Back to Build/check report for BioC 3.14 experimental data
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-04-13 14:50:22 -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
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 curatedBladderData on nebbiolo2


To the developers/maintainers of the curatedBladderData package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 80/408HostnameOS / ArchINSTALLBUILDCHECK
curatedBladderData 1.30.0  (landing page)
Markus Riester
Snapshot Date: 2022-04-13 07:30:01 -0400 (Wed, 13 Apr 2022)
git_url: https://git.bioconductor.org/packages/curatedBladderData
git_branch: RELEASE_3_14
git_last_commit: 052fd77
git_last_commit_date: 2021-10-26 12:04:43 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: curatedBladderData
Version: 1.30.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data curatedBladderData
StartedAt: 2022-04-13 10:17:01 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 10:17:28 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 26.3 seconds
RetCode: 0
Status:   OK  
PackageFile: curatedBladderData_1.30.0.tar.gz
PackageFileSize: 74.92 MiB

Command output

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


* checking for file ‘curatedBladderData/DESCRIPTION’ ... OK
* preparing ‘curatedBladderData’:
* checking DESCRIPTION meta-information ... OK
* 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}] [2]
Overfull \hbox (494.67865pt too wide) in paragraph at lines 93--93
 []  \T1/zi4/m/n/10 Experimenter name: Kim WJ, Kim EJ, Kim SK, Kim YJ et al. Pr
edictive value of progression-related gene classifier in primary non-muscle inv
asive bladder cancer. Mol Cancer 2010 Jan 8;9:3.[] 

Overfull \hbox (136.39984pt too wide) in paragraph at lines 96--96
 []  \T1/zi4/m/n/10 Title: Predictive value of progression-related gene classif
ier in primary non-muscle invasive bladder cancer.[] 
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
[5]
Overfull \hbox (799.64798pt too wide) in paragraph at lines 216--216
 []  \T1/zi4/m/n/10 Experimenter name: Blaveri E, Simko JP, Korkola JE, Brewer 
JL, Baehner F, Mehta K, Devries S, Koppie T, Pejavar S, Carroll P, Waldman FM. 
Bladder cancer outcome and subtype classification by gene expression.Clin Cance
r Res. 2005 Jun 1;11(11):4044-55.[] 
[6] [7] [8]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 346--346
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 349--349
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 

Underfull \vbox (badness 1881) has occurred while \output is active [9]
[10]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 449--449
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 452--452
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 
[11] [12] [13]
Overfull \hbox (534.67865pt too wide) in paragraph at lines 552--552
 []  \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
ancer Epidemiol Biomarkers Prev 2012 Dec;21(12):2149-58.[] 
[14]
Overfull \hbox (784.64798pt too wide) in paragraph at lines 632--632
 []  \T1/zi4/m/n/10 Experimenter name: Riester M, Taylor JM, Feifer A, Koppie T
 et al. Combination of a novel gene expression signature with a clinical nomogr
am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
 Res 2012 Mar 1;18(5):1323-33.[] 
[15]
Overfull \hbox (303.03925pt too wide) in paragraph at lines 635--635
 []  \T1/zi4/m/n/10 Title: Combination of a novel gene expression signature wit
h a clinical nomogram improves the prediction of survival in high-risk bladder 
cancer.[] 
[16]
Underfull \vbox (badness 10000) has occurred while \output is active [17]
[18]
Overfull \hbox (353.02902pt too wide) in paragraph at lines 794--794
 []  \T1/zi4/m/n/10 Experimenter name: Sj?dahl G, Lauss M, L?vgren K, Chebil G 
et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res 2012 Jun 
15;18(12):3377-86.[] 
[19] [20] [21]
Overfull \hbox (691.3385pt too wide) in paragraph at lines 913--913
 []  \T1/zi4/m/n/10 Experimenter name: Smith SC, Baras AS, Owens CR, Dancik G e
t al. Transcriptional signatures of Ral GTPase are associated with aggressive c
linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[] 

