Hi Leo,
Thanks for bringing that up and making those changes.
We wanted to emphasize software packages first and then address experiment
data and workflow packages since they are fewer anyhow.
I will be adding those as additional files in the gist.
To update experiment data packages, the comman
Hi Marcel,
I noticed that https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653
doesn't include the experiment data and workflow packages. I updated
mine preemptively (derfinderData and recountWorkflow).
By the way, how do I sync experiment data package updates? I forgot
how to do so.
Ah, of course. I should have realized that. Makes sense. I'll get that
fixed in devel soon.
Thanks and sorry for the noise.
~G
On Mon, Jul 16, 2018 at 9:37 AM, Marcel Ramos
wrote:
> Hi Gabe,
>
> Please note that we are only making changes to packages in *bioc-devel*.
>
> BiocManager wouldn't fa
Hi Gabe,
Please note that we are only making changes to packages in *bioc-devel*.
BiocManager wouldn't fail for users with earlier versions of R because
it doesn't apply to them. These users
should be using the respective bioc-release versions and consequently
`BiocInstaller`.
BiocManger is curr
Marcel et al,
My genbankr package is one of the ones that mentions biocLite (in
README.md, actually, not the vignette proper, but still...). Historically
this was just because I had missed your email and hadn't updated it, but
when I sat down to do it I ran into an issue:
BiocManager, while a hug
Hi Jason,
Please check all of your package files and not just the vignette.
The criteria involve a simple `grep` search of all package files for
the words `biocLite` and `BiocInstaller`.
~/Bioconductor/ClusterSignificance (master) $ grep -rn "biocLite" *
README.md:52:source("https://bioconductor
Hello Marcel,
I notice that the package I maintain, ClusterSignificance, is included in this
list although I am unsure why. In your previous mail you say:
After the next couple of weeks or so, we will be identifying packages in
bioc-devel (3.8) that still
mention BiocInstaller / biocLite.
I don
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 pack
ew York 14263
From: Bioc-devel on behalf of Joris Meys
Sent: Thursday, June 21, 2018 4:06:11 AM
To: Ramos Perez, Marcel
Cc: bioc-devel
Subject: Re: [Bioc-devel] BiocManager now on CRAN
Dear Marcel,
A big thanks to you and the entire bioconductor team. I will spread t
Dear Marcel,
A big thanks to you and the entire bioconductor team. I will spread the
word among my colleagues. I also noticed that the installation instructions
aren't adapted yet on the bioconductor site (
https://www.bioconductor.org/install/). Probably I'm just rushing here and
you are working
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/packag
11 matches
Mail list logo
