[Bioc-devel] texi2dvi error at R CMD check

[Martin Morgan]

Hi Mizanur --

"Mizanur Khondoker" <Mizanur.Khondoker at ed.ac.uk> writes:

> I am trying to craete a Bioconductor package 'multiscan'. Everything

Hmm, I don't see multiscan in the Bioc repository. Is it a recent
package / are you using a recent Bioconductor? Ahh, I guess you mean
you're preparing a package for submission? Great! Please include the
output of sessionInfo().

More below...

> installs and checks fine  except for the
> package vignette.
>
> When I run R CMD check, I get  the following error  at the package vignette
> checking satge:
> ----------------------------------------------------------------------------------------------------------------------------
> * checking package vignettes in 'inst/doc' ... NOTE
> --- running texi2dvi on vignettes
> /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
> /usr/bin/texi2dvi: see multiscan.log for errors.
> Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet = TRUE) :
>   running 'texi2dvi' on 'multiscan.tex' failed
> Calls: checkVignettes -> texi2dvi
> Execution halted
> * creating multiscan-manual.tex ... OK
> * checking multiscan-manual.tex using pdflatex ... OK
> ------------------------------------------------------------------------------------------------------------------------------
>
> When I run texi2dvi  on  multiscan.tex produced by  executing
> Sweave("multiscan.Rnw") at the R command prompt, I notice some  "Underfull
> \hbox (badness 10000)"  messages. Are  these the reasons for failure of R
> CMD check?  Can anyboby suggest me a solution to this problem?

No, these are just warnings about less-than-perfect formatting.

> Following is the transcript of "texi2dvi  multiscan.tex"  command:

Since this succeeds, it implies that the tex file produced by Sweave
is valid. Unfortunately, you'll have to dig deeper to find the
problem.  Start with a clean copy of the source for the package. Then
in a shell

% R CMD build multiscan

likely you'll see your error, and you can find the 'log' file (and
also the tex file produced by Sweave) in

multiscan/inst/doc

Likely the log file will have lots of intimidating looking tex
messages, but will end abruptly with something informative. Or at
least something that someone on the list can help you with.

Hope that helps,

Martin

> ------------------------------------------------------------------------------------------------------------------------------
> [mizank at oriol myrpackages]$ texi2dvi  multiscan.tex
> This is TeXk, Version 3.14159 (Web2C 7.4.5)
>  file:line:error style messages enabled.
> (/u02/mizank/myrpackages/multiscan.tex
> LaTeX2e <2001/06/01>
> Babel <v3.7h> and hyphenation patterns for american, french, german,
> ngerman, n
> ohyphenation, loaded.
> (/usr/share/texmf/tex/latex/base/article.cls
> Document Class: article 2001/04/21 v1.4e Standard LaTeX document class
> (/usr/share/texmf/tex/latex/base/size11.clo))
> (/usr/share/texmf/tex/latex/amsmath/amsmath.sty
> For additional information on amsmath, use the `?' option.
> (/usr/share/texmf/tex/latex/amsmath/amstext.sty
> (/usr/share/texmf/tex/latex/amsmath/amsgen.sty))
> (/usr/share/texmf/tex/latex/amsmath/amsbsy.sty)
> (/usr/share/texmf/tex/latex/amsmath/amsopn.sty))
> (/usr/share/texmf/tex/latex/graphics/epsfig.sty
> (/usr/share/texmf/tex/latex/graphics/graphicx.sty
> (/usr/share/texmf/tex/latex/graphics/keyval.sty)
> (/usr/share/texmf/tex/latex/graphics/graphics.sty
> (/usr/share/texmf/tex/latex/graphics/trig.sty)
> (/usr/share/texmf/tex/latex/config/graphics.cfg)
> (/usr/share/texmf/tex/latex/graphics/dvips.def))))
> (/usr/share/texmf/tex/generic/misc/psfig.sty)
> (/usr/share/texmf/tex/latex/preprint/fullpage.sty)
> (/u02/mizank/R-2.7.0/share/texmf/Sweave.sty
>
> LaTeX Warning: You have requested package
> `/u02/mizank/R-2.7.0/share/texmf/Swea
> ve',
>                but the package provides `Sweave'.
>
> (/usr/share/texmf/tex/latex/base/ifthen.sty)
> (/usr/share/texmf/tex/latex/fancyvrb/fancyvrb.sty
> Style option: `fancyvrb' v2.7, with DG/SPQR fixes <2000/03/21> (tvz))
> (/usr/share/texmf/tex/latex/base/fontenc.sty
> (/usr/share/texmf/tex/latex/base/t1enc.def))
> (/usr/share/texmf/tex/latex/ae/ae.sty
> (/usr/share/texmf/tex/latex/base/fontenc.sty
> (/usr/share/texmf/tex/latex/base/t1enc.def)
> (/usr/share/texmf/tex/latex/ae/t1aer.fd)))) (./multiscan.aux)
> (/usr/share/texmf/tex/latex/ae/t1aett.fd)
> Underfull \hbox (badness 10000) in paragraph at lines 33--33
> [][]\T1/aer/m/n/9 Biomathematics & Statis-tics Scot-land, King's Build-ings,
> Ed
> -in-burgh, EH9 3JZ, Scot-land, UK.
> (./multiscan.toc)
> Underfull \hbox (badness 10000) in paragraph at lines 40--47
>
> [1]
> Underfull \hbox (badness 10000) in paragraph at lines 48--51
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 64--65
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 66--67
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 68--72
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 73--74
> [2]
> Underfull \hbox (badness 10000) in paragraph at lines 102--103
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 114--118
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 119--124
>
> [3] [4] <multiscan-fitted.eps> <multiscan-sdres.eps> [5] [6] [7]
> Underfull \hbox (badness 10000) in paragraph at lines 302--310
>
> [8] (./multiscan.aux) )
> (see the transcript file for additional information)
> Output written on multiscan.dvi (8 pages, 15548 bytes).
> Transcript written on multiscan.log.
> --------------------------------------------------------------------------------------------------------------------------
>
>
>
> -- 
> Mizanur Khondoker
> Division of Pathway Medicine (DPM)
> The University of Edinburgh Medical School
> The Chancellor's Building
> 49 Little France Crescent
> Edinburgh EH16 4SB
> United Kingdom
>
> Tel: +44 (0) 131 242 6287
> Fax: +44 (0) 131 242 6244
> http://www.pathwaymedicine.ed.ac.uk/
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793