Overfull \hbox (233.0597pt too wide) in paragraph at lines 916--916
 []  \T1/zi4/m/n/10 Title: Transcriptional signatures of Ral GTPase are associa
ted with aggressive clinicopathologic characteristics in human cancer.[] 
[22]
Underfull \hbox (badness 1092) in paragraph at lines 987--987
[] \T1/ptm/m/it/10 Emm-prin and sur-vivin pre-dict re-sponse and sur-vival fol-
low-ing
[23]
Overfull \hbox (819.64798pt too wide) in paragraph at lines 1005--1005
 []  \T1/zi4/m/n/10 Experimenter name: Als AB, Dyrskj?t L, von der Maase H, Koe
d K et al. Emmprin and survivin predict response and survival following cisplat
in-containing chemotherapy in patients with advanced bladder cancer. Clin Cance
r Res 2007 Aug 1;13(15 Pt 1):4407-14.[] 

Overfull \hbox (299.71954pt too wide) in paragraph at lines 1008--1008
 []  \T1/zi4/m/n/10 Title: Emmprin and survivin predict response and survival f
ollowing cisplatin-containing chemotherapy in patients with advanced bladder ca
ncer.[] 
[24] [25]
Overfull \hbox (433.02902pt too wide) in paragraph at lines 1119--1119
 []  \T1/zi4/m/n/10 Experimenter name: Dyrskj?t L, Thykjaer T, Kruh?ffer M, Jen
sen JL et al. Identifying distinct classes of bladder carcinoma using microarra
ys. Nat Genet 2003 Jan;33(1):90-6.[] 
[26] [27]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1207--1207
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[28] [29] [30]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1315--1315
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[31]
No file Rd2.ind.
[32]
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/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){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (32 pages, 129446 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/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/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/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.out
)
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.out
) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (494.67865pt too wide) in paragraph at lines 93--93
 []  \T1/zi4/m/n/10 Experimenter name: Kim WJ, Kim EJ, Kim SK, Kim YJ et al. Pr
edictive value of progression-related gene classifier in primary non-muscle inv
asive bladder cancer. Mol Cancer 2010 Jan 8;9:3.[] 

Overfull \hbox (136.39984pt too wide) in paragraph at lines 96--96
 []  \T1/zi4/m/n/10 Title: Predictive value of progression-related gene classif
ier in primary non-muscle invasive bladder cancer.[] 
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
[5]
Overfull \hbox (799.64798pt too wide) in paragraph at lines 216--216
 []  \T1/zi4/m/n/10 Experimenter name: Blaveri E, Simko JP, Korkola JE, Brewer 
JL, Baehner F, Mehta K, Devries S, Koppie T, Pejavar S, Carroll P, Waldman FM. 
Bladder cancer outcome and subtype classification by gene expression.Clin Cance
r Res. 2005 Jun 1;11(11):4044-55.[] 
[6] [7] [8]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 346--346
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 349--349
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 
[9] [10]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 449--449
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 452--452
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 
[11] [12] [13]
Overfull \hbox (534.67865pt too wide) in paragraph at lines 552--552
 []  \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
ancer Epidemiol Biomarkers Prev 2012 Dec;21(12):2149-58.[] 
[14] [15]
Overfull \hbox (784.64798pt too wide) in paragraph at lines 632--632
 []  \T1/zi4/m/n/10 Experimenter name: Riester M, Taylor JM, Feifer A, Koppie T
 et al. Combination of a novel gene expression signature with a clinical nomogr
am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
 Res 2012 Mar 1;18(5):1323-33.[] 

Overfull \hbox (303.03925pt too wide) in paragraph at lines 635--635
 []  \T1/zi4/m/n/10 Title: Combination of a novel gene expression signature wit
h a clinical nomogram improves the prediction of survival in high-risk bladder 
cancer.[] 
[16]
Underfull \vbox (badness 10000) has occurred while \output is active [17]
[18]
Overfull \hbox (353.02902pt too wide) in paragraph at lines 794--794
 []  \T1/zi4/m/n/10 Experimenter name: Sj?dahl G, Lauss M, L?vgren K, Chebil G 
et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res 2012 Jun 
15;18(12):3377-86.[] 
[19] [20] [21]
Overfull \hbox (691.3385pt too wide) in paragraph at lines 913--913
 []  \T1/zi4/m/n/10 Experimenter name: Smith SC, Baras AS, Owens CR, Dancik G e
t al. Transcriptional signatures of Ral GTPase are associated with aggressive c
linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[] 

