[Bioc-devel] BiocManager::install

Wolfgang Huber wo||g@ng@huber @end|ng |rom emb|@org
Sat May 6 10:39:45 CEST 2023


I am wondering whether:
1. it could be easier to install Bioconductor packages (devel or release) on R-devel (or other non-standard R versions) using BiocManager::install (I may be stirring a hornet’s nest with that:)
2. whether its documentation needs to be updated and/or its implementation could be deconvoluted (hopefully that’s uncontroversial). 

Re the first point, I appreciate that we’re trying to help non-expert users with simple use cases, and that we had/have a lot of trouble with users working with out-of-sync versions. OTOH, the current solution (rigid, confusing documentation, seemingly buggy implementation) seems to be standing in the way for developers, a dichotomy that we do not really want.

Of course, a workaround is
> install.packages("ggtree", repos = c(“@CRAN@", "https://bioconductor.org/packages/3.18/bioc")
and maybe this is just the answer. So far, my workflows have been based on BiocManager::install, but I get (and cannot seem to get rid of):

> BiocManager::install("ggtree", version = "devel")
Error: Bioconductor does not yet build and check packages for R version 4.4; see

> sessionInfo()
R Under development (unstable) (2023-05-05 r84398)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Users/whuber/R.framework/Versions/4.4/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.20 fortunes_1.5-4     

loaded via a namespace (and not attached):
[1] compiler_4.4.0  tools_4.4.0     rstudioapi_0.14

I noted some discussion on this here: https://github.com/Bioconductor/BiocManager/issues/13 but this was 5 years ago.
It appears that the documentation of BiocManager::install mismatches its implementation, and overall the process for something that's conceptually quite simple seems to have become convoluted. 

One of the most helpful documentation resources on this topic btw is https://solutions.posit.co/envs-pkgs/bioconductor/ which cheerfully concludes "Working with BioConductor packages for code development is possible."

Thanks and best wishes

Wolfgang Huber

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