Re: [R] Unit Testing Frameworks: summary and brief discussion

From: Paul Gilbert <pgilbert_at_bank-banque-canada.ca>
Date: Wed, 09 May 2007 21:18:02 -0400

Tony

Thanks for the summary.

My ad hoc system is pretty good for catching flagged errors, and numerical errors when I have a check. Could you (or someone else) comment on how easy it would be with one of these more formal frameworks to do three things I have not been able to accomplish easily:

Paul Gilbert

anthony.rossini_at_novartis.com wrote:
> Greetings -
>
> I'm finally finished review, here's what I heard:
>
> ============ from Tobias Verbeke:
>
> anthony.rossini_at_novartis.com wrote:

>> Greetings!
>>
>> After a quick look at current programming tools, especially with regards 

>
>> to unit-testing frameworks, I've started looking at both "butler" and 
>> "RUnit".   I would be grateful to receieve real world development 
>> experience and opinions with either/both.    Please send to me directly 
>> (yes, this IS my work email), I will summarize (named or anonymous, as 
>> contributers desire) to the list.
>>

> I'm founding member of an R Competence Center at an international
> consulting company delivering R services
> mainly to the financial and pharmaceutical industries. Unit testing is
> central to our development methodology
> and we've been systematically using RUnit with great satisfaction,
> mainly because of its simplicity. The
> presentation of test reports is basic, though. Experiences concerning
> interaction with the RUnit developers
> are very positive: gentle and responsive people.
>
> We've never used butler. I think it is not actively developed (even if
> the developer is very active).
>
> It should be said that many of our developers (including myself) have
> backgrounds in statistics (more than in cs
> or software engineering) and are not always acquainted with the
> functionality in other unit testing frameworks
> and the way they integrate in IDEs as is common in these other languages.
>
> I'll soon be personally working with a JUnit guru and will take the
> opportunity to benchmark RUnit/ESS/emacs against
> his toolkit (Eclipse with JUnit- and other plugins, working `in perfect
> harmony' (his words)). Even if in my opinion the
> philosophy of test-driven development is much more important than the
> tools used, it is useful to question them from
> time to time and your message reminded me of this... I'll keep you
> posted if it interests you. Why not work out an
> evaluation grid / check list for unit testing frameworks ?
>
> Totally unrelated to the former, it might be interesting to ask oneself
> how ESS could be extended to ease unit testing:
> after refactoring a function some M-x ess-unit-test-function
> automagically launches the unit-test for this particular
> function (based on the test function naming scheme), opens a *test
> report* buffer etc.
>
> Kind regards,
> Tobias
>
> ============ from Tony Plate:
>
> Hi, I've been looking at testing frameworks for R too, so I'm interested
> to hear of your experiences & perspective.
>
> Here's my own experiences & perspective:
> The requirements are:
>
> (1) it should be very easy to construct and maintain tests
> (2) it should be easy to run tests, both automatically and manually
> (3) it should be simple to look at test results and know what went wrong
> where
>
> I've been using a homegrown testing framework for S-PLUS that is loosely
> based on the R transcript style tests (run *.R and compare output with
> *.Rout.save in 'tests' dir). There are two differences between this
> test framework and the standard R one:
> (1) the output to match and the input commands are generated from an
> annotated transcript (annotations can switch some tests in or out
> depending on the version used)
> (2) annotations can include text substitutions (regular expression
> style) to be made on the output before attempting to match (this helps
> make it easier to construct tests that will match across different
> versions that might have minor cosmetic differences in how output is
> formatted).
>
> We use this test framework for both unit-style tests and system testing
> (where multiple libraries interact and also call the database).
> One very nice aspect of this framework is that it is easy to construct
> tests -- just cut and paste from a command window. Many tests can be
> generated very quickly this way (my impression is that is is much much
> faster to build tests by cutting and pasting transcripts from a command
> window than it is to build tests that use functions like all.equal() to
> compare data structures.) It is also easy to maintain tests in the face
> of change (e.g., with a new version of S-PLUS or with bug fixes to
> functions or with changed database contents) -- I use ediff in emacs to
> compare test output with the stored annotated transcript and can usually
> just use ediff commands to update the transcript.
>
> This has worked well for us and now we are looking at porting some code
> to R. I've not seen anything that offers these conveniences in R.
>
> It wouldn't be too difficult to add these features to the built-in R
> testing framework, but I've not had success in getting anyone in R core
> to listen to even consider changes, so I've not pursued that route after
> an initial offer of some simple patches to tests.mk and wintests.mk.
>
> RUnit doesn't have transcript-style tests, but it wasn't very difficult
> to add support for transcript-style tests to it. I'll probably go ahead
> and use some version of that for our porting project. (And offer it to
> the community if the RUnit maintainers want to incorporate it.) I also
> like the idea that RUnit has some code analysis tools -- that might
> support some future project that allowed one to catalogue the number of
> times each code path through a function was exercised by the tests.
>
> I just looked at 'butler' and it looks very much like RUnit to me -- and
> I didn't see any overview that explained differences. Do you know of
> any differences?
>
> cheers,
>
> Tony Plate
>
>
> ============== from Paul Gilbert:
>
> Tony
>
> While this is not exactly your question, I have been using my own system
> based on make and the tools use by R CMD build/check to do something I
> think of as unit testing. This pre-dates the unit-testing frameworks, in
> fact, some of it predates R. I actually wrote something on this at one
> point: Paul Gilbert. R package maintenance. R News, 4(2):21-24,
> September 2004.
>
> I have occasionally thought about trying to use RUnit, but never done
> much because I am relatively happy with what I have. (Inertia is an
> issue too.) I would be happy to hear if you do an assessment of the
> various tools.
>
> Best,
> Paul Gilbert
>
>
> ============= From Seth Falcon:
>
> Hi Tony,
>
> anthony.rossini_at_novartis.com writes:
>> After a quick look at current programming tools, especially with regards 

