Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-04-13 12:06:01 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for survcomp on nebbiolo2


To the developers/maintainers of the survcomp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/survcomp.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1906/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.44.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/survcomp
git_branch: RELEASE_3_14
git_last_commit: 5d966f3
git_last_commit_date: 2021-12-14 16:40:13 -0400 (Tue, 14 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: survcomp
Version: 1.44.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
StartedAt: 2022-04-12 06:03:35 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:03:52 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 17.9 seconds
RetCode: 0
Status:   OK  
PackageFile: survcomp_1.44.1.tar.gz
PackageFileSize: 848.5 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data survcomp
###
##############################################################################
##############################################################################


* checking for file ‘survcomp/DESCRIPTION’ ... OK
* preparing ‘survcomp’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX ....
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/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 378.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 378.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 64--65
[]\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 145--146
[]\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] [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6]
[7] [8] [9] [10]
Overfull \hbox (2.15596pt too wide) in paragraph at lines 525--526
[]\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 663--664
[]\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] [24]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1137--1138
\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
[25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35]
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1677--1677
 []\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 1678--1678
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[36] [37] [38] [39] [40] [41]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1959--1960
[]\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"
[42] [43]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2035--2036
[]\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"
[44] [45] [46] [47] [48] [49]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [50] [51]
[52] [53] [54] [55] [56]
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2621--2622
[]\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 2628--2629
[]\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
[57] [58] [59] [60] [61]
No file Rd2.ind.
[62] (/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/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.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one

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

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

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

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc} </home/biocbuild/.texlive2019/texmf-
var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/f
onts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw
/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.p
fb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/
texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (62 pages, 206706 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/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 378.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 378.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.toc [1{/var/l
ib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 64--65
[]\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 145--146
[]\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] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7]
[8] [9] [10] [11]
Overfull \hbox (2.15596pt too wide) in paragraph at lines 525--526
[]\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] [14]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 663--664
[]\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"
[15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1137--1138
\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
[26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1677--1677
 []\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 1678--1678
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[37] [38] [39] [40] [41] [42]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1959--1960
[]\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"
[43] [44]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2035--2036
[]\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"
[45] [46] [47] [48] [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [51] [52]
[53] [54] [55] [56] [57]
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2621--2622
[]\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 2628--2629
[]\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
[58] [59] [60] [61] [62]
No file Rd2.ind.
[63] (/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/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.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one

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

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

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

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc} </home/biocbuild/.texlive2019/texmf-
var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/f
onts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw
/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.p
fb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/
texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (63 pages, 211797 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (188 entries accepted, 0 rejected).
Sorting entries....done (1441 comparisons).
Generating output file Rd2.ind....done (227 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/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 378.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 378.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.toc [1{/var/l
ib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 64--65
[]\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 145--146
[]\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] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7]
[8] [9] [10] [11]
Overfull \hbox (2.15596pt too wide) in paragraph at lines 525--526
[]\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] [14]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 663--664
[]\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"
[15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1137--1138
\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
[26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1677--1677
 []\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 1678--1678
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[37] [38] [39] [40] [41] [42]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1959--1960
[]\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"
[43] [44]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2035--2036
[]\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"
[45] [46] [47] [48] [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [51] [52]
[53] [54] [55] [56] [57]
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2621--2622
[]\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 2628--2629
[]\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
[58] [59] [60] [61] [62]
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.ind [63]
[64]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 192.

[65]) (/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/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.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one

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

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

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

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc} </home/biocbuild/.texlive2019/texmf-
var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/f
onts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times
/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (65 pages, 229334 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (188 entries accepted, 0 rejected).
Sorting entries....done (1441 comparisons).
Generating output file Rd2.ind....done (227 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/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 378.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 378.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.toc [1{/var/l
ib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 64--65
[]\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 145--146
[]\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] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7]
[8] [9] [10] [11]
Overfull \hbox (2.15596pt too wide) in paragraph at lines 525--526
[]\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] [14]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 663--664
[]\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"
[15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1137--1138
\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
[26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1677--1677
 []\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 1678--1678
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[37] [38] [39] [40] [41] [42]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1959--1960
[]\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"
[43] [44]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2035--2036
[]\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"
[45] [46] [47] [48] [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [51] [52]
[53] [54] [55] [56] [57]
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2621--2622
[]\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 2628--2629
[]\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
[58] [59] [60] [61] [62]
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.ind [63]
[64]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 192.

[65]) (/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/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.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one

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

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

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

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc} </home/biocbuild/.texlive2019/texmf-
var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/f
onts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times
/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (65 pages, 229409 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (188 entries accepted, 0 rejected).
Sorting entries....done (1441 comparisons).
Generating output file Rd2.ind....done (227 lines written, 0 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 2
L3 programming layer <2020-02-14>
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/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 378.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 378.

) (/usr/share/texlive/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.toc [1{/var/l
ib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (7.89719pt too wide) in paragraph at lines 64--65
[]\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 145--146
[]\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] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [7]
[8] [9] [10] [11]
Overfull \hbox (2.15596pt too wide) in paragraph at lines 525--526
[]\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] [14]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 663--664
[]\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"
[15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25]
Overfull \hbox (3.50652pt too wide) in paragraph at lines 1137--1138
\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
[26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
Overfull \hbox (9.76044pt too wide) in paragraph at lines 1677--1677
 []\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 1678--1678
 []\T1/zi4/m/n/10 leg.text, leg.pos = "bottomright", leg.bty = "o", leg.inset =
 0.05, o.text, v.line,[] 
[37] [38] [39] [40] [41] [42]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 1959--1960
[]\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"
[43] [44]
Overfull \hbox (14.50804pt too wide) in paragraph at lines 2035--2036
[]\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"
[45] [46] [47] [48] [49] [50]
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [51] [52]
[53] [54] [55] [56] [57]
Overfull \hbox (0.68686pt too wide) in paragraph at lines 2621--2622
[]\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 2628--2629
[]\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
[58] [59] [60] [61] [62]
(/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/Rd2.ind [63]
[64]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 192.

[65]) (/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/survcomp/.Rd2pdf1880647/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.rcorr.cens} has been referenced but does not ex
ist, replaced by a fixed one

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

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

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

{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/sha
re/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dis
t/fonts/enc/dvips/inconsolata/i4-t1-0.enc} </home/biocbuild/.texlive2019/texmf-
var/fonts/pk/ljfour/jknappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/f
onts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/share/texlive/texmf-di
st/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times
/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texliv
e/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (65 pages, 229409 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpmqUicS/Rbuild1cb247568eb90f/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_1.44.1.tar.gz’