On Mon, Apr 27, 2015 at 6:45 PM, Hervé Pagès wrote:
>
> Hi Henrik,
>
> I know it's not necessary and I know that the WRE manual and
> 'R CMD check' don't like this but I like to list in Imports what
> I import and to list in Depends what I want to see attached to
> the search() path. For the same
Beautiful. Thxs Henrik
On Mon, Apr 27, 2015 at 6:47 PM, Dan Tenenbaum
wrote:
>
>
> - Original Message -
> > From: "Henrik Bengtsson"
> > To: "bioC-devel"
> > Sent: Sunday, April 26, 2015 7:14:20 PM
> > Subject: [Bioc-devel] Bioc package pages: List also BugReports for a
> package?
> >
- Original Message -
> From: "Dario Strbenac"
> To: bioc-devel@r-project.org
> Sent: Monday, April 27, 2015 10:00:10 PM
> Subject: [Bioc-devel] biocUpgrade Wrongly Infers R Version
>
> I can't upgrade BiocInstaller :
>
> root@bioinfo:/home/dario/Documents# R
>
> R version 3.2.0 (2015-
I can't upgrade BiocInstaller :
root@bioinfo:/home/dario/Documents# R
R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welco
- Original Message -
> From: "Henrik Bengtsson"
> To: "bioC-devel"
> Sent: Sunday, April 26, 2015 7:14:20 PM
> Subject: [Bioc-devel] Bioc package pages: List also BugReports for a package?
>
> For affxparser, we've got the following in DESCRIPTION:
>
> URL: https://github.com/HenrikBe
Hi Henrik,
I know it's not necessary and I know that the WRE manual and
'R CMD check' don't like this but I like to list in Imports what
I import and to list in Depends what I want to see attached to
the search() path. For the same reason that I like to explicitly
export the generic functions tha
On 04/27/2015 02:15 PM, Michael Lawrence wrote:
It would be nice to have a single function call that would hide these
details. It could probably be made more efficient also by avoiding
multiple matching, unnecessary revmap lists, etc. tableAsGRanges() is
not a good name but it conveys what I mean
It would be nice to have a single function call that would hide these
details. It could probably be made more efficient also by avoiding multiple
matching, unnecessary revmap lists, etc. tableAsGRanges() is not a good
name but it conveys what I mean (does that make it actually good?).
On Mon, Apr
On 04/24/2015 11:41 AM, Michael Lawrence wrote:
Taking this a bit off topic but it would be nice if we could get the
GRanges equivalent of as.data.frame(table(x)), i.e., unique(x) with a
count mcol. Should be easy to support but what should the API be like?
This was actually the motivating use
Hej Michael and Hervé!
Importing from GenomeInfoDb is what I do at the moment. I will have to check
more extensively - adding more unit tests - but it seems to work so far,
without "depending" on IRanges - thanks Michael I'll keep that in mind while
testing.
I just had the understanding that i
Probably because that would mean genomeIntervals depending on IRanges.
Because GenomeInfoDb needs CompressedList.
On Mon, Apr 27, 2015 at 11:14 AM, Hervé Pagès wrote:
> Hi Nico,
>
> On 04/26/2015 09:58 AM, Nicolas Delhomme wrote:
>
>> Hej Hervé (I guess)!
>>
>> Could it be possible to move the g
Hi Nico,
On 04/26/2015 09:58 AM, Nicolas Delhomme wrote:
Hej Hervé (I guess)!
Could it be possible to move the generic from "seqnames" and "seqnames<-" from GenomeInfoDb to
BiocGenerics? I would then deprecate the "seq_name" and "seq_name<-" functions of the genomeIntervals
package and import
Hi,
I want to unsubscribe from the mail list.
thank you
Jenny
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