Dear Herv?, Thanks for your kind explanation to me. (1) The command R CMD Rd2pdf BSgenome.Alyrata.JGI.v1 can not work. (2) The comman /ebio/abt6/jmao/bin/R-2.13/R-alpha/bin/R CMD Rd2dvi BSgenome.Alyrata.JGI.v1 works for me. (3) My colleague told me that he also find that there is problem for Ubuntu (my computer work by Ubuntu sytem) to building PDFs for Bioconductor and other R packages. (4) intermediate files folder ".Rd2dvi28311/" have gone. (5) dvi file generate by R CMD Rd2dvi was in the attachment. ###################################################################### (1) R CMD Rd2dvi jmao at deimos:~/Aly_test$ /ebio/abt6/jmao/bin/R-2.13/R-alpha/bin/R CMD Rd2dvi BSgenome.Alyrata.JGI.v1 Hmm ... looks like a package Converting Rd files to LaTeX Creating dvi output from LaTeX ... This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (./Rd2.tex LaTeX2e <2009/09/24> Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/ebio/abt6/jmao/bin/R-2.13/R-alpha/share/texmf/tex/latex/Rd.sty (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/bm.sty) (/usr/share/texmf-texlive/tex/latex/base/alltt.sty) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/ebio/abt6/jmao/bin/R-2.13/R-alpha/share/texmf/tex/latex/upquote.sty (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/ae/ae.sty (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def) (/usr/share/texmf-texlive/tex/latex/ae/t1aer.fd))) (/usr/share/texmf-texlive/tex/latex/ae/t1aett.fd) NOT loading times NOT loading lmodern) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/base/inputenc.sty (/usr/share/texmf-texlive/tex/latex/base/utf8.def (/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu)) (/usr/share/texmf-texlive/tex/latex/base/latin1.def)) Writing index file Rd2.idx No file Rd2.aux. (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/ae/t1aess.fd) No file Rd2.toc. (/usr/share/texmf-texlive/tex/latex/base/utf8.def) [1] Overfull \hbox (39.70007pt too wide) in paragraph at lines 46--46 []\T1/aett/m/n/10 all the chr*.fa file from http://genome.jgi-psf.org/Araly1/A raly1.download.ftp.html[] [2] No file Rd2.ind. [3] (./Rd2.aux) ) (see the transcript file for additional information) Output written on Rd2.dvi (3 pages, 4520 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2009] (kpathsea + Thai support). Scanning input file Rd2.idx....done (10 entries accepted, 0 rejected). Sorting entries....done (37 comparisons). Generating output file Rd2.ind....done (26 lines written, 0 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (./Rd2.tex LaTeX2e <2009/09/24> Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/ebio/abt6/jmao/bin/R-2.13/R-alpha/share/texmf/tex/latex/Rd.sty (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/bm.sty) (/usr/share/texmf-texlive/tex/latex/base/alltt.sty) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/ebio/abt6/jmao/bin/R-2.13/R-alpha/share/texmf/tex/latex/upquote.sty (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/ae/ae.sty (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def) (/usr/share/texmf-texlive/tex/latex/ae/t1aer.fd))) (/usr/share/texmf-texlive/tex/latex/ae/t1aett.fd) NOT loading times NOT loading lmodern) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/base/inputenc.sty (/usr/share/texmf-texlive/tex/latex/base/utf8.def (/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu)) (/usr/share/texmf-texlive/tex/latex/base/latin1.def)) Writing index file Rd2.idx (./Rd2.aux) (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/ae/t1aess.fd) (./Rd2.toc) (/usr/share/texmf-texlive/tex/latex/base/utf8.def) [1] Overfull \hbox (39.70007pt too wide) in paragraph at lines 46--46 []\T1/aett/m/n/10 all the chr*.fa file from http://genome.jgi-psf.org/Araly1/A raly1.download.ftp.html[] [2] (./Rd2.ind [3] [4]) (./Rd2.aux) ) (see the transcript file for additional information) Output written on Rd2.dvi (4 pages, 5628 bytes). Transcript written on Rd2.log. Saving output to 'BSgenome.Alyrata.JGI.v1.dvi' ... Done ############################################################### (2) Rd2pdf jmao at deimos:~/Aly_test$ /ebio/abt6/jmao/bin/R-2.13/R-alpha/bin/R CMD Rd2pdf BSgenome.Alyrata.JGI.v1 Hmm ... looks like a package Converting Rd files to LaTeX Creating pdf output from LaTeX ... This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) restricted \write18 enabled. entering extended mode (./Rd2.tex LaTeX2e <2009/09/24> Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/bk10.clo)) (/ebio/abt6/jmao/bin/R-2.13/R-alpha/share/texmf/tex/latex/Rd.sty (/usr/share/texmf-texlive/tex/latex/base/ifthen.sty) (/usr/share/texmf-texlive/tex/latex/tools/longtable.sty) (/usr/share/texmf-texlive/tex/latex/tools/bm.sty) (/usr/share/texmf-texlive/tex/latex/base/alltt.sty) (/usr/share/texmf-texlive/tex/latex/tools/verbatim.sty) (/usr/share/texmf-texlive/tex/latex/ltxmisc/url.sty) (/ebio/abt6/jmao/bin/R-2.13/R-alpha/share/texmf/tex/latex/upquote.sty (/usr/share/texmf-texlive/tex/latex/base/textcomp.sty (/usr/share/texmf-texlive/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/share/texmf-texlive/tex/latex/base/fontenc.sty (/usr/share/texmf-texlive/tex/latex/base/t1enc.def)) (/usr/share/texmf-texlive/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/share/texmf-texlive/tex/latex/graphics/color.sty (/etc/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf-texlive/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-texlive/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-texlive/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-texlive/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-texlive/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf-texlive/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texmf-texlive/tex/latex/oberdiek/kvoptions.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/kvsetkeys.sty)) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-texlive/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texmf-texlive/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-texlive/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 332. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 332. ) (/usr/share/texmf-texlive/tex/latex/base/makeidx.sty) (/usr/share/texmf-texlive/tex/latex/base/inputenc.sty (/usr/share/texmf-texlive/tex/latex/base/utf8.def (/usr/share/texmf-texlive/tex/latex/base/t1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ot1enc.dfu) (/usr/share/texmf-texlive/tex/latex/base/omsenc.dfu) (/usr/share/texmf-texlive/tex/latex/base/ts1enc.dfu)) (/usr/share/texmf-texlive/tex/latex/base/latin1.def)) Writing index file Rd2.idx No file Rd2.aux. (/usr/share/texmf-texlive/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-texlive/tex/latex/psnfss/t1ptm.fd) kpathsea: Running mktextfm ptmr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmr8t ! I can't find file `ptmr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Transcript written on mfput.log. grep: ptmr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t' failed to make ptmr8t.tfm. kpathsea: Appending font creation commands to missfont.log. ! Font T1/ptm/m/n/10=ptmr8t at 10.0pt not loadable: Metric (TFM) file not found . <to be read again> relax l.6 \begin{document} (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf-texlive/tex/latex/hyperref/nameref.sty (/usr/share/texmf-texlive/tex/latex/oberdiek/refcount.sty)) kpathsea: Running mktextfm ptmr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmr8t ! I can't find file `ptmr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Transcript written on mfput.log. grep: ptmr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t' failed to make ptmr8t.tfm. ! Font T1/ptm/m/n/24.88=ptmr8t at 24.88pt not loadable: Metric (TFM) file not f ound. <to be read again> relax l.7 \chapter*{} kpathsea: Running mktextfm ptmb8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmb8t ! I can't find file `ptmb8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Transcript written on mfput.log. grep: ptmb8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t' failed to make ptmb8t.tfm. ! Font T1/ptm/bx/n/24.88=ptmb8t at 24.88pt not loadable: Metric (TFM) file not found. <to be read again> relax l.7 \chapter*{} kpathsea: Running mktextfm nullfont mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf nullfont ! I can't find file `nullfont'. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Please type another input file name ! Emergency stop. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Transcript written on mfput.log. grep: nullfont.