>
>> to unit-testing frameworks, I've started looking at both "butler" and 
>> "RUnit".   I would be grateful to receieve real world development 
>> experience and opinions with either/both.    Please send to me directly 
>> (yes, this IS my work email), I will summarize (named or anonymous, as 
>> contributers desire) to the list.

>
> I've been using RUnit and have been quite happy with it. I had not
> heard of butler until I read your mail (!).
>
> RUnit behaves reasonably similarly to other *Unit frameworks and this
> made it easy to get started with as I have used both JUnit and PyUnit
> (unittest module).
>
> Two things to be wary of:
>
> 1. At last check, you cannot create classes in unit test code and
> this makes it difficult to test some types of functionality. I'm
> really not sure to what extent this is RUnit's fault as opposed
> to limitation of the S4 implemenation in R.
>
> 2. They have chosen a non-default RNG, but recent versions provide a
> way to override this. This provided for some difficult bug
> hunting when unit tests behaved differently than hand-run code
> even with set.seed().
>
> The maintainer has been receptive to feedback and patches. You can
> look at the not-so-beautiful scripts and such we are using if you look
> at inst/UnitTest in: Category, GOstats, Biobase, graph
>
> Best Wishes,
>
> + seth
>
>
> =================== Discussion:
>
> After a bit more cursory use, it looks like RUnit is probably the right
> approach at this time (sorry Hadley!). Both RUnit and butler have a
> range of testing facilities and programming support tools. I support the
> above statements about feasibility and problems -- except that I didn't
> get a chance to checkout the S4 issues that Seth raised above. The one
> piece that I found missing in my version was some form of GUI based
> tester, i.e. push a button and test, but I think I've not thought through
> some of the issues with environments and closures yet that might cause
> problems.
>
> Thanks to everyone for responses! It's clear that there is a good start
> here, but lots of room for improvement exists.
>
> Best regards / Mit freundlichen Grüssen,
> Anthony (Tony) Rossini
> Novartis Pharma AG
> MODELING & SIMULATION
> Group Head a.i., EU Statistical Modeling
> CHBS, WSJ-027.1.012
> Novartis Pharma AG
> Lichtstrasse 35
> CH-4056 Basel
> Switzerland
> Phone: +41 61 324 4186
> Fax: +41 61 324 3039
> Cell: +41 79 367 4557
> Email : anthony.rossini_at_novartis.com
>
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>
>
>
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