On 10/15/2015 11:24 AM, Michael Lawrence wrote:
Btw, a subtle issue here is that elementLengths currently calls NROW(),
not length(), and code might be relying on DataFrameList returning row
counts. That behavior has proven convenient, so it would be nice not to
lose it. I guess nrow() already do
Hi Michael,
On 10/15/2015 10:08 AM, Michael Lawrence wrote:
Tangentially related, it seems like nchar is worth defining in
BiocGenerics, with a signature of "x". I saw that Biostrings uses "type",
but I'm not sure why.
The 2 "nchar" methods that dispatch on the 'type' argument are from
the Bio
Btw, a subtle issue here is that elementLengths currently calls NROW(), not
length(), and code might be relying on DataFrameList returning row counts.
That behavior has proven convenient, so it would be nice not to lose it. I
guess nrow() already does that, but anyway, lengths() is not the equivale
Hi Pete -- looks like a good idea.
I think the generic could be adjusted to pass named (not x, y) args to methods,
rather than trying (incorrectly) to combine them. I don't think the
inefficiency of recursion is a particular concern, because it is not like
hundreds (or even tens) of objects ar
Yes I will try and update the current documentation to address this
situation. When it was first written we (I?) was not aware of all the
issues with prior history, merging and how best to handle them.
On Thu, Oct 15, 2015 at 2:00 PM, Leonardo Collado Torres
wrote:
> Jim,
>
> Thank you! This wor
Ahh, ok! Thanks!
On Thu, Oct 15, 2015 at 12:23 PM, Jim Hester wrote:
> Leo,
>
> This issue is unrelated to having a git-svn bridge, the update script just
> failed during the version bump commit. The git mirrors should be updated to
> the current state soon.
>
> Jim
>
> On Thu, Oct 15, 2015 at 12
Jim,
Thank you! This works perfectly!! It'd be great to have this
information at http://bioconductor.org/developers/how-to/git-mirrors/
I realize now that you already had mentioned using "git cherry-pick"
at https://stat.ethz.ch/pipermail/bioc-devel/2015-September/008013.html
and Siddhartha cover
Tangentially related, it seems like nchar is worth defining in
BiocGenerics, with a signature of "x". I saw that Biostrings uses "type",
but I'm not sure why. But if we're just going to use the signature of 'x',
I can make nchar dispatch internally, so we don't need an R-level generic.
Will that wo
Leo,
This issue is unrelated to having a git-svn bridge, the update script just
failed during the version bump commit. The git mirrors should be updated to
the current state soon.
Jim
On Thu, Oct 15, 2015 at 12:06 PM, Leonardo Collado Torres
wrote:
> I know that the git-svn bridge is deprecate
Leo,
You can use your current git repo, please don't delete it or your history!
The most foolproof way of using git-svn with existing git history is to use
`git cherry-pick` to
pick commits to add to the `devel` branch rather than merging changes from
the master
branch. This will avoid including
I know that the git-svn bridge is deprecated as of the new release
yesterday. I'm migrating to using the git mirror, but they are not
updated for packages that had a bridge.
Thanks for taking a look Dan!
Leo
On Thu, Oct 15, 2015 at 11:52 AM, Dan Tenenbaum wrote:
> The git-svn bridge is deprecate
Hi,
Now that BioC 3.2 is released, I need a little bit of guidance on git-svn.
I know that the bridges won't work anymore and my past attempt at the
new git-svn setup was kind of a mess (see
https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007726.html). But
I'm ready to give it another go.
My
The git-svn bridge is deprecated and we recommend migrating to the git mirrors.
At some point the git-svn bridge will no longer be supported.
I will take a look at this.
Dan
- Original Message -
> From: "Leonardo Collado Torres"
> To: bioc-devel@r-project.org
> Sent: Thursday, October 15
Hi,
I noticed that my repositories that had an active git-svn bridge seem
to not be updated in Bioconductor-mirror.
For example, you can see that the bridge was still working for
derfinder with this commit:
https://github.com/lcolladotor/derfinder/commit/a82112f777415414c234623af15e0c2088c2eea7
b
> -Original Message-
> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> Marcin Cieslik
> Sent: Thursday, October 15, 2015 7:46 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] SV4Vectors installation problem
>
> Dear Bioconductors,
>
> Somewhere in Augu
Dear Bioconductors,
Somewhere in August S4Vectors stopped installing correctly resulting in a:
Creating a generic function for ‘nchar’ from package ‘base’ in package
‘S4Vectors’
message (that cannot be suppressed) each time the package is loaded. The
issue is not fixed by a fresh reinstall of bi
Dear Bioconductor developers,
I am happy to present my new package, available with the new version of
Bioconductor.
MEAL is a package designed to integrate methylation and expression and to
analyze both separately. Integration of these data types can be univariate or
multivariate. The univari
With the release of the new version of Bioconductor I would like to present my
new package.
FindMyFriends is an extensible framework for generating and working with
comparative microbial genomics data or, as it is often referred to, pangenomes.
On the algorithm side, FindMyFriends offers a new
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