Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

BUILD report for survcomp on malbec2

This page was generated on 2020-10-17 11:55:53 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE survcomp PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1760/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.38.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/survcomp
Branch: RELEASE_3_11
Last Commit: 79d64c7
Last Changed Date: 2020-04-27 14:25:04 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ OK ] WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.38.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
StartedAt: 2020-10-16 22:06:23 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:06:43 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 20.2 seconds
RetCode: 0
Status:  OK 
PackageFile: survcomp_1.38.0.tar.gz
PackageFileSize: 853.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
###
##############################################################################
##############################################################################


* 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 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (77.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>\T1/ptm
/m/n/10 , Catha- 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 65--66
[]\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/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (23.47868pt too wide) in paragraph at lines 146--147
[]\T1/ptm/m/n/10 list of data used to com-pute the bal-anced haz-ard ra-tio (\T
1/zi4/m/n/10 x\T1/ptm/m/n/10 , \T1/zi4/m/n/10 surv.time \T1/ptm/m/n/10 and \T1/
zi4/m/n/10 surv.event\T1/ptm/m/n/10 ). 
[3] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9] [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 526--527
[]\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. 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [11] [12]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (14.50804pt too wide) in paragraph at lines 664--665
[]\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/zi4/m/n/10 "two.sided"
[13] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16] [17]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20] [21]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1138--1139
\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
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [31] [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1678--1678
 []\T1/zi4/m/n/10 km.coxph.plot(formula.s, data.s, weight.s, x.label, y.label, 
main.title, sub.title,[] 

Overfull \hbox (1.41006pt too wide) in paragraph at lines 1679--1679
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[33] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [34] [35]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1960--1961
[]\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/zi4/m/n/10 "two.sided"
[39] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2036--2037
[]\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/zi4/m/n/10 "two.sided"
[40] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42] [43]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [48] [49]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2622--2623
[]\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 2629--2630
[]\T1/zi4/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
[52] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [53]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [54]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55] [56]
No file Rd2.ind.
[57] (/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/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.normOrder} has been referenced but does not exi
st, 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.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

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 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.coxph} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/time
s/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (57 pages, 209539 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (77.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>\T1/ptm
/m/n/10 , Catha- 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \vbox (5.64125pt too high) has occurred while \output is active
[2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 65--66
[]\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/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
Overfull \hbox (23.47868pt too wide) in paragraph at lines 146--147
[]\T1/ptm/m/n/10 list of data used to com-pute the bal-anced haz-ard ra-tio (\T
1/zi4/m/n/10 x\T1/ptm/m/n/10 , \T1/zi4/m/n/10 surv.time \T1/ptm/m/n/10 and \T1/
zi4/m/n/10 surv.event\T1/ptm/m/n/10 ). 
[4] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 526--527
[]\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. 
[11] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 664--665
[]\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/zi4/m/n/10 "two.sided"
[14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1138--1139
\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
[23] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29] [30]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [33]
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1678--1678
 []\T1/zi4/m/n/10 km.coxph.plot(formula.s, data.s, weight.s, x.label, y.label, 
main.title, sub.title,[] 

Overfull \hbox (1.41006pt too wide) in paragraph at lines 1679--1679
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1960--1961
[]\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/zi4/m/n/10 "two.sided"
[39] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [40]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2036--2037
[]\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/zi4/m/n/10 "two.sided"
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [43]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [47] [48]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2622--2623
[]\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 2629--2630
[]\T1/zi4/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
[52] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [53] [54]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [56]
No file Rd2.ind.
[57] (/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.aux) )
(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.normOrder} has been referenced but does not exi
st, 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.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

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 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.coxph} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/time
s/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (57 pages, 213993 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (191 entries accepted, 0 rejected).
Sorting entries.....done (1595 comparisons).
Generating output file Rd2.ind....done (229 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (77.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>\T1/ptm
/m/n/10 , Catha- 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \vbox (5.64125pt too high) has occurred while \output is active
[2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 65--66
[]\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/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
Overfull \hbox (23.47868pt too wide) in paragraph at lines 146--147
[]\T1/ptm/m/n/10 list of data used to com-pute the bal-anced haz-ard ra-tio (\T
1/zi4/m/n/10 x\T1/ptm/m/n/10 , \T1/zi4/m/n/10 surv.time \T1/ptm/m/n/10 and \T1/
zi4/m/n/10 surv.event\T1/ptm/m/n/10 ). 
[4] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 526--527
[]\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. 
[11] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [13]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 664--665
[]\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/zi4/m/n/10 "two.sided"
[14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [22]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1138--1139
\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
[23] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [28]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [29] [30]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [33]
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1678--1678
 []\T1/zi4/m/n/10 km.coxph.plot(formula.s, data.s, weight.s, x.label, y.label, 
main.title, sub.title,[] 

Overfull \hbox (1.41006pt too wide) in paragraph at lines 1679--1679
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1960--1961
[]\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/zi4/m/n/10 "two.sided"
[39] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [40]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2036--2037
[]\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/zi4/m/n/10 "two.sided"
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [43]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [47] [48]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2622--2623
[]\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 2629--2630
[]\T1/zi4/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
[52] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [53] [54]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [56]
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.ind [57] [58]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 194.

