Q:

After running R CMD Check, the mypackage.Rcheck directory with PDF manual disappeared

I have installed Rtools v.31 and MKTeX2.9 on my laptop before building my R package. After I ran R CMD check, a directory called mypackage.Rcheck and the source file mypackage_1.x.tar.gz appeared, and while RStudio build package function is checking everything, there is no warning or error message, but at the end when it said (as follows), the corresponding mypackage.Rcheck directory which is supposed to contain the PDF manual disappeared:

checking PDF version of manual ... OK
DONE
NOTE: There were 3 notes.
See
'C:/.../package/mypackage.Rcheck/00check.log'
for details.

R CMD check succeeded
I thought it might be a version conflict between Rtools and R because I'm using R13.1.2 and Rtools v.31, where on the http://cran.r-project.org/bin/windows/Rtools/ website, it said the image isn't frozen (which I don't understand what it means). But I tried all the suggested compatible version pairs between Rtools and R, and still couldn't get it working. So I think this disappearing of mypackage.RCheck is not due to version conflict. 
I don't think it's MiKTeX problem because apparently pdf is generated, but was consequently removed. I also tried using --options in R CMD check, but there is no way to force generation of pdf manual, plus pdf was generated at one point. I also read one post on this website, suggesting the use of Rutils function Rd2pdf: "R CMD Rd2pdf mypackage", but I can't run in on windows, and Rutils package is not available for R13.1.2. 
can someone suggest the source of the problem or if they have seen this problem before and was able to fix it? 

A:

In RStudio:  Tools -> Global Options -> Packages.  There is a setting "Cleanup output after successful R CMD Check".  If this is checked it removes the package.Rcheck folder after a successful check.  If you uncheck this setting, the package.Rcheck folder is not removed and you will find the reference manual pdf there.

