CRAN finds an warning that R CMD check --as-cran does not - r

Question

I am using 32-bit R 3.1.2 on Windows 7.
I recently conducted an R CMD check --as-cran on a recently-developed package and received only the 'New submission' note. Research here and on R-devel suggested this could be ignored. I also used devtools::build_win() and received no notes or warnings, other than the one mentioned previously. Further, I built the package locally with R CMD build and R CMD INSTALL --build and everything worked as it should, including the PDF manual.
Upon submission to CRAN, I was told that a warning was thrown:
This fails to make its manual:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Missing $ inserted.
<inserted text>
$
l.682 }{}
! Missing } inserted.
<inserted text>
}
l.682 }{}
...
The line appears to be
\widehat{R_1} = \frac{\sum\limits_{i=1}^n{c_i/n}}{\sum\limits_{i=1}^n{L_i/n}}
Additional research here suggests that I use win-builder.r-project.org/ to check my package on the development version and results from that test threw only the "New submission" warning.
I'm at loss. I can't replicate the error that CRAN found an everything appears to work correctly on my machine and on win-builder.r-project.org, too.
Can someone please help me with resolving this issue? I freely admit that I am not a LaTeX expert but given that the line wasn't an issue with R 3.1.2 on windows or the development version on win-build, I don't know where to begin.
Package information is available here:
creelSurvey
I used the inlinedocs package to write my functions and comments. The warning is coming from the .R, line 127:
this function
and the .Rd line 39:
this .Rd
Thanks for your help.

Answer 1

I was able to reproduce this problem on Ubuntu 12.04 with r-devel by cloning the Github repo and running
R CMD build creelSurvey
R CMD check --as-cran BusRouteCreelSurvey_0.2.1.tar.gz
I was able to fix it by removing DOS end-of-line markers (^M or Ctrl-M) from man/SimulateBusRoute.Rd. I don't know the easiest way to do this on Windows (you could look for a dos2unix utility, or possibly come up with a readLines solution.
I don't know how it will work across platforms, but this seems to work for me:
fn <- "MakeAnglers.Rd"
r <- readLines(fn)
writeLines(r[nchar(r)>0],con="new.Rd")
I would (1) look for (possibly obscure) warnings in the R Extensions manual about end-of-line markers and then (2) report this, either to the CRAN maintainers or by posting on r-devel#r-project.org.
In general you should be able to detect these problems if you can set up a test build on a Linux system; I don't know of an equivalent of win-builder.r-project.org for Linux systems, but http://travis-ci.org is a good resource, and this Github project is a good way to get started with R projects on Travis. (Or you can set your project up on R-forge.) I recognize that this might be more of a project than you're looking for right now, just including it for future reference.