[59]) (/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/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.normOrder} has been referenced but does not exi
st, 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.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

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 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.coxph} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (59 pages, 231860 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (191 entries accepted, 0 rejected).
Sorting entries.....done (1595 comparisons).
Generating output file Rd2.ind....done (229 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (77.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>\T1/ptm
/m/n/10 , Catha- 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 65--66
[]\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/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
Overfull \hbox (23.47868pt too wide) in paragraph at lines 146--147
[]\T1/ptm/m/n/10 list of data used to com-pute the bal-anced haz-ard ra-tio (\T
1/zi4/m/n/10 x\T1/ptm/m/n/10 , \T1/zi4/m/n/10 surv.time \T1/ptm/m/n/10 and \T1/
zi4/m/n/10 surv.event\T1/ptm/m/n/10 ). 
[4] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10] [11]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 526--527
[]\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. 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [12] [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (14.50804pt too wide) in paragraph at lines 664--665
[]\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/zi4/m/n/10 "two.sided"
[14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21] [22]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1138--1139
\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
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32] [33]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1678--1678
 []\T1/zi4/m/n/10 km.coxph.plot(formula.s, data.s, weight.s, x.label, y.label, 
main.title, sub.title,[] 

Overfull \hbox (1.41006pt too wide) in paragraph at lines 1679--1679
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [35] [36]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1960--1961
[]\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/zi4/m/n/10 "two.sided"
[40] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2036--2037
[]\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/zi4/m/n/10 "two.sided"
[41] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [43] [44]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [52]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2622--2623
[]\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 2629--2630
[]\T1/zi4/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
[53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [54]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [56] [57]
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.ind [58] [59]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 194.

[60]) (/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/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.normOrder} has been referenced but does not exi
st, 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.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

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 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.coxph} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (60 pages, 232608 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (191 entries accepted, 0 rejected).
Sorting entries.....done (1595 comparisons).
Generating output file Rd2.ind....done (231 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
LaTeX2e <2017-04-15>
Babel <3.18> and hyphenation patterns for 33 language(s) loaded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.11-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/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 377.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 377.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
Overfull \hbox (77.29225pt too wide) in paragraph at lines 22--23
\T1/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>\T1/ptm
/m/n/10 , Catha- 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.toc [1{/var/lib/tex
mf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 65--66
[]\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/texlive/texmf-dist/tex/latex/base/utf8.def) [3]
Overfull \hbox (23.47868pt too wide) in paragraph at lines 146--147
[]\T1/ptm/m/n/10 list of data used to com-pute the bal-anced haz-ard ra-tio (\T
1/zi4/m/n/10 x\T1/ptm/m/n/10 , \T1/zi4/m/n/10 surv.time \T1/ptm/m/n/10 and \T1/
zi4/m/n/10 surv.event\T1/ptm/m/n/10 ). 
[4] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [10] [11]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.15596pt too wide) in paragraph at lines 526--527
[]\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. 
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [12] [13]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (14.50804pt too wide) in paragraph at lines 664--665
[]\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/zi4/m/n/10 "two.sided"
[14] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [21] [22]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [23]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1138--1139
\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
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [32] [33]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1678--1678
 []\T1/zi4/m/n/10 km.coxph.plot(formula.s, data.s, weight.s, x.label, y.label, 
main.title, sub.title,[] 

Overfull \hbox (1.41006pt too wide) in paragraph at lines 1679--1679
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[34] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [35] [36]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1960--1961
[]\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/zi4/m/n/10 "two.sided"
[40] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2036--2037
[]\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/zi4/m/n/10 "two.sided"
[41] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [42]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [43] [44]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [52]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2622--2623
[]\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 2629--2630
[]\T1/zi4/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
[53] (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [54]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [56] [57]
(/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/Rd2.ind [58] [59]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 196.

[60]) (/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/.Rd2pdf3037/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.normOrder} has been referenced but does not exi
st, 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.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

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 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.coxph} has been referenced but does not exist, 
replaced by a fixed one

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/
type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/ty
pe1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (60 pages, 232642 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/Rtmp4uJhqk/Rbuildbdd1bdfe8a5/survcomp/build/survcomp.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘survcomp_1.38.0.tar.gz’