Re: [Rd] namespace S3 and S4 generic imports cannot both be satisfied:

2012-12-14 Thread Martin Morgan
On 12/09/2012 08:27 PM, John Chambers wrote: Yes, you are right. Mixing S3 and S4 methods for a generic is fine, although in subtle cases one is safer promoting the S3 method to an S4 method, as you did in your example. Usually, the default method for the S4 generic is the S3 generic. But, in

[Rd] Strange, most probably unjustified, codoc mismatch for S4 method with one argument plus '...' (re-try)

2012-12-14 Thread Ulrich Bodenhofer
Hi, I just figured out that I accidentally posted my message in HTML, so I am retrying in plain text only. Sorry. I am currently extending one of our CRAN packages and ran into an unexpected problem when checking the source package. I got some warnings in the step "* checking for code/docume

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

2012-12-14 Thread Martin Maechler
> "PJ" == Paul Johnson > on Fri, 14 Dec 2012 01:01:19 -0600 writes: PJ> On Thu, Dec 13, 2012 at 9:01 PM, Yi (Alice) Wang wrote: >> I have also encountered a similar problem. My mvabund package runs much >> faster on linux/OSX than on windows with both R/2.15.1 and R/2.15

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

2012-12-14 Thread Uwe Ligges
On 14.12.2012 07:55, Paul Johnson wrote: On Thu, Dec 13, 2012 at 3:33 AM, Uwe Ligges wrote: Long message, but as far as I can see, this is not about base R but the contributed package Amelia: Please discuss possible improvements with its maintainer. Thanks for answering, but I'm really surp

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

2012-12-14 Thread Dirk Eddelbuettel
On 14 December 2012 at 18:07, Uwe Ligges wrote: | without overhead of packages. The CRAN check times of > 4000 packages | are typically a good indicator, and they are a bit slower for R-2.15.2 And sadly less so when you force us to turn tests off. Dirk -- Dirk Eddelbuettel | e...@debian.org

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

2012-12-14 Thread Uwe Ligges
On 14.12.2012 18:11, Dirk Eddelbuettel wrote: On 14 December 2012 at 18:07, Uwe Ligges wrote: | without overhead of packages. The CRAN check times of > 4000 packages | are typically a good indicator, and they are a bit slower for R-2.15.2 Please do not quote only parts of my sentences, that

Re: [Rd] small issue with over-zealous clean.

2012-12-14 Thread Uwe Ligges
On 14.12.2012 04:15, Hin-Tak Leung wrote: --- On Sun, 9/12/12, Dirk Eddelbuettel wrote: Do you REALLY think svn would not know about missing files? There does not seem to be a limit on the disdain for svn among git users. Fascinating. FWIW, as one of the linux kernel maintainers, I don't

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

2012-12-14 Thread Dirk Eddelbuettel
On 14 December 2012 at 18:19, Uwe Ligges wrote: | | | On 14.12.2012 18:11, Dirk Eddelbuettel wrote: | > | > On 14 December 2012 at 18:07, Uwe Ligges wrote: | > | without overhead of packages. The CRAN check times of > 4000 packages | > | are typically a good indicator, and they are a bit slower

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

2012-12-14 Thread Spencer Graves
On 12/14/2012 9:32 AM, Dirk Eddelbuettel wrote: On 14 December 2012 at 18:19, Uwe Ligges wrote: | | | On 14.12.2012 18:11, Dirk Eddelbuettel wrote: | > | > On 14 December 2012 at 18:07, Uwe Ligges wrote: | > | without overhead of packages. The CRAN check times of > 4000 packages | > | are typical

Re: [Rd] small issue with over-zealous clean.

2012-12-14 Thread Hin-Tak Leung
--- On Fri, 14/12/12, Uwe Ligges wrote: > On 14.12.2012 04:15, Hin-Tak Leung wrote: > > --- On Sun, 9/12/12, Dirk Eddelbuettel > wrote: > > > > > >> Do you REALLY think svn would not know about > missing > >> files?  There does not > >> seem to be a limit on the disdain for svn among git > user

Re: [Rd] small issue with over-zealous clean.

2012-12-14 Thread Marc Schwartz
On Dec 14, 2012, at 1:48 PM, Hin-Tak Leung wrote: > --- On Fri, 14/12/12, Uwe Ligges wrote: > >> On 14.12.2012 04:15, Hin-Tak Leung wrote: >>> --- On Sun, 9/12/12, Dirk Eddelbuettel >> wrote: >>> >>> Do you REALLY think svn would not know about >> missing files? There does not >>

[Rd] Found explanation for R-2.15.2 slowdown in one case; caution for any users of La_chol

2012-12-14 Thread Paul Johnson
2 days ago, I posted my long message about the observed slowdown in a package between R-2.15.0 and R-2.15.2. Uwe Ligges urged me to make a self-contained R example. That was the encouragement I needed. I tracked the problem down to a failing use of a LAPACK routine. R's LAPACK C interface changed

Re: [Rd] Strange, most probably unjustified, codoc mismatch for S4 method with one argument plus '...' (re-try)

2012-12-14 Thread Martin Morgan
On 12/14/2012 09:46 AM, Ulrich Bodenhofer wrote: Hi, I just figured out that I accidentally posted my message in HTML, so I am retrying in plain text only. Sorry. I am currently extending one of our CRAN packages and ran into an unexpected problem when checking the source package. I got some wa