[Bioc-devel] BiocManager now on CRAN
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}}
>
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[Bioc-devel] New DESCRIPTION fields in build products
This is an FYI on some changes made to the build products and VIEWS files. The build system code was recently modified to add 5 new fields to the DESCRIPTION file of the build products. These fields only appear in the built tarball or binary (not source code) and are parsed into the VIEWS files. The data in VIEWS are used for building parts of the website such as landing pages, badges, etc. The new fields: git_url: The url for the source code on the git server. git_branch: The git branch (master or RELEASE_3_7). git_last_commit: Last git commit hash. git_last_commit_date: Last git commit date. Date/Publication: Date the built package was propagated to the repo and became available via biocLite(). The VIEWS files for devel: https://bioconductor.org/packages/devel/bioc/VIEWS https://bioconductor.org/packages/devel/workflows/VIEWS https://bioconductor.org/packages/devel/data/experiment/VIEWS The VIEWS file is only updated when a package is propagated (version bump). To make these fields available in the devel VIEWS, we force propagated all devel packages. We did not do the same for release because of consistency issues with 'Date/Publication'. Because of this, the devel VIEWS has the fields for all packages but release VIEWS has them only for packages that had a version bump. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] New Package Submission Tracker
Sorry for the delay. The single package builder was down for updates last week and it slipped through undetected. We have remedied the situation and you should be assigned a reviewer shortly. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Hien To Sent: Tuesday, June 19, 2018 11:05:00 PM To: Shepherd, Lori; bioc-devel@r-project.org Subject: Re: [Bioc-devel] New Package Submission Tracker Hi I've submitted a new package (issues #774) on that day (14/06) and it still doesn't have any label such as 1. awaiting moderation. Just wondering if it was this problem, or something I've done wrong with the submission. Thanks for your help. Hien From: Bioc-devel on behalf of Shepherd, Lori Sent: Thursday, 14 June 2018 10:17:56 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] New Package Submission Tracker The Single Package Builder for new package submissions is experience some intermittent connectivity issues. We are working on the issue and hope to have it resolved soon. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
