[Bioc-devel] BiocManager updates / changes

[Marcel Ramos]

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This is an ongoing effort to replace any outdated BiocInstaller,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
>>>
>>>
>>> This email message may contain legally privileged
>>> and/or...{{dropped:2}}
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
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>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
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