Overfull \hbox (233.0597pt too wide) in paragraph at lines 916--916
 []  \T1/zi4/m/n/10 Title: Transcriptional signatures of Ral GTPase are associa
ted with aggressive clinicopathologic characteristics in human cancer.[] 
[22]
Underfull \hbox (badness 1092) in paragraph at lines 987--987
[] \T1/ptm/m/it/10 Emm-prin and sur-vivin pre-dict re-sponse and sur-vival fol-
low-ing
[23]
Overfull \hbox (819.64798pt too wide) in paragraph at lines 1005--1005
 []  \T1/zi4/m/n/10 Experimenter name: Als AB, Dyrskj?t L, von der Maase H, Koe
d K et al. Emmprin and survivin predict response and survival following cisplat
in-containing chemotherapy in patients with advanced bladder cancer. Clin Cance
r Res 2007 Aug 1;13(15 Pt 1):4407-14.[] 

Overfull \hbox (299.71954pt too wide) in paragraph at lines 1008--1008
 []  \T1/zi4/m/n/10 Title: Emmprin and survivin predict response and survival f
ollowing cisplatin-containing chemotherapy in patients with advanced bladder ca
ncer.[] 
[24] [25] [26]
Overfull \hbox (433.02902pt too wide) in paragraph at lines 1119--1119
 []  \T1/zi4/m/n/10 Experimenter name: Dyrskj?t L, Thykjaer T, Kruh?ffer M, Jen
sen JL et al. Identifying distinct classes of bladder carcinoma using microarra
ys. Nat Genet 2003 Jan;33(1):90-6.[] 
[27]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1207--1207
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[28] [29] [30]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1315--1315
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[31] [32]
No file Rd2.ind.
[33]
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.aux
) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr
8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (33 pages, 133418 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (38 entries accepted, 0 rejected).
Sorting entries....done (207 comparisons).
Generating output file Rd2.ind....done (68 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/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/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/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.out
)
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.out
) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (494.67865pt too wide) in paragraph at lines 93--93
 []  \T1/zi4/m/n/10 Experimenter name: Kim WJ, Kim EJ, Kim SK, Kim YJ et al. Pr
edictive value of progression-related gene classifier in primary non-muscle inv
asive bladder cancer. Mol Cancer 2010 Jan 8;9:3.[] 

Overfull \hbox (136.39984pt too wide) in paragraph at lines 96--96
 []  \T1/zi4/m/n/10 Title: Predictive value of progression-related gene classif
ier in primary non-muscle invasive bladder cancer.[] 
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
[5]
Overfull \hbox (799.64798pt too wide) in paragraph at lines 216--216
 []  \T1/zi4/m/n/10 Experimenter name: Blaveri E, Simko JP, Korkola JE, Brewer 
JL, Baehner F, Mehta K, Devries S, Koppie T, Pejavar S, Carroll P, Waldman FM. 
Bladder cancer outcome and subtype classification by gene expression.Clin Cance
r Res. 2005 Jun 1;11(11):4044-55.[] 
[6] [7] [8]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 346--346
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 349--349
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 
[9] [10]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 449--449
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 452--452
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 
[11] [12] [13]
Overfull \hbox (534.67865pt too wide) in paragraph at lines 552--552
 []  \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
ancer Epidemiol Biomarkers Prev 2012 Dec;21(12):2149-58.[] 
[14] [15]
Overfull \hbox (784.64798pt too wide) in paragraph at lines 632--632
 []  \T1/zi4/m/n/10 Experimenter name: Riester M, Taylor JM, Feifer A, Koppie T
 et al. Combination of a novel gene expression signature with a clinical nomogr
am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
 Res 2012 Mar 1;18(5):1323-33.[] 

Overfull \hbox (303.03925pt too wide) in paragraph at lines 635--635
 []  \T1/zi4/m/n/10 Title: Combination of a novel gene expression signature wit
h a clinical nomogram improves the prediction of survival in high-risk bladder 
cancer.[] 
[16]
Underfull \vbox (badness 10000) has occurred while \output is active [17]
[18]
Overfull \hbox (353.02902pt too wide) in paragraph at lines 794--794
 []  \T1/zi4/m/n/10 Experimenter name: Sj?dahl G, Lauss M, L?vgren K, Chebil G 
et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res 2012 Jun 
15;18(12):3377-86.[] 
[19] [20] [21]
Overfull \hbox (691.3385pt too wide) in paragraph at lines 913--913
 []  \T1/zi4/m/n/10 Experimenter name: Smith SC, Baras AS, Owens CR, Dancik G e
t al. Transcriptional signatures of Ral GTPase are associated with aggressive c
linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[] 

