Hi,
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
```{r}
> 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):
```{r}
> options(BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE)
> BiocManager::install("ggtree", version = "devel")
Error: Bioconductor does not yet build and check packages for R version 4.4; see
https://bioconductor.org/install
> 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
locale:
[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
--
Wolfgang Huber
EMBL
https://www.embl.org/groups/huber
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