Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

BUILD report for survcomp on merida1

This page was generated on 2021-05-06 12:37:02 -0400 (Thu, 06 May 2021).

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 1816/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.40.0  (landing page)
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/survcomp
Branch: RELEASE_3_12
Last Commit: 25b364b
Last Changed Date: 2020-10-27 10:40:57 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
StartedAt: 2021-05-05 22:29:16 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 22:29:48 -0400 (Wed, 05 May 2021)
EllapsedTime: 32.1 seconds
RetCode: 0
Status:   OK  
PackageFile: survcomp_1.40.0.tar.gz
PackageFileSize: 869.7 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/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 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06>
(./Rd2.tex (/usr/local/texlive/2020/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2020/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/local/texlive/2020/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2020/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file Rd2.aux.
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2020/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/usr/local/texlive/2020/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/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1phv.fd

LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 46.

) (/usr/local/texlive/2020/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/te
xlive/2020/texmf-var/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,
[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] [4] (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
[5] [6] [7] [8] [9] [10]
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] [12]
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] [14] [15] [16] [17] [18] [19] [20] [21] [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] [24] [25] [26] [27] [28] [29] [30] [31] [32]
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] [34] [35] [36] [37] [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]
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] [41] [42] [43] [44] [45]
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [46]
[47] [48] [49] [50] [51]
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] [53] [54] [55] [56]
No file Rd2.ind.
[57] (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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/local/texlive/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2020/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
20/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2020/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
020/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2020/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (57 pages, 204686 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06>
(./Rd2.tex (/usr/local/texlive/2020/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2020/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/local/texlive/2020/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2020/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.aux)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2020/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/usr/local/texlive/2020/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/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1phv.fd

LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 46.

) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.toc
[1{/usr/local/texlive/2020/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2020/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,
[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] [5] (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
[6] [7] [8] [9] [10]
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] [12] [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] [15] [16] [17] [18] [19] [20] [21] [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] [24] [25] [26] [27] [28] [29] [30] [31] [32] [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] [35] [36] [37] [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] [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"
[41] [42] [43] [44] [45]
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [46]
[47] [48] [49] [50] [51]
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] [53] [54] [55] [56]
No file Rd2.ind.
[57] (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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/local/texlive/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2020/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
20/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2020/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
020/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2020/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (57 pages, 209096 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2020] (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 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06>
(./Rd2.tex (/usr/local/texlive/2020/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2020/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/local/texlive/2020/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2020/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.aux)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2020/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/usr/local/texlive/2020/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/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1phv.fd

LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 46.

) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.toc
[1{/usr/local/texlive/2020/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2020/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,
[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] [5] (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
[6] [7] [8] [9] [10]
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] [12] [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] [15] [16] [17] [18] [19] [20] [21] [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] [24] [25] [26] [27] [28] [29] [30] [31] [32] [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] [35] [36] [37] [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] [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"
[41] [42] [43] [44] [45]
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [46]
[47] [48] [49] [50] [51]
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] [53] [54] [55] [56]
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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]) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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/local/texlive/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2020/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
20/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2020/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
20/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2020/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (59 pages, 226961 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2020] (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 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06>
(./Rd2.tex (/usr/local/texlive/2020/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2020/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/local/texlive/2020/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2020/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.aux)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2020/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/usr/local/texlive/2020/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/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1phv.fd

LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 46.

) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.toc
[1{/usr/local/texlive/2020/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2020/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,
[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] [5] (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
[6] [7] [8] [9] [10] [11]
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. 
[12] [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] [15] [16] [17] [18] [19] [20] [21] [22] [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
[24] [25] [26] [27] [28] [29] [30] [31] [32] [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] [35] [36] [37] [38] [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]
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] [42] [43] [44] [45] [46]
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [47]
[48] [49] [50] [51] [52]
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] [54] [55] [56] [57]
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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]) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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/local/texlive/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2020/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
20/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2020/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
20/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2020/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (60 pages, 227710 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2020] (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 3.14159265-2.6-1.40.21 (TeX Live 2020) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-03-06>
(./Rd2.tex (/usr/local/texlive/2020/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2020/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2020/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2020/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2020/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2020/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2020/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2020/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty

(/usr/local/texlive/2020/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/local/texlive/2020/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2020/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.aux)
(/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2020/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2020/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2020/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2020/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.out)
(/usr/local/texlive/2020/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/local/texlive/2020/texmf-dist/tex/latex/psnfss/t1phv.fd

LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 20.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 23.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 26.


LaTeX Warning: Font shape declaration has incorrect series value `mc'.
               It should not contain an `m'! Please correct it.
               Found on input line 46.

) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/Rd2.toc
[1{/usr/local/texlive/2020/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2020/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,
[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] [5] (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
[6] [7] [8] [9] [10] [11]
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. 
[12] [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] [15] [16] [17] [18] [19] [20] [21] [22] [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
[24] [25] [26] [27] [28] [29] [30] [31] [32] [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] [35] [36] [37] [38] [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]
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] [42] [43] [44] [45] [46]
(/usr/local/texlive/2020/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [47]
[48] [49] [50] [51] [52]
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] [54] [55] [56] [57]
(/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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]) (/private/tmp/RtmpmhALnU/Rbuild7868619f291/survcomp/.Rd2pdf30824/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/local/texlive/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2020/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2020/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
20/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2020/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2020/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
20/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2020/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2020/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (60 pages, 227772 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpmhALnU/Rbuild7868619f291/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_1.40.0.tar.gz’