[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

[Rd] RFC: is.whole() ? {how to judge if a variable is an integer}

2014-10-28 Thread Martin Maechler
Diverted to R-devel, as I'm requesting comments about a proposal to add is.whole() to R just so this issue does not trail on for centuries (;-), see below. William Dunlap wdun...@tibco.com on Sat, 18 Oct 2014 10:33:05 -0700 writes: 3. all.equal(a, as.integer(a)) Note that this

Re: [Rd] RFC: is.whole() ? {how to judge if a variable is an integer}

2014-10-28 Thread Duncan Murdoch
On 28/10/2014, 5:32 AM, Martin Maechler wrote: Diverted to R-devel, as I'm requesting comments about a proposal to add is.whole() to R just so this issue does not trail on for centuries (;-), see below. I didn't read the thread in question, but I think Bill's comment is crucial: what

Re: [Rd] is.whole()

2014-10-28 Thread Therneau, Terry M., Ph.D.
Martin, I can't imagine using such a function myself, the reason being that as Bill and Duncan point out, the correct answer depends on the situation. But given the regular reappearance of this topic, I think that perhaps creation of your function is a good idea, largely to function as a

Re: [Rd] is.whole()

2014-10-28 Thread Greg Snow
Just to anticipate future discussion from math purists (and hopefully not to throw too much of a wrench in the works), what would be the return of: is.whole(-1) or is.whole(-1L) ? I can see arguments for both TRUE and FALSE from both the math purity group and the what will happen when I try

Re: [Rd] OSX Yosemite (10.10): Are package binaries the same as for OSX Mavericks (10.9)?

2014-10-28 Thread Henrik Bengtsson
On Mon, Oct 27, 2014 at 12:33 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Henrik Bengtsson h...@biostat.ucsf.edu To: Dan Tenenbaum dtene...@fredhutch.org Cc: R-devel r-devel@r-project.org Sent: Monday, October 27, 2014 12:21:49 PM Subject: Re: [Rd]