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

[Shepherd, Lori]

Not sure if its worth mentioning but I saw this type of ERROR when we first started the release in R 4.0.0  when S3 plot functions were not defined in the NAMESPACE. http://bioconductor.org/developers/how-to/troubleshoot-build-report/#s3method

But it could also be from  plot() generic moving from graphics to base


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Martin Morgan <mtmorgan.bioc using gmail.com>
Sent: Tuesday, March 17, 2020 1:33 AM
To: Michael Lawrence <lawrence.michael using gene.com>; Henrik Bengtsson <henrik.bengtsson using gmail.com>
Cc: bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] proper way to define an S4 method for 'plot'

We'll discuss this and other issues at the developer forum on Thursday (12pm US Eastern) https://stat.ethz.ch/pipermail/bioc-devel/2020-March/016347.html.

The builds are a really big mess at the moment http://bioconductor.org/checkResults/3.11/bioc-LATEST/, with many changes in R-devel causing often easy-to-fix changes. We need developers to step forward and fix their packages.

A variant of the plot generic change I saw while troubleshooting the graph package was due to a stale version of Rgraphviz, installed before the move of the generic. It was resolved by re-installing Rgraphviz, but then I see

> requireNamespace("Rgraphviz")
Loading required namespace: Rgraphviz
Warning message:
multiple methods tables found for ‘plot’

which I am still working to resolve. I'll bump Rgraphviz version number to force re-installation when I'm sure I've got everything figured out.

Martin

On 3/16/20, 7:37 PM, "Bioc-devel on behalf of Michael Lawrence via Bioc-devel" <bioc-devel-bounces using r-project.org on behalf of bioc-devel using r-project.org> wrote:

    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

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