Hi Martin,

Thank you for the quick response. I followed your suggestion, and seem to
have figured out the problem. The mistake was that,
 in multiscan.Rnw file I used

<<eval=FALSE, echo=TRUE>>
library(multiscan)
@

for loading the package.

eval=TRUE solves the problem. The package has now passed  R CMD check and R
CMD build without errors/warnings.

Thanks,
Mizan



2008/4/30 Martin Morgan <mtmorgan@fhcrc.org>:

> Hi Mizanur --
>
> "Mizanur Khondoker" <Mizanur.Khondoker@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@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]]
> >
> > _______________________________________________
> > Bioc-devel@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> 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
>
>


-- 
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]]

