Building R package: make pdf & _masked_by_GlobalEnv
I am assembling an R package (under Windows XP, R v.2.3) and have a very basic question. Running R CMD build does not generate a pdf. R CMD check generates a .dvi, but I cannot figure out how to automatically create the pdf. I thought from reading the "writing r extensions' manual that R CMD build was supposed to generate the pdf. I am having no success using various permutations of the Rd2dvi and texi2dvi, and I'm a bit frustrated. I have miktex 2.4, which should (I thought) have the necessary pdftex tools to do this. Maybe it does; I definitely have various directories named 'dvipdfm', 'pdftex', etc on my computer, but I have no idea whether there might be a problem.
You need to give a bit more detail. What is the .pdf being created from? What do things look like when you run a build? Does install work?
I guess I'm not sure what the .pdf is being created from - I don't know how this works. I assumed that my set of .Rd files from the man dir would automatically be converted into .pdf, much like 'check' reads them into a dvi document. When I run a build, I get an archive with all of my .R source files, the DESCRIPTION, the .Rd files, my datafiles, and any documentation I've placed in inst/doc. When I install this from CMD, the html help & chtml files compile, examples are copied from the /man directory to their own .Rd files, and everything - to me - appears OK. 'Install' from R CMD works with no problem - it warns me that my 'examples' directory is empty, but it proceeds to create the examples from my .Rd files anyway. I only get a .dvi manual when running 'check'.
When I install the package, I receive the message that most of my functions are "masked _by_ .GlobalEnv". I have no idea what this means; I'm sure that this is amply documented, but I confess that I have a rather difficult time with much of the documentation on writing packages.
This means that you have variables in your workspace with the same names as ones in your package. You probably want to clean out your workspace, because most uses will find those versions before the ones in the package -- and that really messes up testing, etc.
thanks for the clarification!