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-boun...@r-project.org> on behalf of Martin Morgan <mtmorgan.b...@gmail.com> Sent: Tuesday, March 17, 2020 1:33 AM To: Michael Lawrence <lawrence.mich...@gene.com>; Henrik Bengtsson <henrik.bengts...@gmail.com> Cc: bioc-devel <bioc-devel@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-boun...@r-project.org on behalf of bioc-devel@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.bengts...@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 > <st...@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@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 micha...@gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. 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