[Bioc-devel] EXTERNAL: introducing BiocManager in devel packagepages?

[Martin Morgan]

On 08/06/2018 01:30 AM, Anamaria Elek wrote:
> Hi everyone!
> Now this might be a silly question, but since this is my first time submitting to bioc, please ignore my ignorance. What I’d like to know is this: my package has been accepted, although not yet added to the devel bioc – is it ok if I change biocLite with BiocManager in the Installation section of readme and vignette now, or should I wait for the addition to the Bioconductor git repo before making any new commits to the master branch?

if it has been accepted, then the best thing to do, for this and any 
change, is to wait until it is added to the bioc repository, usually no 
more than a few days after your package is accepted.

Martin


> Thanks in advance,
> Anamaria Elek
> 
> 
> From: Shepherd, Lori
> Sent: 31 July 2018 05:51 PM
> To: jmacdon using u.washington.edu
> Cc: bioc-devel
> Subject: Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel packagepages?
> 
> 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.
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> University of Washington
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