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List: bioc-devel
Subject: [Bioc-devel] BiocManager updates / changes
From: Marcel Ramos <marcel.ramosperez () roswellpark ! org>
Date: 2018-08-31 17:28:49
Message-ID: a9e0b62c-d576-a60a-1427-9190f6e6cc4d () roswellpark ! org
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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This is an ongoing effort to replace any outdated BiocInstaller,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@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:4}}
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
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