[Rd] PATCH: Avoiding extra copies (NAMED bumped) with source(..., print.eval=FALSE) ...and with print.eval=TRUE?

2014-06-17 Thread Henrik Bengtsson
OBJECTIVE: To update source(..., print.eval=FALSE) to not use withVisible() unless really needed. This avoids unnecessary increases of reference counts/NAMED introduced by withVisible(), which in turn avoids unnecessary memory allocations and garbage collection overhead. This has an impact on all

Re: [Rd] what is the current correct repos structure for mac osx binaries?

2014-06-17 Thread Skye Bender-deMoll
Please forgive another comment on this topic. The 'type' argument to tools::write_PACKAGES doesn't currently accept the 'mac.binary.mavericks' value. It seems like it should, to make it possible to pass the same 'type' argument to all of the package generation and manipulation functions? >

Re: [Rd] R CMD check warning with S3 method

2014-06-17 Thread Winston Chang
I forgot to add this - here's the warning: * checking S3 generic/method consistency ... WARNING Warning: declared S3 method 'filter.test' not found See section 'Generic functions and methods' of the 'Writing R Extensions' manual. On Tue, Jun 17, 2014 at 2:21 PM, Winston Chang wrote: > I'm getti

[Rd] R CMD check warning with S3 method

2014-06-17 Thread Winston Chang
I'm getting an R CMD check warning with a package (call it package A) that defines an S3 method but not the generic. The generic is defined in another package (package B). Package A imports the S3 generic from B. And there's one additional detail: the generic overrides a function in the stats packa

Re: [Rd] rJava Java debugger API

2014-06-17 Thread Prof Brian Ripley
*Now* you tell us rJava is involved. Its lists are accessed via http://www.rforge.net/rJava/ On 17/06/2014 07:43, rmohan wrote: Hi, I use rJava and call Java code that uses JVMTI code like this VM vm = VM.getVM(); Universe universe = vm.getUniverse(); CollectedHe

Re: [Rd] model.frame question

2014-06-17 Thread Therneau, Terry M., Ph.D.
Brian, So let me ask an r-core opinion. Should I change the default to model=TRUE? Survival is heavily used and there is something to be said for consistency within the central packages. Sometimes old habits die hard, and there is a "save memory" part of me that hates to save a large objec

Re: [Rd] model.frame and parent environment

2014-06-17 Thread Therneau, Terry M., Ph.D.
Duncan, You missed the point. (I sometimes write too tersely, so I take the blame.) Users are writing their own "myfun". I want model.frame to work for them, without forcing the user to learn environment trickery. The actual question from the user was a call to fit <- coxph(formul

[Rd] rJava Java debugger API

2014-06-17 Thread rmohan
Hi, I use rJava and call Java code that uses JVMTI code like this VM vm = VM.getVM(); Universe universe = vm.getUniverse(); CollectedHeap heap = universe.heap(); This code attaches to another JVM and to get its internals. This is legal Java and it works. But when I use r