Re: [Bioc-devel] IFAA Bioconductor

2024-01-16 Thread Martin Morgan
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,

Re: [Bioc-devel] IFAA Bioconductor

2024-01-16 Thread Zuguang Gu
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 wrote: > Hi There, > > It seems that the error says : >

Re: [Bioc-devel] IFAA Bioconductor

2024-01-16 Thread Ramos Perez, Marcel via Bioc-devel
Hi Zhigang, AFAICT, I don't see `crossprod` as an exported symbol in `MatrixExtra`. > library(MatrixExtra) > ls("package:MatrixExtra") Did you mean Matrix:: or base:: crossprod? Best regards, Marcel On 1/16/24 10:14 AM, Zhigang Li wrote: Hi There, It seems that the error says : " **

Re: [Bioc-devel] IFAA Bioconductor

2024-01-16 Thread Zhigang Li
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

Re: [Bioc-devel] Deprecation Request for openPrimeRui

2024-01-16 Thread Kern, Lori via Bioc-devel
Yes I will take care of the deprecation. Thank you for letting us know. If you change your mind, please remember to request un-deprecation here. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm &