Re: [Bioc-devel] SummarizedExperiment initialisation and manipulation question.

2015-06-30 Thread Nicolas Delhomme
Thanks for the quick action :-) Nico --- Nicolas Delhomme, PhD The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden

[Rd] additional leap second

2015-06-30 Thread Ei-ji Nakama
hi, Index: leap_second/src/library/base/R/zdatetime.R === --- leap_second/src/library/base/R/zdatetime.R(revision 68608) +++ leap_second/src/library/base/R/zdatetime.R(working copy) @@ -24,7 +24,8 @@ 1979-12-31,

Re: [Rd] additional leap second

2015-06-30 Thread Duncan Murdoch
On 01/07/2015 7:20 AM, Ei-ji Nakama wrote: hi, Index: leap_second/src/library/base/R/zdatetime.R === --- leap_second/src/library/base/R/zdatetime.R(revision 68608) +++ leap_second/src/library/base/R/zdatetime.R(working

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Hadley Wickham
A slightly simpler formulation of the problem is: show - function(...) stop(My show!) methods::setClass(Person, slots = list(name = character)) methods::new(Person, name = Tom) # Error in (function (...) : My show! Hadley On Tue, Jun 30, 2015 at 9:02 AM, Dean Attali daatt...@gmail.com wrote:

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Duncan Murdoch
On 30/06/2015 1:57 PM, Hadley Wickham wrote: A slightly simpler formulation of the problem is: show - function(...) stop(My show!) methods::setClass(Person, slots = list(name = character)) methods::new(Person, name = Tom) # Error in (function (...) : My show! Just to be clear: the

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Hadley Wickham
On Tue, Jun 30, 2015 at 2:20 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 30/06/2015 1:57 PM, Hadley Wickham wrote: A slightly simpler formulation of the problem is: show - function(...) stop(My show!) methods::setClass(Person, slots = list(name = character)) methods::new(Person,

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Duncan Murdoch
On 30/06/2015 5:27 PM, Lorenz, David wrote: There is something I'm really missing here. The function show is a standardGeneric function, so the correct way to write it as method like this: That describes methods::show. The problem is that the default print mechanism isn't calling

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Lorenz, David
There is something I'm really missing here. The function show is a standardGeneric function, so the correct way to write it as method like this: setMethod(show, Person, function(object) { for an object of class Person for example. Dave On Tue, Jun 30, 2015 at 10:11 AM, luke-tier...@uiowa.edu

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread luke-tierney
Same thing happens with S3 if you redefine print(). I thought that code was actually calculating the function to call rather than the symbol to use, but apparently not. Shouldn't be too hard to fix. luke On Tue, 30 Jun 2015, Hadley Wickham wrote: On Tue, Jun 30, 2015 at 2:20 PM, Duncan

[Rd] Why doesn't R have a float data type?

2015-06-30 Thread Charles Determan
This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility conflicts. But I wanted to know why R has never

Re: [Rd] Why doesn't R have a float data type?

2015-06-30 Thread Charles Determan
Hi Greg, I was referring to the single precision type. Your points were what I expected. I just wanted to ask the R community if there was any other reason than 'there wasn't any reason to implement it'. Thanks, Charles On Tue, Jun 30, 2015 at 12:29 PM, Greg Snow 538...@gmail.com wrote: My

Re: [Bioc-devel] rtracklayer bug?

2015-06-30 Thread Marc Carlson
Hi Arne, So this time when I look at the bioc-devel email list, I don't see a record for this last name (or this email). In fact the only way I could be sure it was you was that your post was the same... ;) If you want to post from gmail, then you will need to subscribe the gmail address to

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Paul Gilbert
On 06/30/2015 11:33 AM, Duncan Murdoch wrote: On 30/06/2015 5:27 PM, Lorenz, David wrote: There is something I'm really missing here. The function show is a standardGeneric function, so the correct way to write it as method like this: That describes methods::show. The problem is that the

Re: [Rd] Why doesn't R have a float data type?

2015-06-30 Thread Greg Snow
My understanding is that R does have a float type, it is just called double instead of float. If you are referring to a single precision floating point type, then R does have the as.single function, but that does not really change the way the number is stored, just sets a flag so that the proper

Re: [Rd] Why doesn't R have a float data type?

2015-06-30 Thread Prof Brian Ripley
On 30/06/2015 17:42, Charles Determan wrote: This is strictly a curiosity question. I am aware the R doesn't possess a float data type. I also don't mean to request that such functionality be implemented as I'm sure it would require a large amount of work with potential back compatibility

Re: [Rd] Why doesn't R have a float data type?

2015-06-30 Thread Hervé Pagès
Hi Charles, Probably for the same reason it doesn't have short int, short unsigned int, long int, long unsigned int, long long int, long long unsigned int, long double etc... There are many built-in types in C and, in order to keep things simple, I guess the line had to be drew somewhere. Said

Re: [Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Duncan Murdoch
On 30/06/2015 7:04 PM, Paul Gilbert wrote: On 06/30/2015 11:33 AM, Duncan Murdoch wrote: On 30/06/2015 5:27 PM, Lorenz, David wrote: There is something I'm really missing here. The function show is a standardGeneric function, so the correct way to write it as method like this: That

Re: [Bioc-devel] rtracklayer bug?

2015-06-30 Thread Michael Lawrence
I will add ... to the httpGet call. On Tue, Jun 30, 2015 at 10:10 AM, Marc Carlson mcarl...@fredhutch.org wrote: Hi Arne, So this time when I look at the bioc-devel email list, I don't see a record for this last name (or this email). In fact the only way I could be sure it was you was that

[Rd] Defining a `show` function breaks the print-ing of S4 object -- bug or expected?

2015-06-30 Thread Dean Attali
Hi r-devel If you define a function named `show` or attach a package with an exported `show` function, then printing/vieweing S4 objects breaks. This is probably because the `print` function calls `show`, which is now masked. Example: show - function() {} setClass(Person, slots = list(name =

Re: [Rd] Guidelines for S3 regression models

2015-06-30 Thread Stephen Milborrow
Given how much documentation is available on R coding in general, it is surprising how little is available specifically on writing model code. Researchers who come up with a new method of regression, and who want to write an S3 model for that method, must currently go all the way back to the