Re: [Rd] [R] library(): load library from a specified location

2010-04-05 Thread Martin Maechler
[ re-diverted to R-devel ] Barry Rowlingson b.rowling...@lancaster.ac.uk on Tue, 30 Mar 2010 20:15:00 +0100 writes: On Tue, Mar 30, 2010 at 7:58 PM, Rolf Turner r.tur...@auckland.ac.nz wrote: But ***please*** say ``load *package*'', not ``load library''.  The *location*

[Rd] svn.r-project.org with new trusted certificate

2010-04-13 Thread Martin Maechler
using the R development sources, (or had scripts that read the logs, or ...) may need to cache the new certificate by some one-time manual interaction. Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [Rd] difficulties with setMethod([ and ...

2010-05-18 Thread Martin Maechler
if you are on a decent OS and in side the package source directory. -- Martin Maechler, ETH Zurich Let me know if you need any further explanation. Several warnings: * I was using this code with S3 generics and methods. * There are quite possibly better ways of detecting empty

[Rd] BIC() in stats {was [R-sig-ME] how to extract the BIC value}

2010-05-18 Thread Martin Maechler
MM == Martin Maechler maech...@stat.math.ethz.ch on Tue, 18 May 2010 12:37:21 +0200 writes: GaGr == Gabor Grothendieck ggrothendi...@gmail.com on Mon, 17 May 2010 09:45:00 -0400 writes: GaGr BIC seems like something that would logically go into stats in the GaGr core of R

Re: [Rd] BIC() in stats {was [R-sig-ME] how to extract the BIC value}

2010-05-18 Thread Martin Maechler
Adding to my own statements (below) : MM == Martin Maechler maech...@stat.math.ethz.ch on Tue, 18 May 2010 13:05:27 +0200 writes: MM == Martin Maechler maech...@stat.math.ethz.ch on Tue, 18 May 2010 12:37:21 +0200 writes: GaGr == Gabor Grothendieck ggrothendi...@gmail.com

Re: [Rd] [R] avoiding reinstall already installed *package*

2010-05-18 Thread Martin Maechler
On Tue, May 18, 2010 at 22:38, William Dunlap wdun...@tibco.com wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Martin Maechler Sent: Tuesday, May 18, 2010 1:25 PM To: milton ruser Cc: r-h...@r-project.org

Re: [Rd] SVN vs DVCS

2010-05-26 Thread Martin Maechler
Felix Andrews fe...@nfrac.org on Wed, 26 May 2010 11:20:12 +1000 writes: On second thoughts it is really none of my business how the R sources are managed. But I would encourage package developers and/or r-forge maintainers to consider these systems. Thank you, Felix,

Re: [Rd] warning from install.packages()

2010-06-03 Thread Martin Maechler
. the group here does share it}. I'd agree to not put a warning but I'd definitely want a message aka note to the user. The *wording* of that note should not be alarming at all, I agree, just a note to the user. Martin Maechler, ETH Zurich __ R-devel@r

Re: [Rd] warning from install.packages()

2010-06-03 Thread Martin Maechler
VG == Vincent Goulet vincent.gou...@act.ulaval.ca on Thu, 3 Jun 2010 10:24:21 -0400 writes: VG Le jeu. 3 juin à 09:27, Ben Bolker a écrit : Martin Maechler wrote: BB == Ben Bolker bol...@ufl.edu on Wed, 02 Jun 2010 13:45:18 -0400 writes: BB Michael Dewey wrote

Re: [Rd] named empty list

2010-06-04 Thread Martin Maechler
[2.12.0] (only; considering it a new feature). Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Argument recycling in substring()

2010-06-04 Thread Martin Maechler
HP == Hervé Pagès hpa...@fhcrc.org on Thu, 03 Jun 2010 17:53:33 -0700 writes: HP Hi, HP According to its man page substring() expands (its) arguments HP cyclically to the length of the longest _provided_ none are of HP zero length. HP So, as expected, I get an error

