[Rd] Darwinian software development and the library function

Spencer Graves spencer.graves at structuremonitoring.com
Sat Feb 13 20:34:29 CET 2010

Hi, Charlotte:

       I'm with Henrik:  I don't know the global consequences of "print 
= function (...) base::print (...)", but I wouldn't do it.

       Writing "print.foo (x, ...)" may violate your sense of 
aesthetics, but I avoid it.  I've done things like that in the past, 
then changed them to match the standard.  I've also gotten others to 
change their code or agree to let me change it to match the standard.  
As I previously mentioned, some of the code in my "sos" package violates 
a standard.  However, there were more substantive reasons than just 

       I hope you'll entertain other analogies:  If red lipstick is 
required for something I want to support, I'll wear red lipstick, even 
if I think blue would go better with my outfit.  Shaving is a pain in 
the face, and I wore a flaming red beard for a quarter century until it 
finally came in white.  Then I started shaving to avoid projecting the 
image of a broken down old man;  people said I looked 25 years younger.  
(Younger than what?)  You can post a question to r-devel in Urdu or 
Farsi, but I doubt of many people will reply.

       Hope this helps.

On 2/13/2010 7:10 AM, Henrik Bengtsson wrote:
> Hi.
> Here are some guidelines that I find useful:
> - Avoid changing the arguments of generic functions provided by the
> default R packages, especially the ones in base.  Just, accept those
> arguments.  If there are extra arguments you don't like, you can
> always add '...' to your method and they will be accepted/pass the R
> CMD check.
> - Using an S3 generic function that only has '...' arguments seems to
> work well and makes all methods for it pass R CMD check, regardless of
> what arguments you use in your methods.
> - Use R.methodS3 to define your methods, i.e. use setMethodS3("print",
> "foo", function(x, ...) { ... }).  This will check if there is a
> generic function or not, and if missing, it will be created.
> R.methodsS3 was created to make your S3 life easier.
> My $.02
> Henrik
> On Sat, Feb 13, 2010 at 7:40 AM, Charlotte Maia<maiagx at gmail.com>  wrote:
>> Hi Spencer,
>> Sorry, I wasn't very clear in my initial post.
>> The function print.foo (myfoo, ...) won't pass R check (unless one
>> overwrites print first).
>> One has to write print.foo (x, ...), which in my personal opinion, can
>> be problematic.
>> In my oosp package, I have overwritten print (along with a few others).
>> Initially, I overwrote both print and print.default.
>> However now, I merely use print = function (...) base::print (...).
>> Not really a generic, however it acts exactly the same (I think...).
>> Plus Rd documentation still documents print.mymethod in the usual way.
>> kind regards
>> Charlotte
>> On Sat, Feb 13, 2010 at 4:41 AM, spencerg<spencer.graves at prodsyse.com>  wrote:
>>> 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.
>>>      Spencer
>>> 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
>> --
>> Charlotte Maia
>> http://sites.google.com/site/maiagx
>> ______________________________________________
>> R-devel at r-project.org  mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel

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