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

[Laurent Gatto]

FYI - I can reproduce this on linux with R Under development (unstable) (2020-03-19 r78011)


________________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Vincent Carey <stvjc using channing.harvard.edu>
Sent: 16 March 2020 23:52
To: bioc-devel
Subject: [Bioc-devel] proper way to define an S4 method for 'plot'

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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fel-capitan%2Fcontrib%2F4.0&data=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615&sdata=7Pq9i9bWYWJ3AaK%2FnGWpAZuvOa0RFGoXLg3cY6XY660%3D&reserved=0
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fel-capitan%2Fcontrib%2F4.0&data=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615&sdata=7Pq9i9bWYWJ3AaK%2FnGWpAZuvOa0RFGoXLg3cY6XY660%3D&reserved=0>:*

*  cannot open URL
'https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fel-capitan%2Fcontrib%2F4.0%2FPACKAGES&data=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615&sdata=BWqDMETTVk7AEYIj1gpfTYDzjsHADvqmqfD6RloDaK4%3D&reserved=0
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fmacosx%2Fel-capitan%2Fcontrib%2F4.0%2FPACKAGES&data=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615&sdata=BWqDMETTVk7AEYIj1gpfTYDzjsHADvqmqfD6RloDaK4%3D&reserved=0>'*


  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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fsrc%2Fcontrib%2FMLInterfaces_1.67.5.tar.gz&data=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615&sdata=yWBq%2BjSD4xvRKkWUKkjoFXuG074hlVcsLSPRiPc5YAc%3D&reserved=0
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fsrc%2Fcontrib%2FMLInterfaces_1.67.5.tar.gz&data=02%7C01%7Claurent.gatto%40uclouvain.be%7C2b8e5941ab5042bd146308d7c9fcc42d%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637199959771328615&sdata=yWBq%2BjSD4xvRKkWUKkjoFXuG074hlVcsLSPRiPc5YAc%3D&reserved=0>'*

*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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