[Bioc-devel] BiocManager now on CRAN

[Marcel Ramos]

Dear bioc-devs,

About 4 weeks ago, I notified maintainers to make changes to their
bioc-devel vignettes and package code to support the use of `BiocManager`.

There are a number of packages that haven't made the transition in
Bioc-devel.

Please see this GitHub gist for a list of outstanding packages:

https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653

Best regards,

Marcel

Bioconductor Core Team
Roswell Park Cancer Institute
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


On 06/20/2018 12:23 PM, Marcel Ramos wrote:
> Dear bioc-devs,
>
>
> A month ago we notified you about our "next generation" changes to
> BiocInstaller.
>
> Thanks to all beta testers and those who provided feedback and
> suggestions for a new package name.
>
>
> I am pleased to inform you that BiocManager is now on CRAN:
> https://cran.r-project.org/web/packages/BiocManager/index.html
>
>
> As mentioned in our last email, you can now install BiocManager using:
>
> ```
> install.packages("BiocManager")
> BiocManager::install("YourPackageNameHere")
> ```
>
> Action Item:
>
>     -   Please modify the vignettes in your bioc-devel packages to
> reflect the use of BiocManager
>
>
> After the next couple of weeks or so, we will be identifying packages in
> bioc-devel (3.8) that still
> mention BiocInstaller / biocLite.
>
>
> Best regards,
> Marcel
>
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Dept. of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
>
>
> On 05/09/2018 06:11 PM, Martin Morgan 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")
>>    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
>>
>>
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>>
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>
>
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