Hmm ... looks like a package This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./Rd2.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/bk10.clo)) (/usr/local/R-2.15.2/share/texmf/tex/latex/Rd.sty (/usr/share/texmf/tex/latex/base/ifthen.sty) (/usr/share/texmf/tex/latex/tools/longtable.sty) (/usr/share/texmf/tex/latex/tools/bm.sty) (/usr/share/texmf/tex/latex/base/alltt.sty) (/usr/share/texmf/tex/latex/tools/verbatim.sty) (/usr/share/texmf/tex/latex/ltxmisc/url.sty) (/usr/local/R-2.15.2/share/texmf/tex/latex/upquote.sty (/usr/share/texmf/tex/latex/base/textcomp.sty (/usr/share/texmf/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/share/texmf/tex/latex/base/fontenc.sty (/usr/share/texmf/tex/latex/base/t1enc.def)) (/usr/share/texmf/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/share/texmf/tex/latex/graphics/color.sty (/usr/share/texmf/tex/latex/config/color.cfg) (/usr/share/texmf/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf/tex/latex/hyperref/hyperref.sty (/usr/share/texmf/tex/latex/graphics/keyval.sty) (/usr/share/texmf/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined ) *hyperref using default driver hpdftex* (/usr/share/texmf/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 356. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 356. ) (/usr/share/texmf/tex/latex/base/makeidx.sty) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/base/utf8.def (/usr/share/texmf/tex/latex/base/t1enc.dfu) (/usr/share/texmf/tex/latex/base/ot1enc.dfu) (/usr/share/texmf/tex/latex/base/omsenc.dfu) (/usr/share/texmf/tex/latex/base/ts1enc.dfu)) (/usr/share/texmf/tex/latex/base/latin1.def)) Writing index file Rd2.idx No file Rd2.aux. (/usr/share/texmf/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf/tex/context/base/supp-pdf.tex [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf/tex/latex/hyperref/nameref.sty (/usr/share/texmf/tex/latex/oberdiek/refcount.sty)) (/usr/share/texmf/tex/latex/psnfss/t1pcr.fd) (/usr/share/texmf/tex/latex/psnfss/t1phv.fd) (/usr/share/texmf/tex/latex/base/utf8.def) Underfull \vbox (badness 10000) has occurred while \output is active [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (114.78088pt too wide) in paragraph at lines 71--71 []\T1/pcr/m/n/10 est.bes(Y, X, intercept = TRUE, start.vals = rep(0, ncol(X) + as.numeric(intercept)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 104--104 [] \T1/pcr/m/n/9 intercept = intercept, method = "BFGS", control = list (fnscale = -1),[] [2] Overfull \hbox (4.38043pt too wide) in paragraph at lines 121--121 [] \T1/pcr/m/n/9 return(list(ests = beta.hat, varcov = beta.cov, fitted.lp = fitted.lp,[] (/usr/share/texmf/tex/latex/base/utf8.def) (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (294.78088pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/10 gbd(n = 1000, p = 1, intercept = TRUE, betas = rep(0, p + int ercept), mu = rep(0, p), Sigma = diag(1, p), seed = 1)[] [3] (/usr/share/texmf/tex/latex/base/utf8.def) (/usr/share/texmf/tex/latex/base/utf8.def) [4] (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (102.78088pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/10 plot.lrsurf(Y, X, b0 = seq(-2, 2, by = 0.01), b1 = seq(-2, 2, by = 0.01), ncl = 20)[] [5] Overfull \hbox (25.98041pt too wide) in paragraph at lines 345--345 [] \T1/pcr/m/n/9 image(b0, b1, lrs, xlab = expression(beta[0]), ylab = expr ession(beta[1]))[] (/usr/share/texmf/tex/latex/base/utf8.def) No file Rd2.ind. [6] (./Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf/fonts/enc/dvips/base/8r.enc} Output written on Rd2.pdf (6 pages, 87273 bytes). Transcript written on Rd2.log. This is makeindex, version 2.14 [02-Oct-2002] (kpathsea + Thai support). Scanning input file Rd2.idx....done (24 entries accepted, 0 rejected). Sorting entries....done (114 comparisons). Generating output file Rd2.ind....done (47 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./Rd2.