[datatable-help] Playing nice(r) with S4?

[Steve Lianoglou]

Hi,

I think running the tests by invoking the test.data.table from inside
an "Examples" section of an .Rd file are causing some pain.

There are complaints of locked environments:

Error in assign(mname, def, where) :
  cannot add bindings to a locked environment

when defining S4 classes and methods inside the test.data.table function.

Defining the class outside of the function works and lets the tests
pass. Defining functions out there doesn't help, so those tests are
commented out (see lines 552 - 556):

https://github.com/lianos/datatable/blob/master/pkg/R/test.data.table.R

I'm not sure how you feel about this approach, but these work.

IMHO it would be better to use something like testthat or RUnit and
run the test harness for the package with those. I have a feeling we'd
avoid these problems that way. If the devs are willing to consider
that, I'd volunteer to port the tests over.

At any rate, let me know if you're OK with these S4 modifications and
I can commit back to the svn repo.

In summary, I've:

* Added an AllS4.R file to add the setOldClass stuff to include
data.table's in S4 "slots" and defined as(...) methods to convert
data.table to data.frame, and vice versa.

* Modified the namespace to export the data.table class for other
packages to use it.

* Bumped version number in DESCRIPTION to 1.5.2, and added an Imports:
methods to it.

* Made changes to the NEWS file

* Added some tests to test.data.table() function.

I've used this updated package as an import to another package I'm
dev'ing and things seem to work as expected ...

Thanks,
-steve


On Wed, Nov 24, 2010 at 6:01 PM, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
>
> For the setClass call itself that would be ok, and then use the class
> somehow, to test it worked?
>
> setClass("DTS4", representation(info="data.table"))
> test(228, is.data.table(new("DTS4")))
>
>
> On Wed, 2010-11-24 at 14:26 -0500, Steve Lianoglou wrote:
>> Hi,
>>
>> On Wed, Nov 24, 2010 at 2:13 PM, Matthew Dowle <mdowle at mdowle.plus.com> wrote:
>> > Try
>> >
>> >  test(228, setClass("DTS4", representation(info="data.table")), "DTS4")
>>
>> I tried that at first, but you get an error from (I think) defining a
>> new class in the wrong place, specifically:
>>
>> Test 228 Error in assign(mname, def, where) :
>>   cannot add bindings to a locked environment
>>
>> > In test.data.table we only use try() for when the correct result is an
>> > error and the test is that we get the right error message with a grep in
>> > another test just afterwards. Otherwise we can leave test() to try().
>> >
>> > Code that shouldn't fail can just be written (and would cause
>> > test.data.table to stop then and there on error) or inside a test().
>>
>> So, in light of the above problem, would you rather I just write the
>> code that defines the new S4 class and not test that "it worked" since
>> we assume implicitly it works if no error stops test.data.table() form
>> completing?
>>
>> -steve
>>
>
>
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact