Dirk Eddelbuettel
2018-May-29 20:17 UTC
[R-sig-Fedora] CentOS 7 issues with pdf manual / tex conversion
On a CentOS 7 machine, I am at a loss with respect to an inability to run a
full R CMD check as anything involving tex files ends in tears.
We followed the README at CRAN and installed a large number of tex-live
packages on this machine. But when a manual is created, we end up with what
follows below. Here, I chopped some of the error messages, the key seems to
be 'Insufficient extension fonts' which gets repeated a bit.
I have been using latex for a long time, but I can't make heads and tails of
it. Any idea?
Dirk
$ R CMD Rd2pdf pkgKitten ## just because I know the manual builds
Hmm ... looks like a package
Converting Rd files to LaTeX
Creating pdf output from LaTeX ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'Rd2.tex' failed.
LaTeX errors:
! Math formula deleted: Insufficient extension fonts.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
! Emergency stop.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
! ==> Fatal error occurred, no output PDF file produced!
Output:
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang,
nohyphenation, lo
aded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
[...]
(/usr/share/R/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/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/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/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
! Math formula deleted: Insufficient extension fonts.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
?
! Emergency stop.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on Rd2.log.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'Rd2.tex' failed.
LaTeX errors:
! Math formula deleted: Insufficient extension fonts.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
! Emergency stop.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
! ==> Fatal error occurred, no output PDF file produced!
Output:
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang,
nohyphenation, lo
aded.
(./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/usr/share/R/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/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/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/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/share/texlive/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/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/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def)
! Math formula deleted: Insufficient extension fonts.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
?
! Emergency stop.
\@iiiparbox ...bm@#3\endcsname }\if at pboxsw \m at th $
\fi \@end at tempboxa
l.34 ...itten} function.}{pkgKitten.Rdash.package}
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on Rd2.log.
Error in running tools::texi2pdf()
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
R P Herrold
2018-May-29 20:37 UTC
[R-sig-Fedora] CentOS 7 issues with pdf manual / tex conversion
On Tue, 29 May 2018, Dirk Eddelbuettel wrote:> On a CentOS 7 machine, I am at a loss with respect to an inability to run a > full R CMD check as anything involving tex files ends in tears.Hi, Dirk Have fun at the upcoming conference at UIC I seem to have 56 font packages installed under CentOS 7 locally, but then I work pretty carefully to cull them down What is the specific 'leaf node' package you are trying to attain. Long ago and far away, I packaged several hundred, inspired by your Debian effort, and I may have a working .spec file about with my regards, -- Russ herrold
Dirk Eddelbuettel
2018-May-29 20:53 UTC
[R-sig-Fedora] CentOS 7 issues with pdf manual / tex conversion
On 29 May 2018 at 16:37, R P Herrold wrote:
| On Tue, 29 May 2018, Dirk Eddelbuettel wrote:
|
| > On a CentOS 7 machine, I am at a loss with respect to an inability to run
a
| > full R CMD check as anything involving tex files ends in tears.
|
| Hi, Dirk
|
| Have fun at the upcoming conference at UIC
|
| I seem to have 56 font packages installed under CentOS 7
| locally, but then I work pretty carefully to cull them down
|
| What is the specific 'leaf node' package you are trying to
I noticed it with a local, not-public package -- but it appears to apply with
any source package. I replicated with pkgKitten straight off CRAN and after
checking that it has a six page manual there. Here, I get an aborted (!!)
source file, same happens with the local, non-public package:
-----------------------------------------------------------------------------
\documentclass[a4paper]{book}
\usepackage[times,hyper]{Rd}
\usepackage{makeidx}
\usepackage[latin1]{inputenc} % @SET ENCODING@
% \usepackage{graphicx} % @USE GRAPHICX@
\makeindex{}
\begin{document}
\chapter*{}
\begin{center}
{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of
\file{pkgKitten\_0.1.4.tar.gz}}}
\par\bigskip{\large \today}
\end{center}
-----------------------------------------------------------------------------
Note that it ends on \end{center}, not \end{document}.
Dirk
| attain. Long ago and far away, I packaged several hundred,
| inspired by your Debian effort, and I may have a working .spec
| file about
|
| with my regards,
|
| -- Russ herrold
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org