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

[Michael Lawrence]

On Thu, Nov 29, 2018 at 8:32 AM Kasper Daniel Hansen
<kasperdanielhansen using gmail.com> wrote:
>
> 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,.
>

And of course it also considers S4 inheritance.

> 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]]
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
> > --
> > The information in this e-mail is intended only for th...{{dropped:10}}
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel