similar to: `[<-.data.frame` sets rownames incorrectly

Fine with me as long as eliminating the inconveniences associated with it can be put on the roadmap. The alias instability and the fact that the user has no way to know if s/he should do ?`foo,numeric-method` or ?`foo,numeric,ANY-method` to find the method has been a long-standing problem. H. On 3/21/19 21:29, Michael Lawrence wrote: If we started over, I'd try to avoid this sort of

Hi Mehmet, On 11/29/2017 11:22 AM, Suzen, Mehmet wrote: > Hi Herve, > > I think you are confusing subclasses and classes. There is no > contradiction. `is` documentation > is very clear: > > `With one argument, returns all the super-classes of this object's class.` Yes that's indeed very clear. So if "list" is a super-class of "data.frame" (as

Hi Michael, Thanks for looking into this. I suspect that truncation of ANY suffixes from method signatures is also the culprit behind the sudden breakage of aliases of the form \alias{foo,numeric-method} when a method without the ANY suffix in its signature gets added to the ecosystem. See my post about this to the Bioc-devel mailing list a couple of months ago:

Not sure why the performance penalty of nonstandard evaluation would be more of a concern here than for something like switch(). If that can't/won't be fixed, what about fixing the man page so it's in sync with the current behavior? Thanks, H. On 05/03/2017 02:26 AM, peter dalgaard wrote: > The first line of stopifnot is > > n <- length(ll <- list(...)) > >

Hi Gabe, On 09/29/2015 02:51 PM, Gabriel Becker wrote: > Herve, > > The problem then would be that for A a refClass whose fields take up N > bytes (in the sense that you mean), if we do > > B <- A > > A and B would look like the BOTH take up N bytes, for a total of 2N, > whereas AFAIK R would only be using ~ N + 2*56 bytes, right? Yes, but that's still a *much*

On 03/19/2016 01:22 AM, Michael Lawrence wrote: > > > On Sat, Mar 19, 2016 at 12:10 AM, Herv? Pag?s <hpages at fredhutch.org > <mailto:hpages at fredhutch.org>> wrote: > > On 03/18/2016 03:28 PM, Michael Lawrence wrote: > > > On Fri, Mar 18, 2016 at 2:53 PM, Herv? Pag?s > <hpages at fredhutch.org <mailto:hpages at

by() does not always return a list. In Gabe's example, it returns an integer, thus it is coerced to a list. as.list() means that it should be a VECSXP, not necessarily with "list" in the class attribute. Michael On Tue, Jan 30, 2018 at 2:41 PM, Herv? Pag?s <hpages at fredhutch.org> wrote: > Hi Gabe, > > Interestingly the behavior of as.list() on by objects seem to

Hi, Currently object.size() is not very useful on environments as it always returns 56 bytes, no matter how big the environment is: env1 <- new.env() object.size(env1) # 56 bytes env2 <- new.env(hash=TRUE, size=75000000L) object.size(env2) # 56 bytes env3 <- list2env(list(a=runif(25000000), L=LETTERS)) object.size(env3) # 56 bytes This makes it pretty useless on

Hi, The following error message misspells the name of the 'dim' argument: > array(integer(0), dim=integer(0)) Error in array(integer(0), dim = integer(0)) : 'dims' cannot be of length 0 The name of the argument is 'dim' not 'dims': > args(array) function (data = NA, dim = length(data), dimnames = NULL) NULL Cheers, H. -- Herv? Pag?s

>>>>> Herv? Pag?s <hpages at fredhutch.org> >>>>> on Wed, 3 May 2017 12:08:26 -0700 writes: > On 05/03/2017 12:04 PM, Herv? Pag?s wrote: >> Not sure why the performance penalty of nonstandard evaluation would >> be more of a concern here than for something like switch(). > which is actually a primitive. So it seems that

I agree with Herve, processing collapse happens last so collapse=non-NULL always leads to a single character string being returned, the same as paste(collapse=""). See the altPaste function I posted yesterday. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, May 22, 2020 at 9:12 AM Herv? Pag?s <hpages at fredhutch.org> wrote: > I think that > >

Here is an example: setGeneric("foo", function(x, y) standardGeneric("foo")) setMethod("foo", c("numeric", "ANY"), function(x, y) cat("I'm the foo#numeric#ANY method\n") ) Dispatch works as expected but selectMethod() fails to find the method: > foo(1, TRUE) I'm the foo#numeric#ANY method >

Hi, The unary forms of is() and extends() report that data.frame extends list, oldClass, and vector: > is(data.frame()) [1] "data.frame" "list" "oldClass" "vector" > extends("data.frame") [1] "data.frame" "list" "oldClass" "vector" However, the binary form of is()

On 05/15/2018 09:13 PM, Michael Lawrence wrote: > My understanding is that array (or any other structure) does not > "simply" inherit from vector, because structures are not vectors in > the strictest sense. Basically, once a vector gains attributes, it is > a structure, not a vector. The methods package accommodates this by > defining an "is" relationship

Gabe, It's the current behavior of paste() that is a major source of bugs: ## Add "rs" prefix to SNP ids and collapse them in a ## comma-separated string. collapse_snp_ids <- function(snp_ids) paste("rs", snp_ids, sep="", collapse=",") snp_groups <- list( group1=c(55, 22, 200), group2=integer(0), group3=c(99,

Hi, It's surprising that stopifnot() keeps evaluating its arguments after it reaches the first one that is not TRUE: > stopifnot(3 == 5, as.integer(2^32), a <- 12) Error: 3 == 5 is not TRUE In addition: Warning message: In stopifnot(3 == 5, as.integer(2^32), a <- 12) : NAs introduced by coercion to integer range > a [1] 12 The details section in its man

On 05/16/2018 10:22 AM, Michael Lawrence wrote: > Factors and data.frames are not structures, because they must have a > class attribute. Just call them "objects". They are higher level than > structures, which in practice just shape data without adding a lot of > semantics. Compare getClass("matrix") and getClass("factor"). > > I agree that

On 3/27/20 15:19, Hadley Wickham wrote: > > > On Fri, Mar 27, 2020 at 4:01 PM Herv? Pag?s <hpages at fredhutch.org > <mailto:hpages at fredhutch.org>> wrote: > > > > On 3/27/20 12:00, Hadley Wickham wrote: > > > > > > On Fri, Mar 27, 2020 at 10:39 AM Herv? Pag?s > <hpages at fredhutch.org <mailto:hpages at

On 03/18/2016 03:28 PM, Michael Lawrence wrote: > > On Fri, Mar 18, 2016 at 2:53 PM, Herv? Pag?s <hpages at fredhutch.org > <mailto:hpages at fredhutch.org>> wrote: > > Hi, > > Short story > ----------- > > setClassUnion("ArrayLike", "array") > > showClass("ArrayLike") # no slot > >

I just meant that the minimal contract for as.list() appears to be that it returns a VECSXP. To the user, we might say that is.list() will always return TRUE. I'm not sure we can expect consistency across methods beyond that, nor is it feasible at this point to match the semantics of the methods package. It deals in "class space" while as.list() deals in "typeof() space".