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

[Michael Lawrence]

At least with 2020-03-16 r77987 (Mac OS) I wasn't able to reproduce this.
Btw, there's no real need for an S4 method in this case. An S3 method would
work just as well.

On Mon, Mar 16, 2020 at 4:12 PM Henrik Bengtsson <henrik.bengtsson using gmail.com>
wrote:

> 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
> >
> > --
> > The information in this e-mail is intended only for th...{{dropped:6}}
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla using gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

	[[alternative HTML version deleted]]