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

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Sep 28 19:00:10 CEST 2017

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 http://r.789695.n4.nabble.com/Using-a-mock-of-an-S4-class-
> 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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