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 wrote: > Hi, > > On 10/28/2014 08:51 PM, Vincent Carey wrote: > >> >> >> On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès > > wrote: >> >> >> >> On 10/28/2014 12:42 PM, Vincent Carey wrote: >> >> >> >> On Tue, Oct

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

2014-10-29 Thread Hervé Pagès
On 10/29/2014 01:07 PM, Vincent Carey wrote: On Wed, Oct 29, 2014 at 2:15 PM, Hervé Pagès mailto: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 mailto:hpa...@fredhutch.org>

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 wrote: > On Wed, Oct 29, 2014 at 2:15 PM, Hervé Pagès wrote: > >> Hi, >> >> On 10/28/2014 08:51 PM, Vincent Carey wrote: >> >>> >>> >>> On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès >> > wrote: >>> >>> >>> >>> On 10/28

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

2014-10-29 Thread Vincent Carey
On Wed, Oct 29, 2014 at 2:15 PM, Hervé Pagès wrote: > Hi, > > On 10/28/2014 08:51 PM, Vincent Carey wrote: > >> >> >> On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès > > wrote: >> >> >> >> On 10/28/2014 12:42 PM, Vincent Carey wrote: >> >> >> >> On Tue, Oct 2

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

2014-10-29 Thread Hervé Pagès
Hi, On 10/28/2014 08:51 PM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote: On 10/28/2014 12:42 PM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès mailto:hpa...@fredhutch.org>

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

2014-10-28 Thread Vincent Carey
On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès wrote: > > > On 10/28/2014 12:42 PM, Vincent Carey wrote: > >> >> >> On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès > > wrote: >> >> Hi, >> >> On 10/28/2014 08:48 AM, Vincent Carey wrote: >> >> On Tue, Oct 28,

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

2014-10-28 Thread Michael Lawrence
On Tue, Oct 28, 2014 at 2:48 PM, Hervé Pagès wrote: > > > On 10/28/2014 12:42 PM, Vincent Carey wrote: > >> >> >> On Tue, Oct 28, 2014 at 2:29 PM, Hervé Pagès > > wrote: >> >> Hi, >> >> On 10/28/2014 08:48 AM, Vincent Carey wrote: >> >> On Tue, Oct 28,

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

2014-10-28 Thread Michael Lawrence
This is a recent change to R; I think 3.1.1. I think many of us (including myself) are (ab)using Depends to deploy a convenient "context" for performing the sorts of work related to the package. This includes the ability to construct inputs and manipulate outputs. But in many ways that context is

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 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 < kasperdanielhan...@gmail.com

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 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 >>> regarding

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. S

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

2014-10-28 Thread Vincent Carey
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. > > Second, while I agree with Jim's general opin

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

2014-10-28 Thread Kasper Daniel Hansen
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. Second, while I agree with Jim's general opinion, it is a little bit different when I have return objects which are defined in other packages. If I d

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

2014-10-28 Thread James W. MacDonald
I agree with Vince. It's your job as a package developer to make available to your package all the functions necessary for the package to work. But I am not sure it is your job to load all the packages that your end user might need. Best, Jim On Tue, Oct 28, 2014 at 11:04 AM, Vincent Carey wr

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

2014-10-28 Thread Vincent Carey
On Tue, Oct 28, 2014 at 10:19 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > 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 d

[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 comma