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont' failed to make nullfont.tfm. ! Font \T1/ptm/b/n/24.88=nullfont not loadable: Metric (TFM) file not found. <to be read again> \relax l.7 \chapter*{} kpathsea: Running mktextfm ptmb8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmb8t ! I can't find file `ptmb8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Transcript written on mfput.log. grep: ptmb8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t' failed to make ptmb8t.tfm. ! Font T1/ptm/bx/n/10=ptmb8t at 10.0pt not loadable: Metric (TFM) file not foun d. <to be read again> relax l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'} } kpathsea: Running mktextfm nullfont mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf nullfont ! I can't find file `nullfont'. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Please type another input file name ! Emergency stop. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Transcript written on mfput.log. grep: nullfont.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont' failed to make nullfont.tfm. ! Font \T1/ptm/b/n/10=nullfont not loadable: Metric (TFM) file not found. <to be read again> \relax l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'} } kpathsea: Running mktextfm ptmb8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmb8t ! I can't find file `ptmb8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Transcript written on mfput.log. grep: ptmb8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t' failed to make ptmb8t.tfm. ! Font T1/ptm/bx/n/20.74=ptmb8t at 20.74pt not loadable: Metric (TFM) file not found. <to be read again> relax l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'} } kpathsea: Running mktextfm nullfont mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf nullfont ! I can't find file `nullfont'. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Please type another input file name ! Emergency stop. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Transcript written on mfput.log. grep: nullfont.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont' failed to make nullfont.tfm. ! Font \T1/ptm/b/n/20.74=nullfont not loadable: Metric (TFM) file not found. <to be read again> \relax l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'} } kpathsea: Running mktextfm ptmr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmr8t ! I can't find file `ptmr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Transcript written on mfput.log. grep: ptmr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t' failed to make ptmr8t.tfm. ! Font T1/ptm/m/n/12=ptmr8t at 12.0pt not loadable: Metric (TFM) file not found . <to be read again> relax l.10 \par\bigskip{\large \today} (/usr/share/texmf-texlive/tex/latex/psnfss/t1pcr.fd) kpathsea: Running mktextfm pcrr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input pcrr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf pcrr8t ! I can't find file `pcrr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t Transcript written on mfput.log. grep: pcrr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input pcrr8t' failed to make pcrr8t.tfm. ! Font T1/pcr/m/n/10=pcrr8t at 10.0pt not loadable: Metric (TFM) file not found . <to be read again> relax l.18 ...n-Feng Mao }\email{jianfeng.mao at gmail.com} \AsIs{} (/usr/share/texmf-texlive/tex/latex/base/utf8.def) kpathsea: Running mktextfm ptmr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmr8t ! I can't find file `ptmr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Transcript written on mfput.log. grep: ptmr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t' failed to make ptmr8t.tfm. ! Font T1/ptm/m/n/14.4=ptmr8t at 14.4pt not loadable: Metric (TFM) file not fou nd. <to be read again> relax l.33 ...a full genome (JGI version V1.0)}{Alyrata} kpathsea: Running mktextfm ptmb8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmb8t ! I can't find file `ptmb8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmb8t Transcript written on mfput.log. grep: ptmb8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmb8t' failed to make ptmb8t.tfm. ! Font T1/ptm/bx/n/14.4=ptmb8t at 14.4pt not loadable: Metric (TFM) file not fo und. <to be read again> relax l.33 ...a full genome (JGI version V1.0)}{Alyrata} kpathsea: Running mktextfm nullfont mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf nullfont ! I can't find file `nullfont'. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Please type another input file name ! Emergency stop. <*> ...ljfour; mag:=1; nonstopmode; input nullfont Transcript written on mfput.log. grep: nullfont.