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

[Kasper Daniel Hansen]

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 using channing.harvard.edu>
wrote:

> 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 using hotmail.com> wrote:
>
> > 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
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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