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