[Bioc-devel] Latex errors in R CMD check a new built BSgenome data package in R-2.13.0
Mao Jianfeng
jianfeng.mao at gmail.com
Fri Apr 1 11:15:41 CEST 2011
Dear Hervé,
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)
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(/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)
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(/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))
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(/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
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(/usr/share/texmf-texlive/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texmf-texlive/tex/generic/oberdiek/atbegshi.sty))
*hyperref using default driver hpdftex*
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Package hyperref Warning: Option `hyperindex' has already been used,
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Package hyperref Warning: Option `pagebackref' has already been used,
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) (/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
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mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode;
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l.7 \chapter*{}
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d.
<to be read again>
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l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'}
}
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l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'}
}
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l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'}
}
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l.9 ...bf{\huge Package `BSgenome.Alyrata.JGI.v1'}
}
kpathsea: Running mktextfm ptmr8t
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l.10 \par\bigskip{\large
\today}
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l.18 ...n-Feng Mao }\email{jianfeng.mao at gmail.com}
\AsIs{}
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l.33 ...a full genome (JGI version V1.0)}{Alyrata}
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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
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