############################################################################## ############################################################################## ### ### 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. 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(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} 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. 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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. 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[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} Output written on Rd2.pdf (65 pages, 229409 bytes). 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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. 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[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} Output written on Rd2.pdf (65 pages, 229409 bytes). 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