From therneau at mayo.edu  Mon Mar  9 16:29:48 2009
From: therneau at mayo.edu (Terry Therneau)
Date: Mon, 9 Mar 2009 10:29:48 -0500 (CDT)
Subject: [Rd] Package issue
Message-ID: <200903091529.n29FTmg00011@hsrnfs-101.mayo.edu>

> 2. R CMD check gives dozens of warnings ...

 Yes, I see a lot of warnings too, but I think that they can and should be 
ignored.
  1. There is a set where the generic function has "..." and my realization of 
the generic has a named argument.  But this is exactly what the ... is for in a 
generic!  
  
  2. Undocumented objects and classes.  I have a couple to fill in, agreed.  But 
I don't agree with CMD check's admonition to add a page for every instance of a 
method.  For instance diag() for a bdsmatrix is no different than for any other 
matrix, so what is there to document?
  
  I'm willing to be corrected on this.

  3. The 00install.out file showed one mismatched brace in one .Rd file.  I'll 
fix that.
  
  4. The 00check.log file gives a WARNING that the src directory contains object 
files.  This is very odd, since the CMD check process itself put them there.

---

> .... before it stops in gtest.R.  There is no gchol2.R!

 This was my mistake in the original message.  It perhaps comes from trying to 
send something out as I was heading for the door.  My apologies.

  To reprise, my problem was a test (gtest.R) that ran perfectly when the code 
was local, but failed when it was attached as a library.
  To understand the error better I used R CMD INSTALL to create a local library 
and ran the tests there.  The problem was not diag() as I had supposed but 
as.matrix.gchol.  I had forgotton one S3method line in the NAMESPACE file.
 
  The library now loads and tests correctly.  
  
  	Terry T.



[Rd] Package issue
Terry Therneau