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/bk10.clo)) (/usr/local/R-2.15.2/share/texmf/tex/latex/Rd.sty (/usr/share/texmf/tex/latex/base/ifthen.sty) (/usr/share/texmf/tex/latex/tools/longtable.sty) (/usr/share/texmf/tex/latex/tools/bm.sty) (/usr/share/texmf/tex/latex/base/alltt.sty) (/usr/share/texmf/tex/latex/tools/verbatim.sty) (/usr/share/texmf/tex/latex/ltxmisc/url.sty) (/usr/local/R-2.15.2/share/texmf/tex/latex/upquote.sty (/usr/share/texmf/tex/latex/base/textcomp.sty (/usr/share/texmf/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/share/texmf/tex/latex/base/fontenc.sty (/usr/share/texmf/tex/latex/base/t1enc.def)) (/usr/share/texmf/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/share/texmf/tex/latex/graphics/color.sty (/usr/share/texmf/tex/latex/config/color.cfg) (/usr/share/texmf/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf/tex/latex/hyperref/hyperref.sty (/usr/share/texmf/tex/latex/graphics/keyval.sty) (/usr/share/texmf/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined ) *hyperref using default driver hpdftex* (/usr/share/texmf/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 356. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 356. ) (/usr/share/texmf/tex/latex/base/makeidx.sty) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/base/utf8.def (/usr/share/texmf/tex/latex/base/t1enc.dfu) (/usr/share/texmf/tex/latex/base/ot1enc.dfu) (/usr/share/texmf/tex/latex/base/omsenc.dfu) (/usr/share/texmf/tex/latex/base/ts1enc.dfu)) (/usr/share/texmf/tex/latex/base/latin1.def)) Writing index file Rd2.idx (./Rd2.aux) (/usr/share/texmf/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf/tex/context/base/supp-pdf.tex [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf/tex/latex/hyperref/nameref.sty (/usr/share/texmf/tex/latex/oberdiek/refcount.sty)) (./Rd2.out) (./Rd2.out) (/usr/share/texmf/tex/latex/psnfss/t1pcr.fd) (/usr/share/texmf/tex/latex/psnfss/t1phv.fd) (./Rd2.toc) (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \vbox (30.37697pt too high) has occurred while \output is active [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (114.78088pt too wide) in paragraph at lines 71--71 []\T1/pcr/m/n/10 est.bes(Y, X, intercept = TRUE, start.vals = rep(0, ncol(X) + as.numeric(intercept)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 104--104 [] \T1/pcr/m/n/9 intercept = intercept, method = "BFGS", control = list (fnscale = -1),[] [2] Overfull \hbox (4.38043pt too wide) in paragraph at lines 121--121 [] \T1/pcr/m/n/9 return(list(ests = beta.hat, varcov = beta.cov, fitted.lp = fitted.lp,[] (/usr/share/texmf/tex/latex/base/utf8.def) (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (294.78088pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/10 gbd(n = 1000, p = 1, intercept = TRUE, betas = rep(0, p + int ercept), mu = rep(0, p), Sigma = diag(1, p), seed = 1)[] [3] (/usr/share/texmf/tex/latex/base/utf8.def) (/usr/share/texmf/tex/latex/base/utf8.def) [4] (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (102.78088pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/10 plot.lrsurf(Y, X, b0 = seq(-2, 2, by = 0.01), b1 = seq(-2, 2, by = 0.01), ncl = 20)[] [5] Overfull \hbox (25.98041pt too wide) in paragraph at lines 345--345 [] \T1/pcr/m/n/9 image(b0, b1, lrs, xlab = expression(beta[0]), ylab = expr ession(beta[1]))[] (/usr/share/texmf/tex/latex/base/utf8.def) (./Rd2.ind [6] [7]) (./Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf/fonts/enc/dvips/base/8r.enc} Output written on Rd2.pdf (7 pages, 106546 bytes). Transcript written on Rd2.log. This is makeindex, version 2.14 [02-Oct-2002] (kpathsea + Thai support). Scanning input file Rd2.idx....done (24 entries accepted, 0 rejected). Sorting entries....done (114 comparisons). Generating output file Rd2.ind....done (47 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) %&-line parsing enabled. entering extended mode (./Rd2.