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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