Re: [Rd] seek() and gzfile() on 32-bit R2.12.0 in linux

2010-06-24 Thread Martin Maechler
the CRAN maintainers that indeed this is a bug in R-devel, or probably in zlib 1.2.4 (R 2.11.x uses zlib 1.2.3). Within R-core, Brian Ripley has been the zlib principal investigator, and I'd wait a bit for his comment on this issue. Martin Maechler, ETH Zurich and R-Core Team BW cheers

Re: [Rd] NAs and weighted.mean

2010-06-24 Thread Martin Maechler
at first, and R-patched later after a while. Martin Maechler, ETH Zurich RobMcG Here's the full note from the NEWS file. RobMcG o The default method of weighted.mean(x, w) coerces 'w' to be RobMcG numeric (aka double); previously only integer weights were RobMcG coerced. Zero

Re: [Rd] POSIXlt matching bug

2010-07-02 Thread Martin Maechler
the tests in C code, so that the resulting R code would simply be match - function(x, table, nomatch = NA_integer_, incomparables = NULL) .Internal(x, table, nomatch, incomparables) Martin Maechler, ETH Zurich RobMcG and may prefer a simple change to the ?match RobMcG documentation

Re: [Rd] POSIXlt matching bug

2010-07-02 Thread Martin Maechler
MM == Martin Maechler maech...@stat.math.ethz.ch on Fri, 2 Jul 2010 12:22:07 +0200 writes: RobMcG == McGehee, Robert robert.mcge...@geodecapital.com on Tue, 29 Jun 2010 10:46:06 -0400 writes: RobMcG I came across the below mis-feature/bug using match with POSIXlt objects

Re: [Rd] Best way to determine if you're running 32 or 64 bit R on windows

2010-07-02 Thread Martin Maechler
Jeffrey Horner jeffrey.horner at gmail.com writes: Is this sufficient? if (.Machine$sizeof.pointer==4){ cat('32\n') } else { cat('64\n') } Or is it better to test something in R.version, say os? No, the above is perfect, as it also works on other platforms to distinguish 32-bit

Re: [Rd] kmeans

2010-07-05 Thread Martin Maechler
Gabor Grothendieck ggrothendi...@gmail.com on Fri, 2 Jul 2010 18:50:28 -0400 writes: In kmeans() in stats one gets an error message with the default clustering algorithm if centers = 1. Its often useful to calculate the sum of squares for 1 cluster, 2 clusters, etc. and this

Re: [Rd] arr.ind argument to which.min and which.max

2010-07-06 Thread Martin Maechler
help(arrayInd). yes... and if you wondered *who* re-factored which() into its internal the arrayInd() part . . had not known about the R.utils function. [] On Mon, Jul 5, 2010 at 8:27 PM, Patrick Burns pbu...@pburns.seanet.com wrote: On 05/07/2010 10:56, Martin

Re: [Rd] Large discrepancies in the same object being saved to .RData

2010-07-12 Thread Martin Maechler
(.) original x attr(x, .Environment) - NULL print.default(unclass(x), ...) if (showEnv) print(e) invisible(.x) } -- Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] broken link to new features in R-devel: no NEWS file

2010-07-21 Thread Martin Maechler
updated) web page is that it's really about *NON RELEASED* versions of R. Martin Maechler, ETH ZUrich On Wed, 21 Jul 2010, mark.braving...@csiro.au wrote: Hi The link from CRAN to new features in R-devel hasn't been working for a few days. Specifically

Re: [Rd] R CMD build wiped my computer

2010-07-28 Thread Martin Maechler
'~' as your home directory. But I can hardly believe it. This seems explanation seems a bit doubtful to me.. ... and even more importantly if I can I restore what was lost. well, you just get it from the backup. You do daily backups, do you? Regards, Martin Maechler, ETH Zurich

Re: [Rd] rbind on data.frame that contains a column that is also a data.frame

2010-08-07 Thread Martin Maechler
. But getting back to 'matrices', I think they should work without problems, at least for basic R operations such as rbind(). I don't have time to analyze the Surv - example below, but at the moment think, that we'd be interested in fixing the problems.. Martin Maechler, ETH Zurich Heinz

Re: [Rd] R support for 64 bit integers

2010-08-10 Thread Martin Maechler
, e.g., one big challenge will be to go there in a way such that not all R packages using compiled code will have to be patched extensively... another aspect is how the BLAS / Lapack team will address the problem. Martin Maechler, ETH Zurich __ R-devel@r

