From therne@u @end|ng |rom m@yo@edu  Mon Jan 13 21:51:19 2020
From: therne@u @end|ng |rom m@yo@edu (Therneau, Terry M., Ph.D.)
Date: Mon, 13 Jan 2020 14:51:19 -0600
Subject: [Rd] as-cran issue, SOLVED
In-Reply-To: <4d4df998-9a1c-ce8b-7abf-7c4bc476165f@gmail.com>
References: <28fddd$d2evua@ironport10.mayo.edu>
 <4d4df998-9a1c-ce8b-7abf-7c4bc476165f@gmail.com>
Message-ID: <28fddd$d2i78g@ironport10.mayo.edu>

Thank you to all who replied with helpful suggestions.?? I had to run off to meetings and 
talks for a bit so am now processing it all.

1. It turns out that the issue was not with coxme, but with bsdmatrix, a package that 
coxme calls.? It just happens to have a function ismat() with the same general purpose and 
some similar variable names, which led me down the rabbit hole.?? That package contained a 
"class(x) == " flaw, now fixed.?? (The fact that bdsmatrix has been stable and unchanged 
for nearly a decade helped with the deception.)

2. As pointed out by Duncan and Kurt, the coxme function also had a class(x)== flaw.? None 
of my test cases triggered this, but since 'x' is an argument that can be supplied by a 
user, it certainly would have happened in package use.? Good catch.

3. Dirk gave good input about the flags in R CMD check and how to find them.?? One more 
line in the "Writing R Extensions" manual would have been helpful, namely that many of the 
options are NOT available in the options() command nor as arguments to R.??? As near as I 
can tell, there is no way to turn on these logic checks within a standard R session.?? A 
desire to do this is where I started: I would have set options(warn=2, error=recover) and 
found the actual offender in a few minutes; and never had to bother all you worthy readers.

4. I agree completely with Martin that errors like this should not be ignored.? In fact, 
except for? "variable may be used before initialized" messages from the C compiler, I have 
become grateful for EVERY complaint that comes out R CMD check.?? Notice the verb "have 
become" -- I did not start out so enthusiastic.

Again, thanks for the help.

Terry T.




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[Rd] as-cran issue, SOLVED
Therneau, Terry M., Ph.D.