Re: [Bioc-devel] depends on packages providing classes

2014-10-29 Thread Henrik Bengtsson
On Wed, Oct 29, 2014 at 1:07 PM, Vincent Carey st...@channing.harvard.edu wrote: On Wed, Oct 29, 2014 at 2:15 PM, Hervé Pagès hpa...@fredhutch.org wrote: Hi, On 10/28/2014 08:51 PM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès hpa...@fredhutch.org

Re: [Bioc-devel] depends on packages providing classes

2014-10-29 Thread Michael Lawrence
On Wed, Oct 29, 2014 at 11:15 AM, Hervé Pagès hpa...@fredhutch.org wrote: Hi, On 10/28/2014 08:51 PM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès hpa...@fredhutch.org mailto:hpa...@fredhutch.org wrote: On 10/28/2014 12:42 PM, Vincent Carey wrote:

[Bioc-devel] depends on packages providing classes

2014-10-28 Thread Kasper Daniel Hansen
What is the current best paradigm for using all the classes in S4Vectors/GenomeInfoDb/GenomicRanges/IRanges I obviously import methods and classes from the relevant packages. But shouldn't I depend on these packages as well? Since I basically want the user to have this functionality at the

Re: [Bioc-devel] depends on packages providing classes

2014-10-28 Thread Hervé Pagès
Hi, On 10/28/2014 08:48 AM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 11:23 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Well, first I want to make sure that there is not something special regarding S4 methods and classes. I have a feeling that they are a special case.

Re: [Bioc-devel] depends on packages providing classes

2014-10-28 Thread Vincent Carey
On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès hpa...@fredhutch.org wrote: Hi, On 10/28/2014 08:48 AM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 11:23 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Well, first I want to make sure that there is not something special

Re: [Bioc-devel] depends on packages providing classes

2014-10-28 Thread Hervé Pagès
On 10/28/2014 12:42 PM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès hpa...@fredhutch.org mailto:hpa...@fredhutch.org wrote: Hi, On 10/28/2014 08:48 AM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 11:23 AM, Kasper Daniel Hansen