Re: [Rd] install.packages on unix / su (PR#8760)

2006-04-10 Thread ripley
On Mon, 10 Apr 2006, Thomas Friedrichsmeier wrote: >> | Wishlist item: >> | >> | There is a small problem using intall.packages() (and update.packages()): >> | Typically I want to install packages for system-wide use, not in a user >> | directory. Obviously this does not work without superuser rig

[Rd] eapply() fails on baseenv() (PR#8761)

2006-04-10 Thread murdoch
eapply() works on most environments, but not on baseenv(). For example, > x <- 1 > eapply(globalenv(), function(x) x) $x [1] 1 > eapply(baseenv(), function(x) x) list() I'm probably not going to have time to work on this before 2.3.0, but I don't think it's really urgent; if no one else fix

Re: [Rd] Suggestions to speed up median() and has.na()

2006-04-10 Thread Duncan Murdoch
On 4/10/2006 8:08 PM, Thomas Lumley wrote: > On Mon, 10 Apr 2006, Duncan Murdoch wrote: > >> On 4/10/2006 7:22 PM, Thomas Lumley wrote: >>> On Mon, 10 Apr 2006, Henrik Bengtsson wrote: >>> Suggestion 2: Create a has.na(x) function to replace any(is.na(x)) that returns TRUE as soon a

Re: [Rd] Suggestions to speed up median() and has.na()

2006-04-10 Thread Thomas Lumley
On Mon, 10 Apr 2006, Duncan Murdoch wrote: > On 4/10/2006 7:22 PM, Thomas Lumley wrote: >> On Mon, 10 Apr 2006, Henrik Bengtsson wrote: >> >>> Suggestion 2: >>> Create a has.na(x) function to replace any(is.na(x)) that returns TRUE >>> as soon as a NA value is detected. In the best case it retur

Re: [Rd] Suggestions to speed up median() and has.na()

2006-04-10 Thread Duncan Murdoch
On 4/10/2006 7:22 PM, Thomas Lumley wrote: > On Mon, 10 Apr 2006, Henrik Bengtsson wrote: > >> Hi, >> >> I've got two suggestions how to speed up median() about 50%. For all >> iterative methods calling median() in the loops this has a major >> impact. The second suggestion will apply to other m

Re: [Rd] Suggestions to speed up median() and has.na()

2006-04-10 Thread Bill Dunlap
On Mon, 10 Apr 2006, Thomas Lumley wrote: > On Mon, 10 Apr 2006, Henrik Bengtsson wrote: > > > Hi, > > > > I've got two suggestions how to speed up median() about 50%. For all > > iterative methods calling median() in the loops this has a major > > impact. The second suggestion will apply to oth

Re: [Rd] Suggestions to speed up median() and has.na()

2006-04-10 Thread Thomas Lumley
On Mon, 10 Apr 2006, Henrik Bengtsson wrote: > Hi, > > I've got two suggestions how to speed up median() about 50%. For all > iterative methods calling median() in the loops this has a major > impact. The second suggestion will apply to other methods too. I'm surprised this has a major impact -

Re: [Rd] install.packages on unix / su (PR#8760)

2006-04-10 Thread Thomas Friedrichsmeier
> | Wishlist item: > | > | There is a small problem using intall.packages() (and update.packages()): > | Typically I want to install packages for system-wide use, not in a user > | directory. Obviously this does not work without superuser rights. > > One can see this problem as a local system manag

Re: [Rd] install.packages on unix / su (PR#8760)

2006-04-10 Thread Dirk Eddelbuettel
On 10 April 2006 at 21:14, [EMAIL PROTECTED] wrote: | Full_Name: Thomas Friedrichsmeier | Version: R 2.2.1 | OS: Debian / Linux | Submission from: (NULL) (84.60.123.243) | | | Wishlist item: | | There is a small problem using intall.packages() (and update.packages()): | Typically I want to inst

Re: [Rd] setIs and method dispatch in S4 classes

2006-04-10 Thread Peter Ruckdeschel
Hi Seth and John, Thank you for your helpful responses, >John Chambers <[EMAIL PROTECTED]> writes: >>From your description of the application, it sounds like you would be >>better off just forcing "+" to behave as you want. Using inheritance is >>a much more powerful mechanism & can introduce re

