Re: [Rd] R 2.14.1 memory management under Windows

2012-03-21 Thread Joshua Wiley
On Wed, Mar 21, 2012 at 10:14 PM, Spencer Graves wrote: > I computed "system.time(diag(3))" with R 2.12.0 on Fedora 13 Linux with > 4 GB RAM and with R 2.14.1 on Windows 7 with 8 GB RAM: > > > Linux (4 GB RAM):  0, 0.21, 0.21 -- a fifth of a second > > > Windows 7 (8 GB RAM):  11.37 7.47 93.19

[Rd] R 2.14.1 memory management under Windows

2012-03-21 Thread Spencer Graves
I computed "system.time(diag(3))" with R 2.12.0 on Fedora 13 Linux with 4 GB RAM and with R 2.14.1 on Windows 7 with 8 GB RAM: Linux (4 GB RAM): 0, 0.21, 0.21 -- a fifth of a second Windows 7 (8 GB RAM): 11.37 7.47 93.19 -- over 1.5 minutes. Moreover, during most of that time, I could

[Rd] Thai vignette, cross-compile for Mac OS X, universal/multiarch (Fwd: Mac OS X builds of CelQuantileNorm, vcftools/samtools/tabix, and snpStats)

2012-03-21 Thread Hin-Tak Leung
FYI. There is a Thai vignette - and it went a lot further doing some Thai text processing in R, than the earlier Chinese/Tibetan/LiangshanYi/Arabic vignette, which was in reality just Chinese + Cairo graphics. Managed to cross-compile an R package for Mac OS X from Linux; and it seems to be

Re: [Rd] R's copying of arguments (Re: Julia)

2012-03-21 Thread Simon Urbanek
On Mar 21, 2012, at 9:31 PM, Hervé Pagès wrote: > On 03/21/2012 06:23 PM, Simon Urbanek wrote: >> >> On Mar 20, 2012, at 3:08 PM, Hervé Pagès wrote: >> >>> Hi Oliver, >>> >>> On 03/17/2012 08:35 AM, oliver wrote: Hello, regarding the copying issue, I would like to point to

Re: [Rd] R's copying of arguments (Re: Julia)

2012-03-21 Thread Hervé Pagès
On 03/21/2012 06:23 PM, Simon Urbanek wrote: On Mar 20, 2012, at 3:08 PM, Hervé Pagès wrote: Hi Oliver, On 03/17/2012 08:35 AM, oliver wrote: Hello, regarding the copying issue, I would like to point to the "Writing R-Extensions" documentation. There it is mentio9ned, that functions of ex

Re: [Rd] R's copying of arguments (Re: Julia)

2012-03-21 Thread Simon Urbanek
On Mar 20, 2012, at 3:08 PM, Hervé Pagès wrote: > Hi Oliver, > > On 03/17/2012 08:35 AM, oliver wrote: >> Hello, >> >> regarding the copying issue, >> I would like to point to the >> >> "Writing R-Extensions" documentation. >> >> There it is mentio9ned, that functions of extensions >> that us

Re: [Rd] Why is there no within.environment function?

2012-03-21 Thread Gavin Simpson
On Wed, 2012-03-21 at 22:01 +, William Dunlap wrote: > Wouldn't within.environment be identical to with.environment? > > e <- new.env() > > with(e, { One <- 1 ; Two <- 2+2i ; Theee <- One + Two }) > > objects(e) > [1] "One" "Theee" "Two" > It might make the transition between lists an

Re: [Rd] Why is there no within.environment function?

2012-03-21 Thread peter dalgaard
On Mar 21, 2012, at 23:01 , William Dunlap wrote: > Wouldn't within.environment be identical to with.environment? >> e <- new.env() >> with(e, { One <- 1 ; Two <- 2+2i ; Theee <- One + Two }) >> objects(e) > [1] "One" "Theee" "Two" > It might make the transition between lists and environments

Re: [Rd] Why is there no within.environment function?

2012-03-21 Thread William Dunlap
Wouldn't within.environment be identical to with.environment? > e <- new.env() > with(e, { One <- 1 ; Two <- 2+2i ; Theee <- One + Two }) > objects(e) [1] "One" "Theee" "Two" It might make the transition between lists and environments simpler if within.environment existed. Bill Dunlap S

Re: [Rd] Why is there no within.environment function?

2012-03-21 Thread Gabor Grothendieck
On Wed, Mar 21, 2012 at 5:51 PM, Richard Cotton wrote: > If I want to assign some variables into an environment, it seems > natural to do something like > > e <- new.env() > within(e, >    { >      x <- 1:5 >      y <- runif(5) >    } > ) > > This throws an error, since within.environment doesn't

[Rd] Why is there no within.environment function?

