[Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?

[Shepherd, Lori]

We assume most users are using release not devel.  So this page is appropriate for the majority users using release 3.7.  This page is scheduled to be updated when the next release happens and BiocManager goes live in the Bioc3.8 release.


It has been pointed out and we have it as a task to update the useDevel page asap http://www.bioconductor.org/developers/how-to/useDevel/    as this should be updated now for BiocManager.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: James W. MacDonald <jmacdon using uw.edu>
Sent: Tuesday, July 31, 2018 11:24:32 AM
To: Shepherd, Lori
Cc: Tim Triche, Jr.; bioc-devel
Subject: Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?

Well, there's this:

Package Archives

Follow Installation<https://bioconductor.org/install/#install-bioconductor-packages> instructions to use this package in your R session.

And the link for the Installation instructions directs you to the page that says to use biocLite.

Jim



On Tue, Jul 31, 2018 at 10:59 AM, Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:
Yes DropletUtils has a release and a devel page; as most of the Bioconductor package do. The devel pages have been updated for the BiocManager while the release still are BiocInstaller.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Tim Triche, Jr. <tim.triche using gmail.com<mailto:tim.triche using gmail.com>>
Sent: Tuesday, July 31, 2018 10:26:31 AM
To: Shepherd, Lori
Cc: bioc-devel
Subject: Re: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package pages?

Now I am wondering about my sanity... it seems like perhaps DropletUtils has a release package page too?  In any event, looks like things are all set.

thanks!

--t


On Tue, Jul 31, 2018 at 9:21 AM Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org><mailto:Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>>> wrote:

Where exactly did you see this?  It will be up to the package maintainers to update their package documentation (vignettes and such).  We have updated the devel package landing pages to include the new BiocManager instructions already:


https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org><mailto:bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>>> on behalf of Tim Triche, Jr. <tim.triche using gmail.com<mailto:tim.triche using gmail.com><mailto:tim.triche using gmail.com<mailto:tim.triche using gmail.com>>>
Sent: Tuesday, July 31, 2018 9:14:24 AM
To: bioc-devel
Subject: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package pages?

So I was looking at DropletUtils and stumbled on this:

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DropletUtils")


It seems like maybe devel might be a sensible place to start migrating
users to BiocManager::install(...).  Thoughts?

--t

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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099


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