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....@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-boun...@r-project.org> on behalf of > Zuguang Gu <joker...@gmail.com> > *Date: *Tuesday, January 16, 2024 at 11:49 AM > *To: *Zhigang Li <lzg2...@gmail.com> > *Cc: *bioc-devel@r-project.org <bioc-devel@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 <lzg2...@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 < > > > bioconductorcoret...@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@r-project.org > > >> > > >> We appreciate your quick attention to this matter > > >> > > >> Cheers, > > >> On behalf of the Bioconductor Core Team > > >> > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel