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[Bioc-devel] Latex/Rd problems?

3 messages · Dykema, Karl, Ting-Yuan Liu (FHCRC), Seth Falcon

#
I seem to be having a new problem with my ideogram package passing the
CHECK on 3 of the 4 systems on the daily package check results page.
Packages biocViews and geneSpring also have similar errors.

I have gone through my .Rd and .Rnw files without finding any problems
that are obvious. I have hopefully overlooked something rudimentary that
a LaTex guru will easily spot. I can replicate the error on my windows
PC with the current development version of R, but have not been able to
figure anything out on my own. Thanks in advance if anyone can help!


The error message: 

* checking ideogram-manual.tex ... ERROR LaTeX errors when creating DVI
version.
This typically indicates Rd problems.
LaTeX errors found:

! LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.



Here is my session info:
R version 2.2.0, 2005-08-25, i386-pc-mingw32 

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
"datasets"  "base"     

other attached packages:
  ideogram   annotate golubEsets    Biobase     hu6800 
   "1.2.2"   "1.5.15"      "1.0"    "1.6.7"    "1.8.4"



-------------------------------
Karl Dykema
Bioinformatics Programmer/Analyst
Laboratory of Computational Biology
Van Andel Research Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503
This email message, including any attachments, is for the so...{{dropped}}
#
Hi Karl,

The message said "! LaTeX Error: Something's wrong--perhaps a missing 
\item." I will guess you have a \begin{itemize} and \end{itemize} 
session but no \item inside the session.  Check this...

HTH,
Ting-Yuan
On Tue, 27 Sep 2005, Dykema, Karl wrote:

            
#
On 27 Sep 2005, Karl.Dykema at vai.org wrote:

            
I just committed a fix for you.  The problem seemed to be that you had
unespaped '$' characters.  Wrapping them in \code{something$else}
fixed things.  

I also converted a few files that had mixed line ending style (a
little Windows a little unix) to unix style.  Files should be one or
the other.

How did I find the error?

After running R CMD check, look in the ideograph.Rcheck dir and browse
the ideogram-manual.log file.  This told me where to look in the
ideograpm-manual.tex file and this told me where to fix the problem in
the Rd file.

+ seth