[Bioc-devel] BiocManager updates / changes

[Marcel Ramos]

Dear Bioc-devs,

We have successfully completed the migration from BiocInstaller to
BiocManager.
Together, we modified about 570 packages that were using old
BiocInstaller code.

Please ensure that your package(s) install / build / check without
errors and that all
dependencies are properly documented in the DESCRIPTION file.

If you have any issues with your package related to our BiocManager
commits. Feel
free to reach out to me.


Thank you all for your continued cooperation.


Best regards,

Marcel


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

On 08/31/2018 01:28 PM, Marcel Ramos wrote:
> Dear bioc-devs,
>
> Thank you to all maintainers who have made appropriate changes to their
> packages *in devel*.
>
> This is an ongoing effort to replace any outdated BiocInstaller,
> biocLite, etc.
> code from packages as we transition to `BiocManager` before the next
> release.
>
> You may have noticed a recent commit to your package. These commits are
> the result
> of a script to automatically replace a set number of lines of code with
> BiocManager code.
>
> These lines include `library(BiocInstaller)`,
> `source("https://bioconductor.org/biocLite.R")`, and
> `biocLite("pkgname")`.
>
> All in all, we have changed about 314 packages from about 578 packages.
> There are still
> about 264 packages left with `BiocInstaller` and `biocLite` calls.
>
> Please DO ensure that:
>
>     * The language around these new changes is in concordance with the
> actual code
>
>     * You update your package to use BiocManager, if you haven't already
>
>     * Your package is building and dependencies are accounted for
>
>
> For a list of outstanding packages please see:
> https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
>
> For example code see devel landing pages such as:
> http://bioconductor.org/packages/devel/bioc/html/RaggedExperiment.html
>
>
> Best regards,
> Marcel
>
> --
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
>
> On 07/13/2018 05:11 PM, Marcel Ramos wrote:
>> 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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>>
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