[Bioc-devel] texi2dvi error at R CMD check

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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/

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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
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