############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-data-experiment/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-3.15-data-experiment/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 396. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 396. ) (/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 94--94 [] \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 97--97 [] \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 217--217 [] \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 347--347 [] \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 350--350 [] \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 450--450 [] \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 453--453 [] \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 553--553 [] \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 633--633 [] \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 636--636 [] \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 795--795 [] \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 914--914 [] \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 917--917 [] \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 988--988 [] \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 1006--1006 [] \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 1009--1009 [] \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 1120--1120 [] \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 1208--1208 [] \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 1316--1316 [] \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/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/Rd2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. 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Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 396. ) (/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/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/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/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/Rd2.out) (/tmp/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/Rd2.out) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/tmp/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/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 94--94 [] \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 97--97 [] \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 217--217 [] \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 347--347 [] \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 350--350 [] \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 450--450 [] \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 453--453 [] \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 553--553 [] \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 633--633 [] \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 636--636 [] \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 795--795 [] \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 914--914 [] \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 917--917 [] \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 988--988 [] \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 1006--1006 [] \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 1009--1009 [] \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 1120--1120 [] \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 1208--1208 [] \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 1316--1316 [] \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/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/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} Output written on Rd2.pdf (33 pages, 133414 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. 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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 97--97 [] \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 217--217 [] \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 347--347 [] \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 350--350 [] \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 450--450 [] \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 453--453 [] \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 553--553 [] \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 633--633 [] \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 636--636 [] \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 795--795 [] \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 914--914 [] \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 917--917 [] \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 988--988 [] \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 1006--1006 [] \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 1009--1009 [] \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 1120--1120 [] \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 1208--1208 [] \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 1316--1316 [] \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/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/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/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/Rd2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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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 97--97 [] \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 217--217 [] \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 347--347 [] \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 350--350 [] \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 450--450 [] \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 453--453 [] \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 553--553 [] \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 633--633 [] \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 636--636 [] \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 795--795 [] \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 914--914 [] \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 917--917 [] \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 988--988 [] \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 1006--1006 [] \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 1009--1009 [] \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 1120--1120 [] \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 1208--1208 [] \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 1316--1316 [] \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/Rtmpkgsw9J/Rbuildfc72177f6c3ca/curatedBladderData/.Rd2pdf1034017/Rd2.ind [33] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 19. 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