r-project.org> wrote:
Date: Tue, 7 Jan 2020 19:40:02 +
From: Martin Morgan mailto:mtmorgan.b...@gmail.com>>
To: Karl Stamm mailto:karl.st...@gmail.com>>,
"bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>"
mailto:bioc-devel@r-project.org>>
Subj
Hi,
On 1/7/20 10:47, Karl Stamm wrote:
> I was notified recently my package has build errors going in to bioc 3.11.
> So begins the biannual saga of updating everything to see what's new.
> My package has quite a few dependencies, so it's normal for someone to
> change their API and break my scrip
I went on a dependency diet and went from 114 to 87 in devel now.
I would like to trim more, but I think trimming any of the rest would just
be pushing burden over for the user to install packages when they run core
functions, so not very helpful. But if someone spots one I can trim, I'd be
happy
I'm not an expert on macOS, but generally one wants to follow documented R
procedures.
Instructions for installing binary versions of R on macOS, including managing
multiple versions, are provide at
http://mac.r-project.org/man/R-admin.html#Installing-R-under-macOS.
The section about installin
Thanks for the note Karl, and sorry for the break.
For others, the change in DESeq2::lfcShrink is that now type="apeglm"
is the default instead of type="normal".
For the past two releases, users have been getting a message when they
run with the default argument that type="normal" performs worse
I was notified recently my package has build errors going in to bioc 3.11.
So begins the biannual saga of updating everything to see what's new.
My package has quite a few dependencies, so it's normal for someone to
change their API and break my scripted usage. This time a default parameter
changed
