[Bioc-devel] proper way to define an S4 method for 'plot'

[Henrik Bengtsson]

Maybe it's related to:

* The plot() S3 generic function is now in package base rather than
package graphics, as it is reasonable to have methods that do not use
the graphics package. The generic is currently re-exported from the
graphics namespace to allow packages importing it from there to
continue working, but this may change in future.

mentioned in the R 4.0.0 NEWS
(https://cran.r-project.org/doc/manuals/r-devel/NEWS.html)?

/Henrik

On Mon, Mar 16, 2020 at 3:52 PM Vincent Carey
<stvjc using channing.harvard.edu> wrote:
>
> I just updated my R and I am getting into trouble with MLInterfaces
> maintenance.
>
> > BiocManager::install("MLInterfaces")
>
> *Bioconductor version 3.11 (BiocManager 1.30.10), R Under development
> (unstable)*
>
> *  (2020-03-15 r77975)*
>
> *Installing package(s) 'MLInterfaces'*
>
> *Warning: unable to access index for repository
> https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0
> <https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0>:*
>
> *  cannot open URL
> 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0/PACKAGES
> <https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0/PACKAGES>'*
>
>
>   There is a binary version available but the source version is later:
>
>              binary source needs_compilation
>
> MLInterfaces 1.67.2 1.67.5             FALSE
>
>
> *installing the source package ‘MLInterfaces’*
>
>
> *trying URL
> 'https://bioconductor.org/packages/3.11/bioc/src/contrib/MLInterfaces_1.67.5.tar.gz
> <https://bioconductor.org/packages/3.11/bioc/src/contrib/MLInterfaces_1.67.5.tar.gz>'*
>
> *Content type 'application/x-gzip' length 1071876 bytes (1.0 MB)*
>
> *==================================================*
>
> *downloaded 1.0 MB*
>
>
> * installing *source* package ‘MLInterfaces’ ...
>
> ** using staged installation
>
> ** R
>
> ** inst
>
> ** byte-compile and prepare package for lazy loading
>
> Error in getGeneric(f, TRUE, envir, package) :
>
>   no generic function found for ‘plot’
>
> Calls: <Anonymous> ... namespaceImportFrom -> .mergeImportMethods ->
> <Anonymous> -> getGeneric
>
> recover called non-interactively; frames dumped, use debugger() to view
>
> ** help
>
> *** installing help indices
>
> ** building package indices
>
> ** installing vignettes
>
> ** testing if installed package can be loaded from temporary location
>
> Error: package or namespace load failed for ‘MLInterfaces’ in getGeneric(f,
> TRUE, envir, package):
>
>  no generic function found for ‘plot’
>
>
> ...
>
>
> > sessionInfo()
>
> R Under development (unstable) (2020-03-15 r77975)
>
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>
> Running under: macOS Mojave 10.14.6
>
>
> Matrix products: default
>
> BLAS:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib
>
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
>
> [1] rmarkdown_2.1
>
>
> loaded via a namespace (and not attached):
>
>  [1] BiocManager_1.30.10 compiler_4.0.0      startup_0.14.0
>
>  [4] tools_4.0.0         htmltools_0.4.0     Rcpp_1.0.3
>
>  [7] codetools_0.2-16    knitr_1.28          xfun_0.12
>
> [10] digest_0.6.25       rlang_0.4.5         evaluate_0.14
>
> --
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