search for: ismethodsdispatchon

...precation warning only when not called by method dispatch from as.data.frame(): - bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !identical(sys.function(-1L), as.data.frame))) + bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !( + identical(sys.function(-1L), as.data.frame) || ( + .isMethodsDispatchOn() && + methods::is(sys.function(-1L), 'derivedDefaultMethod') && + identical( + sys.function(-1L)@generic, + structure('as.data.frame', package = 'base') + ))))) .Deprecated( msg = gettextf( "Direct call of '%s()' is depr...

...eck), or even if I try to load it using devtools::load_all() I tried to investigate the problem, and I found that the error arises in the base::namespaceImportFrom() function, and more precisely in this block: for (n in impnames) if (exists(n, envir = impenv, inherits = FALSE)) { if (.isMethodsDispatchOn() && methods:::isGeneric(n, ns)) { genNs <- get(n, envir = ns)@package Here n is '[', and the get(n, envir = ns) expression returns .Primitive("["), which is a function and has no @package slot. This will only occur if exists(n, envir = impenv, inherits =...

See also .isMethodsDispatchOn, which is what trace uses to decide if the methods package needs to be loaded. ~G On Tue, Apr 19, 2016 at 5:34 AM, Michael Lawrence <lawrence.michael at gene.com > wrote: > Not sure why R_has_methods_attached() exists. Maybe Martin could shed > some light on that. > > On Mon, A...

I have encountered an issue which I have been unable to resolve, involving an S3 generic (print) being declared S4 generic in a package, and the method being exported. This all works fine - the problem occurs when I try to import the method to another package. Here is the bit that works fine. ------------- #the .r file for package bar

...rks after fixing the check to ensure that R_MethodsNamespace > is not R_GlobalEnv, but one could load a serialized S4 object and > expect S3 dispatch to work with Rscript. > > On Tue, Apr 19, 2016 at 6:51 AM, Gabriel Becker <gmbecker at ucdavis.edu> > wrote: > > See also .isMethodsDispatchOn, which is what trace uses to decide if the > > methods package needs to be loaded. > > > > ~G > > > > On Tue, Apr 19, 2016 at 5:34 AM, Michael Lawrence > > <lawrence.michael at gene.com> wrote: > >> > >> Not sure why R_has_methods_attached...

...ision 49278) +++ src/library/base/R/namespace.R (working copy) @@ -797,8 +797,12 @@ } } for (n in impnames) - if (exists(n, envir = impenv, inherits = FALSE)) - warning(msg, " ", n) + if (exists(n, envir = impenv, inherits = FALSE)) { + if (.isMethodsDispatchOn() && methods:::isGeneric(n, ns)) { + if (methods:::isGeneric(n, impenv)) + warning("replacing previous generic import: ", n) + } else warning(msg, " ", n) + } importIntoEnv(impenv, impnames, ns, impvars) if (r...

...ported. If so, a patch for library() is: >svn diff library.R Index: library.R =================================================================== --- library.R (revision 51296) +++ library.R (working copy) @@ -312,7 +312,7 @@ nogenerics <- !.isMethodsDispatchOn() || checkNoGenerics(env, package ) if(warn.conflicts && - !exists(".conflicts.OK", envir = env, inherits = FALSE)) + !exists(".conflicts.OK", envir = ns, inherits = FALSE)) checkC...

Hi, The acrobatics that as.data.frame.factor() is going thru in order to recognize a direct call don't play nice if as.data.frame() is an S4 generic: ??? df <- as.data.frame(factor(11:12)) ??? suppressPackageStartupMessages(library(BiocGenerics)) ??? isGeneric("as.data.frame") ??? # [1] TRUE ??? df <- as.data.frame(factor(11:12)) ??? # Warning message: ??? # In

...package? The above example works after fixing the check to ensure that R_MethodsNamespace is not R_GlobalEnv, but one could load a serialized S4 object and expect S3 dispatch to work with Rscript. On Tue, Apr 19, 2016 at 6:51 AM, Gabriel Becker <gmbecker at ucdavis.edu> wrote: > See also .isMethodsDispatchOn, which is what trace uses to decide if the > methods package needs to be loaded. > > ~G > > On Tue, Apr 19, 2016 at 5:34 AM, Michael Lawrence > <lawrence.michael at gene.com> wrote: >> >> Not sure why R_has_methods_attached() exists. Maybe Martin could shed >&...

...ck to ensure that R_MethodsNamespace >> is not R_GlobalEnv, but one could load a serialized S4 object and >> expect S3 dispatch to work with Rscript. >> >> On Tue, Apr 19, 2016 at 6:51 AM, Gabriel Becker <gmbecker at ucdavis.edu> >> wrote: >> > See also .isMethodsDispatchOn, which is what trace uses to decide if the >> > methods package needs to be loaded. >> > >> > ~G >> > >> > On Tue, Apr 19, 2016 at 5:34 AM, Michael Lawrence >> > <lawrence.michael at gene.com> wrote: >> >> >> >> Not...

...ly when not called by method dispatch from as.data.frame(): > - bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !identical(sys.function(-1L), as.data.frame))) > + bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !( > + identical(sys.function(-1L), as.data.frame) || ( > + .isMethodsDispatchOn() && > + methods::is(sys.function(-1L), 'derivedDefaultMethod') && > + identical( > + sys.function(-1L)@generic, > + structure('as.data.frame', package = 'base') > + ))))) > .Deprecated( > msg = gettextf( > &qu...

Hi all, I know I shouldn't really expect the following to work, but it provokes a crash of the GUI on my computer (Win xp professional). --- >sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base"

I know I said that I had no further comments on object oriented semantics. However, I found a contradiction in the R documentation. Gabriel Becker wrote: > So, there are implicit classes, but *only when the data object is NOT an "R object" In the R Language Definition: > The R specific function typeof returns the type of an R object. > Lists have elements, each of which can

Thanks for looking into it, your approach sounds good to me. See also R_has_methods_attached() (https://github.com/wch/r-source/blob/42ecf5f492a005f5398cbb4c9becd4aa5af9d05c/src/main/objects.c#L258-L265). I'm fine with Rscript not loading "methods", as long as everything works properly with "methods" loaded but not attached. -Kirill On 19.04.2016 04:10, Michael

Merry Xmas to all, I am writing a function and curiously this runs sometimes on one data set and fails on another and i cannot figure out why. Any help much appreciated. If i run the code below with data <- iris[ ,1:4] The code runs fine, but if i run on a large dataset i get the following error (showing data structures as matrix is large) > str(cluster.data) num [1:9985, 1:811] 0 0 0 0

R-1.7.0 built on NetBSD 1.6, but the validation test suite failed: Machinetype: Intel Pentium III (600 MHz); NetBSD 1.6 (GENERIC) Remote gcc version: gcc (GCC) 3.2.2 Remote g++ version: g++ (GCC) 3.2.2 Configure environment: CC=gcc CXX=g++ LDFLAGS=-Wl,-rpath,/usr/local/lib make[5]: Entering directory `/local/build/R-1.7.0/src/library' >>> Building/Updating