[Rd] Darwinian software development and the library function

spencerg spencer.graves at prodsyse.com
Fri Feb 12 16:41:03 CET 2010

Hi, Charlotte: 

      I'm not sure what you mean.  If you mean writing something like 
"print.foo (myfoo, ...)", this is relatively benign I suppose, but I 
avoid it where feasible.  On multiple occasions, I've pushed 
collaborators and even maintainers of other packages to change this or 
allow me to change it to conform to the standard;  if my memory is 
correct, there have been several violations of this standard in the 
"fda" package, which are no longer there because I changed them.  If a 
user with an object "x" of class "foo" writes print(x=x) or 
print(foo=x), I'm not sure what it would do, but it might not be what 
you want. 

      My "sos" package masks "?".  However, I don't like it.  I 
generally consider such to be potentially user hostile, and whenever 
feasible, I prefer to avoid such code.  I did it in this case for a 
couple of reasons.  First, using "?" (actually "???") seems so much 
easier to remember than "findFn" that it justifies this transgression of 
standard protocol.  Second, one of the leading figures in the R 
community (Duncan Murdoch) contributed suggested we do this and 
contributed the code. 

      If you change the definition of "print" itself, that seems to me 
to be a much bigger issue, with consequences much more difficult to 
predict.  If someone else also overwrites "print" making it different 
and incompatible with yours, then your code may not work or theirs may 
not, depending on which gets loaded first in the search path.  Worse, 
your code cannot possibly have been tested as thoroughly as the standard 
code.  If your code includes a subtle bug that only occurs under special 
circumstances, it may be hard for the person experiencing the problem to 
find, because they don't expect it. 

      Hope this helps.

Charlotte Maia wrote:
> Hi all,
> Legend has it, that polite R programmers don't overwrite, say, the
> print function.
> However, this seems quite un-Darwinian to me (especially given that I
> don't want to call all my arguments x and y).
> I might want a function print.foo (myfoo, ...).
> So I decided to be very impolite (in one of my packages) and overwrite
> a few standard generics.
> Plus, to the best of my knowledge it doesn't interfere with normal use (yay...).
> This brings us to the library function.
> Which by default gives a whole lot of warnings loading my package (and
> any other package that does something similar), scaring off polite R
> programmers and perhaps some mainstream R users.
> I'm starting to think that the default for library, should be
> warn.conflicts=FALSE.
> However, just reading the documentation, I noticed a reference to
> something called .conflicts.OK.
> Not sure what that does, however if it does what it sounds like, then
> it largely fixes the problem.
> The biggest issue though, is whether or not one should be impolite
> (i.e. Darwinian) and overwrite print etc in the first place...?
> I'm inclined to go in favour of overwriting the functions.
> However, it has the potential to introduce some technical problems.
> Other's opinions appreciated.
> kind regards

Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph:  408-655-4567

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