Re: [Bioc-devel] avoiding clashes of different S4 methods with the same generic

2016-04-27 Thread Michael Lawrence
On Wed, Apr 27, 2016 at 10:52 AM, Hervé Pagès wrote: > On 04/27/2016 04:24 AM, Michael Lawrence wrote: >> >> On Tue, Apr 26, 2016 at 11:12 PM, Hervé Pagès >> wrote: >>> >>> Hi, >>> >>> I would not discard defining a SummarizedExperiment subclass so

Re: [Bioc-devel] avoiding clashes of different S4 methods with the same generic

2016-04-27 Thread Hervé Pagès
On 04/27/2016 04:24 AM, Michael Lawrence wrote: On Tue, Apr 26, 2016 at 11:12 PM, Hervé Pagès wrote: Hi, I would not discard defining a SummarizedExperiment subclass so quickly. SummarizedExperiment is very generic and can contain any kind of data. IIUC the csaw package

Re: [Bioc-devel] avoiding clashes of different S4 methods with the same generic

2016-04-27 Thread Hervé Pagès
On 04/27/2016 03:18 AM, Martin Morgan wrote: On 04/27/2016 02:12 AM, Hervé Pagès wrote: Hi, I would not discard defining a SummarizedExperiment subclass so quickly. SummarizedExperiment is very generic and can contain any kind of data. IIUC the csaw package uses SummarizedExperiment to

Re: [Bioc-devel] avoiding clashes of different S4 methods with the same generic

2016-04-27 Thread Kasper Daniel Hansen
I agree with Herve that making a subclass (is that the technical term?) might be a good idea. This is what I would do. And this is what has been done historically for all the extensions of ExpressionSet and eSet from Biobase. The issue with a general class like SummarizedExperiment is that

Re: [Bioc-devel] avoiding clashes of different S4 methods with the same generic

2016-04-27 Thread Michael Lawrence
On Tue, Apr 26, 2016 at 11:12 PM, Hervé Pagès wrote: > Hi, > > I would not discard defining a SummarizedExperiment subclass so quickly. > SummarizedExperiment is very generic and can contain any kind of data. > IIUC the csaw package uses SummarizedExperiment to store a

Re: [Bioc-devel] avoiding clashes of different S4 methods with the same generic

2016-04-27 Thread Martin Morgan
On 04/27/2016 02:12 AM, Hervé Pagès wrote: Hi, I would not discard defining a SummarizedExperiment subclass so quickly. SummarizedExperiment is very generic and can contain any kind of data. IIUC the csaw package uses SummarizedExperiment to store a particular kind of data (ChIP-seq data) and

Re: [Bioc-devel] build reports are not updated

2016-04-27 Thread Martin Morgan
On 04/27/2016 05:30 AM, Andrzej Oleś wrote: Dear Ludwig, according to http://bioconductor.org/developers/release-schedule/ release (BioC 3.2) builds were to stop on April 22. That's probably why they are not updated anymore. yes the _release_ builds have stopped. Devel builds still continue

Re: [Bioc-devel] build reports are not updated

2016-04-27 Thread Andrzej Oleś
Dear Ludwig, according to http://bioconductor.org/developers/release-schedule/ release (BioC 3.2) builds were to stop on April 22. That's probably why they are not updated anymore. Cheers, Andrzej On Wed, Apr 27, 2016 at 11:08 AM, Ludwig Geistlinger < ludwig.geistlin...@bio.ifi.lmu.de> wrote:

[Bioc-devel] build reports are not updated

2016-04-27 Thread Ludwig Geistlinger
Dear Dan, For some reason, the build reports are still showing the snapshot of Saturday: http://bioconductor.org/checkResults/release/bioc-LATEST/EnrichmentBrowser/ As there is an error, I would like to know whether this is something persistent or only something temporary. Thanks, Ludwig --

Re: [Bioc-devel] avoiding clashes of different S4 methods with the same generic

2016-04-27 Thread Hervé Pagès
Hi, I would not discard defining a SummarizedExperiment subclass so quickly. SummarizedExperiment is very generic and can contain any kind of data. IIUC the csaw package uses SummarizedExperiment to store a particular kind of data (ChIP-seq data) and I believe specialization is a legitimate