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: jmac...@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 <jmac...@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.sheph...@roswellpark.org<mailto:lori.sheph...@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.tri...@gmail.com<mailto:tim.tri...@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.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org><mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org><mailto:bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>>>
on behalf of Tim Triche, Jr.
<tim.tri...@gmail.com<mailto:tim.tri...@gmail.com><mailto:tim.tri...@gmail.com<mailto:tim.tri...@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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