Re: [Rd] setIs and method dispatch in S4 classes

2006-04-10 Thread John Chambers
Seth Falcon wrote: >Hi John, > >I found your comments helpful, even though this isn't _my_ question. >But now I have one of my own :-) > >John Chambers <[EMAIL PROTECTED]> writes: > > >>>Of course, I could also declare explicitly "+" methods for signatures >>>c("Exp", "Exp"), c("Exp", "Gammad"),

[Rd] install.packages on unix / su (PR#8760)

2006-04-10 Thread thomas . friedrichsmeier
Full_Name: Thomas Friedrichsmeier Version: R 2.2.1 OS: Debian / Linux Submission from: (NULL) (84.60.123.243) Wishlist item: There is a small problem using intall.packages() (and update.packages()): Typically I want to install packages for system-wide use, not in a user directory. Obviously this

[Rd] Suggestions to speed up median() and has.na()

2006-04-10 Thread Henrik Bengtsson
Hi, I've got two suggestions how to speed up median() about 50%. For all iterative methods calling median() in the loops this has a major impact. The second suggestion will apply to other methods too. This is what the functions look like today: > median function (x, na.rm = FALSE) { if (is

Re: [Rd] setIs and method dispatch in S4 classes

2006-04-10 Thread Seth Falcon
Hi John, I found your comments helpful, even though this isn't _my_ question. But now I have one of my own :-) John Chambers <[EMAIL PROTECTED]> writes: >>Of course, I could also declare explicitly "+" methods for signatures >>c("Exp", "Exp"), c("Exp", "Gammad"), and c("Gammad", "Exp") in >>whic

Re: [Rd] setIs and method dispatch in S4 classes

2006-04-10 Thread John Chambers
From your description of the application, it sounds like you would be better off just forcing "+" to behave as you want. Using inheritance is a much more powerful mechanism & can introduce results you don't want, as it seems to have in this case. An important point about using inheritance is

[Rd] get(name, envir=envir) : formal argument "envir" matched by multiple actual arguments

2006-04-10 Thread Henrik Bengtsson
Hi, very sporadic and non-reproducible, I get the following type of errors: Error in get(name, envir = envir) : formal argument "envir" matched by multiple actual arguments Error in exists(cacheName, envir = envir, inherit = FALSE) : formal argument "envir" matched by multiple actual arguments

Re: [Rd] Run package code on R shutdown?

2006-04-10 Thread Duncan Murdoch
On 4/10/2006 6:16 AM, Prof Brian Ripley wrote: > On Sun, 9 Apr 2006, Duncan Murdoch wrote: > >> I'm sure I've seen this discussed before, but haven't been able to find >> it. I'd like some package code to be run when R is shut down >> (approximately when a user's .Last function would be run), to

Re: [Rd] Should demo files be run as part of R CMD check?

2006-04-10 Thread hadley wickham
> > The rationale may be that a demo is entitled to assume it is being run > > interactively. Checking demo(tkdensity), for example, would be > > unproductive. > > Also, it is easy for a package author to arrange to check the demos by a > test in the package's tests directory. Thanks for your com

Re: [Rd] Run package code on R shutdown?

2006-04-10 Thread Henrik Bengtsson
On 4/10/06, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > I'm sure I've seen this discussed before, but haven't been able to find > it. I'd like some package code to be run when R is shut down > (approximately when a user's .Last function would be run), to clean up > properly. What is the best way

[Rd] Example in ?order

2006-04-10 Thread Gregor Gorjanc
Hello! On R Version 2.2.1 (2005-12-20 r36812) and in SVN The following part of the example in ?order says ## For character vectors we can make use of rank: cy <- as.character(y) rbind(x,y,z)[, order(x, -rank(y), z)] But "cy" is not used in there. -- Lep pozdrav / With regards,

Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta

2006-04-10 Thread Dirk Eddelbuettel
On 10 April 2006 at 14:31, Bjørn-Helge Mevik wrote: | Dirk Eddelbuettel wrote: | | > Fair point, especially as you have to insist on using gcc 3.3.* on Debian: | > -- 3.3.6 is the current 3.3.* one whereas Bjørn-Helge used 3.3.5 | > -- 3.4.5 is the latest 3.* one supplanting 3.3.(5,6) | > -- 4.0.

Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta

2006-04-10 Thread Bjørn-Helge Mevik
Dirk Eddelbuettel wrote: > Fair point, especially as you have to insist on using gcc 3.3.* on Debian: > -- 3.3.6 is the current 3.3.* one whereas Bjørn-Helge used 3.3.5 > -- 3.4.5 is the latest 3.* one supplanting 3.3.(5,6) > -- 4.0.3 is the current default > -- 4.1.0 is available too > > That app

Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta

2006-04-10 Thread Dirk Eddelbuettel
On 10 April 2006 at 10:06, Prof Brian Ripley wrote: | Since that compiler is not even the last in the 3.3.x series, and there | are now three later (released) gcc series, I think we have to write that | off to an optimization bug in gcc 3.3.x. Fair point, especially as you have to insist on usi

Re: [Rd] Branch changes at feature freeze

2006-04-10 Thread Duncan Murdoch
On 4/10/2006 5:16 AM, Prof Brian Ripley wrote: > Peter Dalgaard is travelling today, so this is a 'heads up' on the effects > of having gone today into feature freeze on 2.3.0. > > R-devel (the SVN trunk and the tarballs made available from ETHZ) is now > labelled '2.4.0 Under development' and w

Re: [Rd] setIs and method dispatch in S4 classes

2006-04-10 Thread Peter Ruckdeschel
Hi Seth , thank you for your reply. Seth Falcon <[EMAIL PROTECTED]> writes: >Peter Ruckdeschel <[EMAIL PROTECTED]> writes: > > >> ## now: B00 mother class to B01 and B02, and again B02 "contains" B01 by >> setIs: >> setClass("B00", representation(a="numeric")) >> setClass("B01", representatio

Re: [Rd] Run package code on R shutdown?

2006-04-10 Thread Prof Brian Ripley
On Sun, 9 Apr 2006, Duncan Murdoch wrote: > I'm sure I've seen this discussed before, but haven't been able to find > it. I'd like some package code to be run when R is shut down > (approximately when a user's .Last function would be run), to clean up > properly. What is the best way to do this?

Re: [Rd] Should demo files be run as part of R CMD check?

2006-04-10 Thread Prof Brian Ripley
On Fri, 7 Apr 2006, Thomas Lumley wrote: > On Fri, 7 Apr 2006, hadley wickham wrote: > >> I was a bit suprised to note that demo files are not run as part of R >> CMD check. This seems out of keeping with the philosophy of running >> all code contained in the package (in the source, in examples e

[Rd] Branch changes at feature freeze

2006-04-10 Thread Prof Brian Ripley
Peter Dalgaard is travelling today, so this is a 'heads up' on the effects of having gone today into feature freeze on 2.3.0. R-devel (the SVN trunk and the tarballs made available from ETHZ) is now labelled '2.4.0 Under development' and will shortly include changes intended for 2.4.0 (and not

Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta

2006-04-10 Thread Prof Brian Ripley
Since that compiler is not even the last in the 3.3.x series, and there are now three later (released) gcc series, I think we have to write that off to an optimization bug in gcc 3.3.x. On Mon, 10 Apr 2006, Bjørn-Helge Mevik wrote: Peter Dalgaard wrote: I don't see it with a current version

Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta

2006-04-10 Thread Bjørn-Helge Mevik
Peter Dalgaard wrote: > I don't see it with a current version either. What happens if you > reduce the optimization level? (I've tried both "-g" and -g "-O3"). > Is that -std=gnu99 bit necessary? My gcc is gcc (GCC) 3.3.5 (Debian 1:3.3.5-13). I've now tried with ./configure CFLAGS="-g [-O|-O2|-O

[Rd] Spelling of "parameter" in summary.nls(..., correlation = TRUE) (PR#8759)

2006-04-10 Thread henric . nilsson
Full_Name: Henric Nilsson Version: 2.3.0 alpha (2006-04-08 r37675) OS: Windows XP SP2 Submission from: (NULL) (212.209.13.15) The text preceeding the correlation matrix in summary.nls(..., correlation = TRUE) has a spelling error: parameter is spelled paraneter. > DNase1 <- subset(DNase, Run ==