[Rd] Is there a way to disable / warn about forking?

2011-10-04 Thread Thomas Friedrichsmeier
Dear R developers, with the inclusion of the package "parallel" in the upcoming release of R, users and package developers are likely to make increasing usage of parallelization features. In part, these features rely on forking the R process. As ?mcfork points out, fork()ing in a GUI process is

Re: [Rd] Finding inter-function dependencies within a package

2011-10-04 Thread Keith Jewell
Following helpful correspondence with Mark Bravington, mvbutils::foodweb and callers.of can do exactly what I wanted very neatly and easily. The trick is to use base::asNamespace to see non-exported objects in the package. base::asNamespace is described as "Internal name space support functions

Re: [Rd] Is there a way to disable / warn about forking?

2011-10-04 Thread Simon Urbanek
On Oct 4, 2011, at 4:43 AM, Thomas Friedrichsmeier wrote: > Dear R developers, > > with the inclusion of the package "parallel" in the upcoming release of R, > users and package developers are likely to make increasing usage of > parallelization features. In part, these features rely on forkin

Re: [Rd] number of copies - summary

2011-10-04 Thread Terry Therneau
My thanks to Bill Dunlap and Simon Urbanek for clarifying many of the details. This gives me what I need to go forward. Yes, I will likely convert more and more things to .Call over time. This clearly gives the most control over excess memory copies. I am getting more comments from people usi

Re: [Rd] Is there a way to disable / warn about forking?

2011-10-04 Thread Thomas Friedrichsmeier
Hi, On Tuesday 04 October 2011, Simon Urbanek wrote: > I don't see why this should be anything new - this is already happening > since both packages that were folded into parallel (snow and multicore) > are well known and well used. > > In multicore we were explicitly warning about this and also

[Rd] segfault after .C call.

2011-10-04 Thread Adrin
Hi there, I think I'm encountering a bug, and I already reported it here: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14695 But meanwhile, could you help me by any suggestions about the problem? I'll place the content of the reported bug here. You can find attachments on bugzilla if you

[Rd] R-devel (2.14 alpha) Windows binary

2011-10-04 Thread Dan Tenenbaum
Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan -- Forwarded message -- From: Stefan

Re: [Rd] segfault after .C call.

2011-10-04 Thread Simon Urbanek
The bug is in your code! (I see at least one - many buffer overflows in all char** output arguments). Please don't abuse the bug tracking system for usage questions. You may want to consider using either .Call (if you are familiar with R) or Rcpp (if you are more familiar with C++), .C is not th

[Rd] Moderating consequences of garbage collection when in C

2011-10-04 Thread Martin Morgan
Allocating many small objects triggers numerous garbage collections as R grows its memory, seriously degrading performance. The specific use case is in creating a STRSXP of several 1,000,000's of elements of 60-100 characters each; a simplified illustration understating the effects (because the

Re: [Rd] R-devel (2.14 alpha) Windows binary

2011-10-04 Thread Peter Dalgaard
I suspect that the Windows build system just hasn't caught on to the short time between 2.13.2 and the start of run-in for 2.14.0. I think the usual logic is that pre-releases of the next version replace the patch releases of the old one (by definition, there shouldn't be updates to 2.13.2 anywa