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input nullfont' failed to make nullfont.tfm. ! Font \T1/ptm/b/n/14.4=nullfont not loadable: Metric (TFM) file not found. <to be read again> \relax l.33 ...a full genome (JGI version V1.0)}{Alyrata} (/usr/share/texmf-texlive/tex/latex/psnfss/t1phv.fd) kpathsea: Running mktextfm phvr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input phvr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf phvr8t ! I can't find file `phvr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input phvr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input phvr8t Transcript written on mfput.log. grep: phvr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input phvr8t' failed to make phvr8t.tfm. ! Font T1/phv/m/n/14.4=phvr8t at 14.4pt not loadable: Metric (TFM) file not fou nd. <to be read again> relax l.33 ...a full genome (JGI version V1.0)}{Alyrata} kpathsea: Running mktextfm ptmri8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmri8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmri8t ! I can't find file `ptmri8t'. <*> ...=ljfour; mag:=1; nonstopmode; input ptmri8t Please type another input file name ! Emergency stop. <*> ...=ljfour; mag:=1; nonstopmode; input ptmri8t Transcript written on mfput.log. grep: ptmri8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmri8t' failed to make ptmri8t.tfm. ! Font T1/ptm/m/it/10=ptmri8t at 10.0pt not loadable: Metric (TFM) file not fou nd. <to be read again> relax l.33 ...a full genome (JGI version V1.0)}{Alyrata} [1] kpathsea: Running mktextfm ptmr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmr8t ! I can't find file `ptmr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input ptmr8t Transcript written on mfput.log. grep: ptmr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmr8t' failed to make ptmr8t.tfm. ! Font T1/ptm/m/n/9=ptmr8t at 9.0pt not loadable: Metric (TFM) file not found. <to be read again> relax l.71 \begin{ExampleCode} kpathsea: Running mktextfm pcrr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input pcrr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf pcrr8t ! I can't find file `pcrr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input pcrr8t Transcript written on mfput.log. grep: pcrr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input pcrr8t' failed to make pcrr8t.tfm. ! Font T1/pcr/m/n/9=pcrr8t at 9.0pt not loadable: Metric (TFM) file not found. <to be read again> relax l.71 \begin{ExampleCode} kpathsea: Running mktextfm ptmro8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmro8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf ptmro8t ! I can't find file `ptmro8t'. <*> ...=ljfour; mag:=1; nonstopmode; input ptmro8t Please type another input file name ! Emergency stop. <*> ...=ljfour; mag:=1; nonstopmode; input ptmro8t Transcript written on mfput.log. grep: ptmro8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input ptmro8t' failed to make ptmro8t.tfm. ! Font T1/ptm/m/sl/10=ptmro8t at 10.0pt not loadable: Metric (TFM) file not fou nd. <to be read again> relax l.103 if (interactive()) kpathsea: Running mktextfm phvr8t mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input phvr8t This is METAFONT, Version 2.718281 (TeX Live 2009/Debian) kpathsea: Running mktexmf phvr8t ! I can't find file `phvr8t'. <*> ...:=ljfour; mag:=1; nonstopmode; input phvr8t Please type another input file name ! Emergency stop. <*> ...:=ljfour; mag:=1; nonstopmode; input phvr8t Transcript written on mfput.log. grep: phvr8t.log: No such file or directory mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input phvr8t' failed to make phvr8t.tfm. ! Font T1/phv/m/n/10=phvr8t at 10.0pt not loadable: Metric (TFM) file not found . <to be read again> relax l.103 if (interactive()) [2] No file Rd2.ind. [3] (./Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.available.genomes} has been referenced but does not exist, replaced by a f ixed one pdfTeX warning (dest): name{Rfn.DNAString.Rdash.class} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.BSgenome.Rdash.class} has been referenced but d oes not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.BSgenomeForge} has been referenced but does not exist, replaced by a fixed one Output written on Rd2.pdf (3 pages, 5159 bytes). Transcript written on Rd2.log. Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, : unable to run 'pdflatex' on 'Rd2.tex' Error in running tools::texi2dvi
[Bioc-devel] Latex errors in R CMD check a new built BSgenome data package in R-2.13.0
1 message · Mao Jianfeng