Hi, 

I sent this to the Bioconductor mailing list (q.v.), replies recommended this 
forum. Here it is: 
A suggestion. Typically a package provides documentation of two types, one or 
more vignettes and a reference manual; and they have the same file name, 
PackageName.pdf.  When downloaded some file name manipulation is required, or 
accept PackageName(1).pdf.

I suggest the documents be given different names, for example the reference 
manual could be named PackageNameRefMan.pdf. Package checking could enforce the 
rule. 
Jerry 


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