[Bioc-devel] writing unit tests for functions in an initializer

[Hervé Pagès]

Yep. And w.r.t. empty objects, make sure new("MyClass") works and
returns a valid object. This should produce an "empty" object.

Note that the explicit constructor function should be named as the
class itself (e.g. MyClass()). It's up to you to decide whether
it should support being called with no arguments (and behave just
like new("MyClass") in that case).

Cheers,
H.

On 09/28/2017 10:13 AM, Michael Lawrence wrote:
> I agree with Kasper. You are better off just leaving initialize() to
> its default implementation. Violating that abstraction for the purpose
> of testing is only going to put your software more at risk, defeating
> the purpose of testing.
>
> Overriding initialize() makes it do more than just set slots, but then
> there's no simple way to just initialize an object with specific slot
> values.
>
> Put another way, if you think of software as an onion of abstraction
> layers, initialize() is at the bottom, and making it do more raises it
> up a level, which is disruptive.
>
> Michael
>
> On Thu, Sep 28, 2017 at 10:00 AM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com> wrote:
>> Ok, this is answering a different question, but the recommendation is to
>> avoid spending time on the initialize method and instead write am explicit
>> constructor function.
>>
>> On Thu, Sep 28, 2017 at 10:48 AM, Zach Skidmore <zskidmor at wustl.edu> wrote:
>>
>>> Hi All,
>>>
>>> I maintain the GenVisR package and am currently converting it to S4
>>> classes. I'm running into a problem however when writing unit tests for
>>> functions within the initalizer. What I really need is a "mock" object of
>>> the class for which the initializer unit tests are being performed but
>>> which hold no data. This will allow me to step through the initializer "sub
>>> functions" and write tests for each one. The problem is I don't see a way
>>> in the S4 system to create a mock object. I've found this post that will do
>>> what I want https://urldefense.proofpoint.com/v2/url?u=http-3A__r.789695.n4.nabble.com_Using-2Da-2Dmock-2Dof-2Dan-2DS4-2Dclass-2D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=E7E1IgOkbh8tTHxd1nMRLxG0TSoO1bPovE9KbCJqkcc&s=09aZdeqljGIeuqC3xMM9jZiWiYiGk8FLCdpazy2oAZ8&e=
>>> td4728547.html, however when using this solution R CMD CHECK throws
>>> errors:
>>>
>>> * checking dependencies in R code ... WARNING
>>> Unexported object imported by a ':::' call: ‘methods:::C_new_object’
>>>    See the note in ?`:::` about the use of this operator.
>>>    Including base/recommended package(s):
>>>    ‘methods’
>>> * checking S3 generic/method consistency ... OK
>>> * checking replacement functions ... OK
>>> * checking foreign function calls ... WARNING
>>> Foreign function call to a base package:
>>>    .Call(methods:::C_new_object, ...)
>>> Packages should not make .C/.Call/.External/.Fortran calls to a base
>>> package. They are not part of the API, for use only by R itself and
>>> subject to change without notice.
>>>
>>> I'm wondering if anyone has any ideas on the best way to handle this. I
>>> suppose i could create a "test" flag within the initalizer that would
>>> create an empty object of that class and use that but it seems hacky to do
>>> this.
>>>
>>> thanks!
>>> Zach
>>>
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-- 
Hervé Pagès

Program in Computational Biology
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