Overfull \hbox (233.0597pt too wide) in paragraph at lines 916--916
 []  \T1/zi4/m/n/10 Title: Transcriptional signatures of Ral GTPase are associa
ted with aggressive clinicopathologic characteristics in human cancer.[] 
[22]
Underfull \hbox (badness 1092) in paragraph at lines 987--987
[] \T1/ptm/m/it/10 Emm-prin and sur-vivin pre-dict re-sponse and sur-vival fol-
low-ing
[23]
Overfull \hbox (819.64798pt too wide) in paragraph at lines 1005--1005
 []  \T1/zi4/m/n/10 Experimenter name: Als AB, Dyrskj?t L, von der Maase H, Koe
d K et al. Emmprin and survivin predict response and survival following cisplat
in-containing chemotherapy in patients with advanced bladder cancer. Clin Cance
r Res 2007 Aug 1;13(15 Pt 1):4407-14.[] 

Overfull \hbox (299.71954pt too wide) in paragraph at lines 1008--1008
 []  \T1/zi4/m/n/10 Title: Emmprin and survivin predict response and survival f
ollowing cisplatin-containing chemotherapy in patients with advanced bladder ca
ncer.[] 
[24] [25] [26]
Overfull \hbox (433.02902pt too wide) in paragraph at lines 1119--1119
 []  \T1/zi4/m/n/10 Experimenter name: Dyrskj?t L, Thykjaer T, Kruh?ffer M, Jen
sen JL et al. Identifying distinct classes of bladder carcinoma using microarra
ys. Nat Genet 2003 Jan;33(1):90-6.[] 
[27]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1207--1207
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[28] [29] [30]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1315--1315
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[31] [32]
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.ind
[33]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 19.

[34])
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/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){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (34 pages, 143076 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (38 entries accepted, 0 rejected).
Sorting entries....done (207 comparisons).
Generating output file Rd2.ind....done (68 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/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/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/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.out
)
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.out
) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.toc
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (494.67865pt too wide) in paragraph at lines 93--93
 []  \T1/zi4/m/n/10 Experimenter name: Kim WJ, Kim EJ, Kim SK, Kim YJ et al. Pr
edictive value of progression-related gene classifier in primary non-muscle inv
asive bladder cancer. Mol Cancer 2010 Jan 8;9:3.[] 

Overfull \hbox (136.39984pt too wide) in paragraph at lines 96--96
 []  \T1/zi4/m/n/10 Title: Predictive value of progression-related gene classif
ier in primary non-muscle invasive bladder cancer.[] 
(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [3] [4]
[5]
Overfull \hbox (799.64798pt too wide) in paragraph at lines 216--216
 []  \T1/zi4/m/n/10 Experimenter name: Blaveri E, Simko JP, Korkola JE, Brewer 
JL, Baehner F, Mehta K, Devries S, Koppie T, Pejavar S, Carroll P, Waldman FM. 
Bladder cancer outcome and subtype classification by gene expression.Clin Cance
r Res. 2005 Jun 1;11(11):4044-55.[] 
[6] [7] [8]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 346--346
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 349--349
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 
[9] [10]
Overfull \hbox (922.9779pt too wide) in paragraph at lines 449--449
 []  \T1/zi4/m/n/10 Experimenter name: Lindgren D, Frigyesi A, Gudjonsson S, Sj
?dahl G et al. Combined gene expression and genomic profiling define two intrin
sic molecular subtypes of urothelial carcinoma and gene signatures for molecula
r grading and outcome. Cancer Res 2010 May 1;70(9):3463-72[] 

Overfull \hbox (434.6991pt too wide) in paragraph at lines 452--452
 []  \T1/zi4/m/n/10 Title: Combined gene expression and genomic profiling defin
e two intrinsic molecular subtypes of urothelial carcinoma and gene signatures 
for molecular grading and outcome.[] 
[11] [12] [13]
Overfull \hbox (534.67865pt too wide) in paragraph at lines 552--552
 []  \T1/zi4/m/n/10 Experimenter name: Urquidi V, Goodison S, Cai Y, Sun Y et a
l. A candidate molecular biomarker panel for the detection of bladder cancer. C
ancer Epidemiol Biomarkers Prev 2012 Dec;21(12):2149-58.[] 
[14] [15]
Overfull \hbox (784.64798pt too wide) in paragraph at lines 632--632
 []  \T1/zi4/m/n/10 Experimenter name: Riester M, Taylor JM, Feifer A, Koppie T
 et al. Combination of a novel gene expression signature with a clinical nomogr
am improves the prediction of survival in high-risk bladder cancer. Clin Cancer
 Res 2012 Mar 1;18(5):1323-33.[] 

Overfull \hbox (303.03925pt too wide) in paragraph at lines 635--635
 []  \T1/zi4/m/n/10 Title: Combination of a novel gene expression signature wit
h a clinical nomogram improves the prediction of survival in high-risk bladder 
cancer.[] 
[16]
Underfull \vbox (badness 10000) has occurred while \output is active [17]
[18]
Overfull \hbox (353.02902pt too wide) in paragraph at lines 794--794
 []  \T1/zi4/m/n/10 Experimenter name: Sj?dahl G, Lauss M, L?vgren K, Chebil G 
et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res 2012 Jun 
15;18(12):3377-86.[] 
[19] [20] [21]
Overfull \hbox (691.3385pt too wide) in paragraph at lines 913--913
 []  \T1/zi4/m/n/10 Experimenter name: Smith SC, Baras AS, Owens CR, Dancik G e
t al. Transcriptional signatures of Ral GTPase are associated with aggressive c
linicopathologic characteristics in human cancer. Cancer Res 2012 Jul 15;72(14)
:3480-91.[] 

Overfull \hbox (233.0597pt too wide) in paragraph at lines 916--916
 []  \T1/zi4/m/n/10 Title: Transcriptional signatures of Ral GTPase are associa
ted with aggressive clinicopathologic characteristics in human cancer.[] 
[22]
Underfull \hbox (badness 1092) in paragraph at lines 987--987
[] \T1/ptm/m/it/10 Emm-prin and sur-vivin pre-dict re-sponse and sur-vival fol-
low-ing
[23]
Overfull \hbox (819.64798pt too wide) in paragraph at lines 1005--1005
 []  \T1/zi4/m/n/10 Experimenter name: Als AB, Dyrskj?t L, von der Maase H, Koe
d K et al. Emmprin and survivin predict response and survival following cisplat
in-containing chemotherapy in patients with advanced bladder cancer. Clin Cance
r Res 2007 Aug 1;13(15 Pt 1):4407-14.[] 

Overfull \hbox (299.71954pt too wide) in paragraph at lines 1008--1008
 []  \T1/zi4/m/n/10 Title: Emmprin and survivin predict response and survival f
ollowing cisplatin-containing chemotherapy in patients with advanced bladder ca
ncer.[] 
[24] [25] [26]
Overfull \hbox (433.02902pt too wide) in paragraph at lines 1119--1119
 []  \T1/zi4/m/n/10 Experimenter name: Dyrskj?t L, Thykjaer T, Kruh?ffer M, Jen
sen JL et al. Identifying distinct classes of bladder carcinoma using microarra
ys. Nat Genet 2003 Jan;33(1):90-6.[] 
[27]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1207--1207
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[28] [29] [30]
Overfull \hbox (1407.90634pt too wide) in paragraph at lines 1315--1315
 []  \T1/zi4/m/n/10 Experimenter name: Stransky N, Vallot C, Reyal F, Bernard-P
ierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C,
 Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP
, Chopin DK, Pinkel D, Radvanyi F. Regional copy number-independent deregulatio
n of transcription in cancer. Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov
 12.[] 
[31] [32]
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.ind
[33]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 19.

[34])
(/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/.Rd2pdf2016389/Rd2.aux
)

LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dist/fonts
/enc/dvips/base/8r.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsola
ta/i4-t1-0.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/inconsolata/In
consolata-zi4r.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb
></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on Rd2.pdf (34 pages, 143956 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmpoblCG3/Rbuild1ec4853db7badb/curatedBladderData/build/curatedBladderData.pdf’ ...
Done
* creating vignettes ... OK
* 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 ‘curatedBladderData_1.30.0.tar.gz’