Re: [Rd] R 2.6.0 S4 data breakage, R _data_class(), class-, etc.

2007-10-08 Thread Bjørn-Helge Mevik
Martin Morgan wrote: But both 'new' and 'as' appear to produce invalid (in a different sense, I guess) objects: setClass(snp, contains=raw, + validity=function(object) { + if (length(object) 1) too short + else TRUE + }) Well, you _have_

Re: [Rd] R 2.6.0 S4 data breakage, R _data_class(), class-, etc.

2007-10-08 Thread Martin Morgan
[EMAIL PROTECTED] (Bjørn-Helge Mevik) writes: Martin Morgan wrote: But both 'new' and 'as' appear to produce invalid (in a different sense, I guess) objects: setClass(snp, contains=raw, + validity=function(object) { + if (length(object) 1) too short +

Re: [Rd] R 2.6.0 S4 data breakage, R _data_class(), class-, etc.

2007-10-07 Thread John Chambers
Most of your problems seem related to assigning an S4 class to an arbitrary object--a really bad idea, since it can produce invalid objects. Objects from S4 classes are created by calling the function new(), and in principal _only_ by calling that function. Objects from one class are coerced

Re: [Rd] R 2.6.0 S4 data breakage, R _data_class(), class-, etc.

2007-10-07 Thread Martin Morgan
John Chambers [EMAIL PROTECTED] writes: Most of your problems seem related to assigning an S4 class to an arbitrary object--a really bad idea, since it can produce invalid objects. Objects from S4 classes are created by calling the function new(), and in principal _only_ by calling that

[Rd] R 2.6.0 S4 data breakage, R _data_class(), class-, etc.

2007-10-06 Thread Hin-Tak Leung
Hi, (somebody would probably yell at me for not checking 2.6.0rc, for which I can only apologize...) Our R package (snpMatrix in http://www-gene.cimr.cam.ac.uk/clayton/software/) is broken rather badly in 2.6.0 ; I have fixed most of it now so a new release is imminent; but I'd like to mention