[Bioc-devel] BiocManager updates / changes

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This is an ongoing effort to replace any outdated BiocInstaller,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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