2012-03-21 Thread Richard Cotton
If I want to assign some variables into an environment, it seems natural to do something like e <- new.env() within(e, { x <- 1:5 y <- runif(5) } ) This throws an error, since within.environment doesn't exist.  I realise I can work around it using as.environment(within(as.lis

Re: [Rd] enableJIT() and internal R completions (was: [ESS-bugs] ess-mode 12.03; ess hangs emacs)

2012-03-21 Thread luke-tierney
The compiler/JIT is behaving as expected. The idea of compiling on duplicate, which level 2 enables, is to address some idioms where functions are modified at runtime. Ideally it would be good to avoid these idioms, and we may eventually get there, but for now they are an issue. In this particul

Re: [Rd] bzip2'ed data under data/

2012-03-21 Thread Prof Brian Ripley
On 19/03/2012 20:25, Sebastian P. Luque wrote: Hi, R CMD check PACKAGE_VERSION_tar.gz gives warning: Files not of a type allowed in a ‘data’ directory: ‘tser1.csv.bz2’ ‘tser2.csv.bz2’ Please use e.g. ‘inst/extdata’ for non-R data files which I didn't expect, based on section 1.1.5 (Data in

Re: [Rd] overriding "summary.default" or "summary.data.frame". How?

2012-03-21 Thread Uwe Ligges
Simple answer: Never ever override R base functionality. Best, Uwe Ligges On 20.03.2012 16:24, Paul Johnson wrote: I suppose everybody who makes a package for the first time thinks "I can change anything!" and then runs into this same question. Has anybody written out information on how a p

Re: [Rd] uncompressed saves warning

2012-03-21 Thread Uwe Ligges
On 21.03.2012 14:58, Michael Friendly wrote: [Env: Windows XP Pro / R 2.14.1 / StatET / R-Forge] A package of mine now generates a Warning under R 2.15.0 beta on CRAN checks: * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained

Re: [Rd] enableJIT() prohibits usual R debugging

2012-03-21 Thread luke-tierney
On Wed, 21 Mar 2012, Vitalie Spinu wrote: Vitalie Spinu on Wed, 21 Mar 2012 14:39:52 +0100 wrote: on Wed, 21 Mar 2012 07:46:21 -0500 wrote: >> I can't reproduce this in either 2.14.1 or R-devel. > Hm .. I cannot reproduce it, nor with the latest R-devel, nor with 2.14.2 > anymore. Som

Re: [Rd] enableJIT() prohibits usual R debugging

2012-03-21 Thread Vitalie Spinu
Vitalie Spinu on Wed, 21 Mar 2012 14:39:52 +0100 wrote: on Wed, 21 Mar 2012 07:46:21 -0500 wrote: >> I can't reproduce this in either 2.14.1 or R-devel. > Hm .. I cannot reproduce it, nor with the latest R-devel, nor with 2.14.2 > anymore. Some local glitch or somethi

[Rd] uncompressed saves warning

2012-03-21 Thread Michael Friendly
[Env: Windows XP Pro / R 2.14.1 / StatET / R-Forge] A package of mine now generates a Warning under R 2.15.0 beta on CRAN checks: * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data

Re: [Rd] enableJIT() prohibits usual R debugging

2012-03-21 Thread Vitalie Spinu
on Wed, 21 Mar 2012 07:46:21 -0500 wrote: > I can't reproduce this in either 2.14.1 or R-devel. Hm .. I cannot reproduce it, nor with the latest R-devel, nor with 2.14.2 anymore. Some local glitch or something ... Vitalie. __ R-devel@r-pr

Re: [Rd] enableJIT() prohibits usual R debugging

2012-03-21 Thread luke-tierney
I can't reproduce this in either 2.14.1 or R-devel. luke On Wed, 21 Mar 2012, Vitalie Spinu wrote: Hi, Browser doesn't work properly with the compiler enabled. It might be intended behavior, but it's not documented. compiler::enableJIT(1) foo <- function(){ browser() cat("here\n") }

Re: [Rd] enableJIT() prohibits usual R debugging

2012-03-21 Thread Feng Li
FYI https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14594 On 03/21/2012 10:19 AM, Vitalie Spinu wrote: Hi, Browser doesn't work properly with the compiler enabled. It might be intended behavior, but it's not documented. compiler::enableJIT(1) foo<- function(){ browser() cat(

[Rd] enableJIT() prohibits usual R debugging

2012-03-21 Thread Vitalie Spinu
Hi, Browser doesn't work properly with the compiler enabled. It might be intended behavior, but it's not documented. compiler::enableJIT(1) foo <- function(){ browser() cat("here\n") } Browser doesn't stop, and I am getting: > foo() Called from: foo() Browse[1]> here > Thanks, V

[Rd] enableJIT() and internal R completions (was: [ESS-bugs] ess-mode 12.03; ess hangs emacs)

2012-03-21 Thread Vitalie Spinu
Hello, JIT compiler interferes with internal R completions: compiler::enableJIT(2) utils:::functionArgs("density", '') gives: utils:::functionArgs("density", '') Note: no visible global function definition for 'bw.nrd0' Note: no visible global function definition for 'bw.nrd' Note: no visib

Re: [Rd] S3 methods with full name in documentation?

2012-03-21 Thread Spencer Graves
Hi, Duncan: On 3/20/2012 6:43 PM, Duncan Murdoch wrote: On 12-03-20 4:40 PM, Spencer Graves wrote: Hello: Is there a recommended way to inform "R CMD check" that a function like "as.numeric" is NOT a method for the S3 generic function "as" for objects of class "numeric"? I