##############################################################################
##############################################################################
###
### 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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2016/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/2016/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2016/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,
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] [6]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9] [10]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [11] [12]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [16] [17]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [20] [21]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [23]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [29]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [31] [32]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.78088pt 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 (8.78088pt 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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [34] [35]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2016/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/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [42] [43]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [48] [49]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [53]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [54]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [55] [56]
No file Rd2.ind.
[57] (./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/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2016/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
16/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2016/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
016/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (57 pages, 209638 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2016] (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 (230 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2016/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/2016/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2016/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/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [12]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [21]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [28]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [29] [30]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [33]
Overfull \hbox (13.78088pt 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 (8.78088pt 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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2016/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/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [42]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [43]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [47] [48]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [49]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [53] [54]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [56] (./Rd2.ind
[57] [58]
LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font) using `T1/zi4/m/n' instead on input line 195.
[59]) (./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/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2016/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
16/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2016/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
16/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (59 pages, 231999 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2016] (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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2016/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/2016/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2016/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/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [10] [11]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [12] [13]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [21] [22]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [32] [33]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.78088pt 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 (8.78088pt 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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [35] [36]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/local/texlive/2016/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/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [42]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [43] [44]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [52]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [54]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [56] [57]
(./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]) (./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/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2016/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
16/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2016/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
16/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (60 pages, 232729 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2016] (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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2016/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/2016/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2016/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/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [8]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [10] [11]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [12] [13]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [16]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [21] [22]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [32] [33]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.78088pt 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 (8.78088pt 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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [35] [36]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/local/texlive/2016/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/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [42]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [43] [44]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [52]
(/usr/local/texlive/2016/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/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [54]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [56] [57]
(./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]) (./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/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2016/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
16/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/tex
live/2016/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
16/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (60 pages, 232762 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpTEBT2I/Rbuild14fc0108d34bf/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_1.30.0.tar.gz’
