[Bioc-devel] BiocInstaller: next generation

[Martin Morgan]

On 05/11/2018 03:33 AM, Lluís Revilla wrote:
> Dear Bioconductor team,
> 
> Bioconductor packages can be installed via install.packages when they 
> are a dependency of another package if there is in the DESCRIPTION file 
> a "biocViews:" section (see 
> https://github.com/r-lib/devtools/issues/700#issuecomment-235127291 
> <https://github.com/r-lib/devtools/issues/700#issuecomment-235127291>) .
> I don't know how install.packages handles these packages in Bioconductor 
> but would it be possible to use this trick to directly install the 
> packages in Bioconductor?

biocLite() actually user install.packages(). the 'trick' is to have the 
correct 'repos' argument. In essence that is what biocLite() / 
BiocManager::install() does -- sets the repository argument to include 
the location where Bioconductor version x is available for R version y.

Users of base R can `setRepositories()`; then install.packages() 
installs Bioconductor packages. The problem is that the version of 
Bioconductor installed by this approach is hard-coded in R, so the user 
gets the version of Bioc available at the time of the release of R, 
rather than the most recent version available for their version of R. 
After setRepositories() and selecting all bioc options, in my 'devel' 
install I have

 > getOption("repos")
                                                    CRAN
                                                "@CRAN@"
                                                BioCsoft
            "https://bioconductor.org/packages/3.7/bioc"
                                                 BioCann
"https://bioconductor.org/packages/3.7/data/annotation"
                                                 BioCexp
"https://bioconductor.org/packages/3.7/data/experiment"

whereas I actually want

 > BiocManager::repositories()
                                                BioCsoft
            "https://bioconductor.org/packages/3.8/bioc"
                                                 BioCann
"https://bioconductor.org/packages/3.8/data/annotation"
                                                 BioCexp
"https://bioconductor.org/packages/3.8/data/experiment"
                                           BioCworkflows
       "https://bioconductor.org/packages/3.8/workflows"
                                                    CRAN
                              "https://cran.rstudio.com"


install.packages() does not pay attention to biocViews; the comment you 
reference is incorrect (here's the sole reference to 'biocViews' in the 
R source code: 
https://github.com/wch/r-source/blob/3137a19986dfa547eba59b46ed8dc02b0dbf888c/src/library/tools/R/utils.R#L1249)

> 
> What will happen with BiocInstaller package? The package has the same 
> description and purpose of the proposed new package.
> Wouldn't be better to move this new functionality to BiocInstaller and 
> move it to CRAN?

Package names need to be unique across CRAN and Bioconductor, so there 
can only be one BiocInstaller. BiocInstaller as it exists in 
Bioconductor supports two different interfaces to package management 
already ('legacy' biocLite, plus more recent BiocInstaller::biocLite()) 
and has 15 years of code; it is better to start with a clean implementation.

Martin

> Best,
> 
> Lluís
> 
> 
> 
> On 10 May 2018 at 00:11, Martin Morgan <martin.morgan at roswellpark.org 
> <mailto:martin.morgan at roswellpark.org>> wrote:
> 
>     Developers --
> 
>     A preliminary heads-up and request for comments.
> 
>     Almost since project inception, we've used the commands
> 
>        source("https://bioconductor.org/biocLite.R
>     <https://bioconductor.org/biocLite.R>")
>        biocLite(pkgs)
> 
>     to install packages. This poses security risks (e.g., typos in the
>     url) and deviates from standard R package installation procedures.
> 
> 
>     We'd like to move to a different system where a base package, call
>     it 'BiocManager', is installed from CRAN and used to install
>     Bioconductor packages
> 
>        if (!"BiocManager" %in% rownames(installed.packages()))
>            install.packages("BiocManager")
>        BiocManager::install(pkgs)
> 
>     This establishes a secure chain from user R session to Bioconductor
>     package installation. It is also more consistent with base R package
>     installation procedures.
> 
>     BiocManager exposes four functions
> 
>        - install() or update packages
> 
>        - version() version of Bioconductor in use
> 
>        - valid() are all Bioconductor packages from the same
>     Bioconductor version?
> 
>        - repositories() url location for Bioconductor version-specific
>     repositories
> 
>     install() behaves like biocLite(), using the most current version of
>     Bioconductor for the version of R in use. It stores this state using
>     a Bioconductor package 'BiocVersion', which is nothing more than a
>     sentinel for the version in use. One can also 'use devel' or a
>     particular version of Bioconductor (consistent with the version of
>     R) with
> 
>        BiocManager::install(version = "3.8")   # or the synonym "devel"
> 
> 
>     We intend to phase this in over several release cycles, and to
>     continue to support the traditional biocLite() route for versions
>     before BiocManager becomes available.
> 
>     We also intend to change the overall versioning of 'Bioconductor'
>     itself, where releases are always even (3.8, 3.10, 3.12, ...) and
>     'devel' always odd.
> 
>     Obviously this is a large change, eventually requiring updates to
>     many locations on our web site and individual vignettes.
> 
> 
>     Of course the key question is the name of the 'BiocManager' package.
>     It cannot easily be 'BiocInstaller', because of the differences in
>     way CRAN and Bioconductor version packages. Some possible names are
>     '
>     BiocInstall::install()
>     BiocPackages::install()
>     BiocManager
>     BiocMaestro
> 
> 
>     Your comments are welcome...
> 
>     Martin
> 
> 
>     This email message may contain legally privileged and/or...{{dropped:2}}
> 
>     _______________________________________________
>     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> 
> 


This email message may contain legally privileged and/or...{{dropped:2}}