similar to: issue with .local() hack used in S4 methods

>>>>> Herv? Pag?s >>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes: > Hi list, > Here is an example: > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx > ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?

Hi list, Here is an example: ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library? ??? * installing *source* package ?CoreGx? ... ??? ** using staged installation ??? ** R ??? ** data ??? *** moving datasets to lazyload DB ??? ** inst ??? ** byte-compile and prepare package for lazy loading ??? Error : in method for

Dear all, I am using caret package to analyze a microarray dataset with feature selection using sbf(). My dataset is 3500 samples with 2200 genes, the outcome Y variable is a factor of 12 levels. I used the following script to run the feature selection: library(caret) ctrl <- sbfControl(functions=rfSBF, method='repeatedcv', repeats=5) ### x is a matrix of 3500x2200, y is a factor

Agreed but I'm not sure we want users accessing documentation with those types of aliases. One option is the method?foo("numeric") syntax. On Thu, Mar 21, 2019 at 9:52 PM Pages, Herve <hpages at fredhutch.org> wrote: > 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

If we started over, I'd try to avoid this sort of complexity, but "ANY" truncation has been happening since at least 2003. > matchSignature(c("numeric", "ANY"), foo) x "numeric" So I'm not sure we want to mess with it. Michael On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at fredhutch.org> wrote: > Hi Michael, >

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:

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

This is due to the intentional truncation of ANY suffixes from method signatures. I've hacked selectMethod() to be robust to that and will commit soon. Thanks for the report. Michael On Thu, Mar 14, 2019 at 9:32 AM Pages, Herve <hpages at fredhutch.org> wrote: > Here is an example: > > setGeneric("foo", function(x, y) standardGeneric("foo")) > >

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 >

Dear All, Here is my reproducible example: > library(stargazer) Please cite as: Hlavac, Marek (2018). stargazer: Well-Formatted Regression and Summary Statistics Tables. R package version 5.2.2. https://CRAN.R-project.org/package=stargazer > x1=1:1000 ; y = 2 * x1+ rnorm(1000) > stargazer(lm(y~x1)) Error in (.format.s.statistics.list != "p25") &&

Dear All, I had done an automatic upgrade of my Debian 10 system which had also upgraded R. I reinstalled the stargazer package and the error went away. Query : Do I need to reinstall all packages with each upgrade of R ? Best, Ashim On Thu, Jun 8, 2023 at 11:11?AM Ashim Kapoor <ashimkapoor at gmail.com> wrote: > > Dear All, > > Here is my reproducible example: > >

Hi, Strange things happen. Here is a simple example: > setClass("A", contains="integer") > setMethod("as.matrix", "A", function(x, ...) t(callNextMethod())) Creating a generic function for ?as.matrix? from package ?base? in the global environment [1] "as.matrix" > a <- new("A", 1:3) > as.matrix(a)

On Thu, 08 Jun 2023, Ashim Kapoor writes: > Dear All, > > I had done an automatic upgrade of my Debian 10 system which had also > upgraded R. > > I reinstalled the stargazer package and the error went away. > > Query : Do I need to reinstall all packages with each upgrade of R ? > > Best, > Ashim Your session info says "stargazer 5.2.2". What version

Hi, as(x, "<vector-type>") is supported and does as.<vector-type>(x) for all vector types except for raw. For example all the following coercions work and do what you'd expect: as(1L, "logical"), as(1L, "double"), as(1L, "complex"), as(1L, "character"), as(1L, "list"). But as(1L, "raw") does not: ??? >

Hi, In the situation below the note issued by the dispatch algo doesn't seem right: setClass("A", representation(stuff="complex")) setAs("ANY", "A", function(from) new("A", stuff=as.complex(from))) > as(6, "A") An object of class "A" Slot "stuff": [1] 6+0i > as(6L, "A")

Hi, Many S4 objects in Bioconductor support "combining" via a "c" method. A common use case is to combine a collection of S4 objects stored in a list with the following idiom: do.call("c", list_of_objects) For many users this doesn't return what they expect though, because their 'list_of_objects' is a named list and this seems to "break"

Dear Yihui, Thanks a lot for your help! Unfortunately, I was not able to reproduce this. I've tried creating files with Chinese characters in their names and populating them with valid UTF-8 and valid non-UTF-8 text, but R seems to be able to list them all in my case. I'm running a US English evaluation ISO image of a slightly newer build of Windows 10, and I also compiled R-4.3.1 from

Hi, First a bit of disclaimer... I haven't isolated this problem into an easy to reproduce case, and I won't be surprised if the root cause is a fault in my code's use of name spaces or some such. The error I'm seeing is one in which the desired method is not found. What worries me in terms of my expectations of how to debug the problem is that showMethods and selectMethod both

From Peter Dalgaard announcement earlier today. CHANGES IN R 3.4.3: INSTALLATION on a UNIX-ALIKE: * A workaround has been added for the changes in location of time-zone files in macOS 10.13 'High Sierra' and again in 10.13.1, so the default time zone is deduced correctly from the system setting when R is configured with --with-internal-tzcode (the default on

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 inheritance through explicit coercion is confusing. As far as I know, there are only