[Bioc-devel] BiocManager::install

[Vincent Carey]

Thanks for these observations Wolfgang, I am glad I read to the end,
because as you say,

https://solutions.posit.co/envs-pkgs/bioconductor/

has lots of interesting information.  As I personally have no
experience with renv or Connect
much of the motivating detail is opaque to me.

I would question the proposition

"Given the structural differences between BioConductor and CRAN
repositories, it is not straightforward to work with both types. "

with at least 10 years of history of effective usage of both together
by many hundreds of users.  "Straightforward" is
subjective.  The existence of some shortcomings, like the specific
ones you mention, is acknowledged, and setting
up priorities to ameliorate them would be worthwhile.  Part of the
prioritization would need to be based on user
data and user experiences.  In the case of this posit.co article, what
is known about the significance of Connect
for genomic data science?  I have not had great difficulty publishing
apps to shinyapps.io that use Bioconductor
and CRAN, but perhaps it can be made easier if that is a key concern.

The problem of smoothly supporting multiple versions of R/Bioc
simultaneously is also acknowledged.  At this
time we do not have sufficient resources to make a big charge in the
direction of increasing support for this
"use case".  Users and sysadmins with sufficient expertise can
definitely accomplish much in this area, see
https://bioconductor.org/about/release-announcements/ for the map of
resources supporting this going back to
2005.  If there is a way to simplify this by using recently developed
package management strategies is would
be good to know and document.

This is a good place to continue the discussion from a developer's
perspective, but how can we get more
input from non-developer users?  And from posit.co?

"Publishing Shiny Apps that make use of BioConductor packages to
Connect is not possible for this setup.
BiocManager::install() temporarily adds the BioConductor repository
for the duration of the install process.
During the publishing process rsconnect no longer has any knowledge
about BioConductor." -- is this something
that can be remedied in BiocManager?  Are we able to test Connect for
this use case?


On Sat, May 6, 2023 at 4:40 AM Wolfgang Huber <wolfgang.huber using embl.org> wrote:
>
> 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
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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