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[Bioc-devel] Questions about some checks in the latest BiocCheck

4 messages · Casper Peters, Vincent Carey, Kasper Daniel Hansen +1 more

Original
Casper Peters
# 
So in the package I'm developing, I have a few specific use cases that make BiocCheck not so happy.



1:


```

* WARNING: Avoid class()== or class()!= ; use is() or !is()

```

So my first problem arises with checking the classes of objects. I want the interface to be such that I can allow for case insensitivity and/or allow the object to be NULL in some specific cases. This is easier with using `class()` explicitly (especially in the case of case sensitivity).



2:


```

 * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples. The following pages do not:
```

The second problem arises because of some of my exported functions. I made parser+download functions for the Fantom5 data, as this was not available anywhere inside a package yet. Because of the download being big/taking too long, I want to avoid running the checks in R CMD check. For this I added \dontrun{} at the examples, resulting in BiocCheck not liking this.


Other than that I just have some small notes that I still need to take care of, but with these I am not sure what to do.

Thanks in advance,

-Casper
Vincent Carey
# 
Can you provide the repo for your package in development?  These BiocCheck
issues are important and
should be resolved at your end.  We can give some advice on how to get
better results with BiocCheck.
On Wed, Nov 28, 2018 at 10:34 AM Casper Peters <cp100u at hotmail.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Kasper Daniel Hansen
    

    

      
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First, the issue with using class() is that the return is a vector possibly
with >1 element. This _does_ happen.  This is why is() etc is much better,.

Second, why do you need case insensitivity when testing for class. That
makes NO sense to me. You should be testing for a specific (collection) of
class(es).  Not just anything with a random name.


On Wed, Nov 28, 2018 at 10:44 AM Vincent Carey <stvjc at channing.harvard.edu>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Michael Lawrence
    

    

      
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On Thu, Nov 29, 2018 at 8:32 AM Kasper Daniel Hansen

        
<kasperdanielhansen at gmail.com> wrote:

            

      
      
      
    

        
And of course it also considers S4 inheritance.