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, arabic, basque, bulgarian, coptic, welsh, czech, slovak, german, ng erman, danish, esperanto, spanish, catalan, galician, estonian, farsi, finnish, french, greek, monogreek, ancientgreek, croatian, hungarian, interlingua, ibyc us, indonesian, icelandic, italian, latin, mongolian, dutch, norsk, polish, por tuguese, pinyin, romanian, russian, slovenian, uppersorbian, serbian, swedish, turkish, ukenglish, ukrainian, loaded. (/usr/share/texmf/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf/tex/latex/base/bk10.clo)) (/usr/local/R-2.15.2/share/texmf/tex/latex/Rd.sty (/usr/share/texmf/tex/latex/base/ifthen.sty) (/usr/share/texmf/tex/latex/tools/longtable.sty) (/usr/share/texmf/tex/latex/tools/bm.sty) (/usr/share/texmf/tex/latex/base/alltt.sty) (/usr/share/texmf/tex/latex/tools/verbatim.sty) (/usr/share/texmf/tex/latex/ltxmisc/url.sty) (/usr/local/R-2.15.2/share/texmf/tex/latex/upquote.sty (/usr/share/texmf/tex/latex/base/textcomp.sty (/usr/share/texmf/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/share/texmf/tex/latex/base/fontenc.sty (/usr/share/texmf/tex/latex/base/t1enc.def)) (/usr/share/texmf/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/share/texmf/tex/latex/graphics/color.sty (/usr/share/texmf/tex/latex/config/color.cfg) (/usr/share/texmf/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf/tex/latex/hyperref/hyperref.sty (/usr/share/texmf/tex/latex/graphics/keyval.sty) (/usr/share/texmf/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined ) *hyperref using default driver hpdftex* (/usr/share/texmf/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 356. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 356. ) (/usr/share/texmf/tex/latex/base/makeidx.sty) (/usr/share/texmf/tex/latex/base/inputenc.sty (/usr/share/texmf/tex/latex/base/utf8.def (/usr/share/texmf/tex/latex/base/t1enc.dfu) (/usr/share/texmf/tex/latex/base/ot1enc.dfu) (/usr/share/texmf/tex/latex/base/omsenc.dfu) (/usr/share/texmf/tex/latex/base/ts1enc.dfu)) (/usr/share/texmf/tex/latex/base/latin1.def)) Writing index file Rd2.idx (./Rd2.aux) (/usr/share/texmf/tex/latex/base/ts1cmr.fd) (/usr/share/texmf/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf/tex/context/base/supp-pdf.tex [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf/tex/latex/hyperref/nameref.sty (/usr/share/texmf/tex/latex/oberdiek/refcount.sty)) (./Rd2.out) (./Rd2.out) (/usr/share/texmf/tex/latex/psnfss/t1pcr.fd) (/usr/share/texmf/tex/latex/psnfss/t1phv.fd) (./Rd2.toc) (/usr/share/texmf/tex/latex/base/utf8.def) [1{/var/lib/texmf/fonts/map/pdftex/u pdmap/pdftex.map}] (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (114.78088pt too wide) in paragraph at lines 71--71 []\T1/pcr/m/n/10 est.bes(Y, X, intercept = TRUE, start.vals = rep(0, ncol(X) + as.numeric(intercept)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 104--104 [] \T1/pcr/m/n/9 intercept = intercept, method = "BFGS", control = list (fnscale = -1),[] [2] Overfull \hbox (4.38043pt too wide) in paragraph at lines 121--121 [] \T1/pcr/m/n/9 return(list(ests = beta.hat, varcov = beta.cov, fitted.lp = fitted.lp,[] (/usr/share/texmf/tex/latex/base/utf8.def) (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (294.78088pt too wide) in paragraph at lines 165--165 []\T1/pcr/m/n/10 gbd(n = 1000, p = 1, intercept = TRUE, betas = rep(0, p + int ercept), mu = rep(0, p), Sigma = diag(1, p), seed = 1)[] [3] (/usr/share/texmf/tex/latex/base/utf8.def) (/usr/share/texmf/tex/latex/base/utf8.def) [4] (/usr/share/texmf/tex/latex/base/utf8.def) Overfull \hbox (102.78088pt too wide) in paragraph at lines 306--306 []\T1/pcr/m/n/10 plot.lrsurf(Y, X, b0 = seq(-2, 2, by = 0.01), b1 = seq(-2, 2, by = 0.01), ncl = 20)[] [5] Overfull \hbox (25.98041pt too wide) in paragraph at lines 345--345 [] \T1/pcr/m/n/9 image(b0, b1, lrs, xlab = expression(beta[0]), ylab = expr ession(beta[1]))[] (/usr/share/texmf/tex/latex/base/utf8.def) (./Rd2.ind [6] [7]) (./Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf/fonts/enc/dvips/base/8r.enc} Output written on Rd2.pdf (7 pages, 107063 bytes). Transcript written on Rd2.log. Saving output to 'LogRegLinux-manual.pdf' ... Done You may want to clean up by 'rm -rf /tmp/Rtmpvipbok/Rd2pdf59581b62f025'