[Bioc-devel] IFAA Bioconductor

[Zhigang Li]

Hi Martin,

Thanks for the explanation. We will change all related functions in
MatrixExtra to the following format:
importMethodsFrom(MatrixExtra, crossprod)

Thanks,

Zhigang
https://sites.google.com/view/zlab


On Tue, Jan 16, 2024 at 1:18 PM Martin Morgan <mtmorgan.xyz using gmail.com>
wrote:

> In R-devel I typed
>
>
>
> news()
>
>
>
> and noted
>
>
>
> - The matrix multiplication functions crossprod() and tcrossprod() are now
> also primitive and S3 generic,
>
>
>
> So I wonder if this has changed the 'rules' for how to declare the import
> -- previous behavior was along the lines of 'if the methods are exported,
> then the generic is also (implicitly) exported' and vice versa. I'm guess
> that the generic is no longer exported with the methods, which is how S3
> works. If you're using the methods, then maybe
>
>
>
> importMethodsFrom(MatrixExtra, crossprod)
>
>
>
> if one wants to use the methods. Or, since the S4 generic crossprod is
> defined in the Matrix package,
>
>
>
> importFrom(Matrix, crossprod)
>
>
>
> if one wants to use the S4 generic (e.g., to create a new S4 method).
>
>
>
> This is just a guess, and it's not really clear to me whether this
> behavior apparently associated with the change in crossprod to base is
> intentional or accidental; a post to R-devel might be in order…
>
>
>
> I would avoid import(MatrixExtra) on principle, but perhaps it is a last
> resort.
>
>
>
> Also I'll mention that I could reproduce the problem under R-devel, and
> that changing to importMethodsFrom(MatrixExtra, crossprod) got me past this
> stage (but now I also need to make a change for tcrossprod…)
>
>
>
> Martin Morgan
>
>
>
> *From: *Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
> Zuguang Gu <jokergoo using gmail.com>
> *Date: *Tuesday, January 16, 2024 at 11:49 AM
> *To: *Zhigang Li <lzg2151 using gmail.com>
> *Cc: *bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject: *Re: [Bioc-devel] IFAA Bioconductor
>
> I saw MatrixExtra defines several S4 methods/dispatches for the generic
> `crossprod()` which is actually defined in base.
>
> Maybe you can import the whole MatrixExtra namespace?
>
> import(MatrixExtra)
>
>
>
> On Tue, 16 Jan 2024 at 16:14, Zhigang Li <lzg2151 using gmail.com> wrote:
>
> > Hi There,
> >
> > It seems that the error says :
> > "
> > ** byte-compile and prepare package for lazy loading
> >
> > Error: object ‘crossprod’ is not exported by 'namespace:MatrixExtra'
> >
> > "
> >
> > But we checked and the package "MatrixExtra" still has the function
> > "crossprod". And in the NAMESPACE file, there is a row for
> > "importFrom(MatrixExtra,crossprod)". So we are a bit confused why this
> > error happened. And there was no error for the previous version. Would
> you
> > mind providing some advice? Thanks.
> >
> > Regards,
> > Zhigang
> > https://sites.google.com/view/zlab
> >
> >
> > On Thu, Jan 11, 2024 at 10:11 AM CoreTeam Bioconductor <
> > > bioconductorcoreteam using gmail.com> wrote:
> > >
> > >> Hello Package Maintainer,
> > >>
> > >> We would like to bring to your attention that your package is failing
> in
> > >> devel across all platforms. This is very problematic. Please
> investigate
> > >> the issues and fix the package to avoid deprecation.
> > >>
> > >> https://bioconductor.org/checkResults/devel/bioc-LATEST/
> > >> <
> >
> https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow>
> > >>
> > >> If you have further questions or concerns please reach out on the
> > >> bioc-devel using r-project.org
> > >>
> > >> We appreciate your quick attention to this matter
> > >>
> > >> Cheers,
> > >> On behalf of the Bioconductor Core Team
> > >>
> > >
> >
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> >
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> >
>
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