An-no-tated-DataFrame con-tain-in
g an-no-ta-tions of Affy mi-croar-ray plat-form hgu133a
[48] (/usr/share/texmf/tex/latex/base/utf8.def) [49] [50]
(/usr/share/texmf/tex/latex/base/utf8.def) [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/cm-super/cm-super-t1.enc}{/usr/share/texmf/fo
nts/enc/dvips/base/8r.enc}</usr/share/texmf/fonts/type1/public/amsfonts/cm/cmmi
10.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/
texmf/fonts/type1/public/cm-super/sfrm0900.pfb></usr/share/texmf/fonts/type1/pu
blic/cm-super/sfrm1000.pfb></usr/share/texmf/fonts/type1/urw/helvetic/uhvr8a.pf
b></usr/share/texmf/fonts/type1/urw/times/utmb8a.pfb></usr/share/texmf/fonts/ty
pe1/urw/times/utmr8a.pfb></usr/share/texmf/fonts/type1/urw/times/utmr8a.pfb></u
sr/share/texmf/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (54 pages, 253030 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmplseEJc/Rbuild74877781cf97/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_1.8.1.tar.gz’