Re: [Rd] save() object w/o all of the loaded environment

2010-08-25 Thread Martin Maechler
RL == Roebuck,Paul L proeb...@mdanderson.org on Tue, 24 Aug 2010 11:06:54 -0500 writes: RL I have two packages, one that does the actual work (SC) RL and the other a Tcl/Tk UI (SCUI) that invokes methods RL within the former. Within the SCUI's invocation method, RL I save an

Re: [Rd] No [[-.factor()

2010-08-26 Thread Martin Maechler
(Two, Three) however should continue to give an error. Martin Maechler, ETH Zurich z - factor(c(Two,Two,Three), levels=c(One,Two,Three)) z WD [1] Two Two Three WD Levels: One Two Three str(z) WD Factor w/ 3 levels One,Two,Three: 2 2 3 z[[2]] - One str(z

Re: [Rd] RCMD CHECK and non-methods

2010-08-26 Thread Martin Maechler
not a WARNING (or nothing at all)? {from the above: definitely a warning, if not worse} Best regards, Martin Martin Maechler, ETH Zurich - if not, shouldn't there be a more explicit statement to the effect that if R decides it's a method, then it damned well is a method, whether you think

Re: [Rd] No [[-.factor()

2010-08-30 Thread Martin Maechler
Prof Brian Ripley rip...@stats.ox.ac.uk on Mon, 30 Aug 2010 08:28:24 +0100 (BST) writes: On Thu, 26 Aug 2010, Martin Maechler wrote: WD == William Dunlap wdun...@tibco.com on Wed, 25 Aug 2010 17:31:27 -0700 writes: WD Should there be a [[-.factor() that either

Re: [Rd] S4 Method Signatures

2010-09-03 Thread Martin Maechler
. Martin Maechler, ETH Zurich DS -- DS Dario Strbenac DS Research Assistant DS Cancer Epigenetics DS Garvan Institute of Medical Research DS Darlinghurst NSW 2010 DS Australia DS __ DS R

Re: [Rd] Suggestion: Add DESCRIPTION 'Date' to R CMD check log header

2010-09-15 Thread Martin Maechler
Hi Henrik HB == Henrik Bengtsson h...@stat.berkeley.edu on Tue, 14 Sep 2010 18:26:31 -0700 writes: HB Hi, HB in R CMD check, the version of the package being checked is reported, e.g. HB Thu Sep 9 05:02:30 2010: Checking package R.utils (SVN revision 399) ... HB * using

Re: [Rd] OT: Reason/history behind ## notation for comments?

2010-09-23 Thread Martin Maechler
) programming history. Martin Maechler, ETH Zurich (and R Core) LG Best wishes, LG Laurent LG On 22 September 2010 07:26, Henrik Bengtsson LG h...@stat.berkeley.edu wrote: Off topic, but since I've observe both styles, does anyone know the history behind/reason for using

Re: [Rd] Recursion error after upgrade to R_2.11.1 [Sec=Unclassified] [Sec=Unclassified]

2010-10-07 Thread Martin Maechler
. Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] new.env does not recognize parents from subclassesof environment

2010-10-23 Thread Martin Maechler
2010/10/23 Uwe Ligges lig...@statistik.tu-dortmund.de: On 23.10.2010 17:08, Uwe Ligges wrote: Looks like those ETH pages were nnot updated after the R-2.12.0 release (they do not show current R-tached / R-devel), hence CCing Martin Maechler. ... which I actually do now... Hmm, but why

Re: [Rd] new.env does not recognize parents from subclassesof environment

2010-10-23 Thread Martin Maechler
On Sat, Oct 23, 2010 at 18:23, Peter Dalgaard pda...@gmail.com wrote: On 10/23/2010 05:27 PM, Uwe Ligges wrote: On 23.10.2010 17:25, Martin Maechler wrote: 2010/10/23 Uwe Liggeslig...@statistik.tu-dortmund.de: On 23.10.2010 17:08, Uwe Ligges wrote: Looks like those ETH pages were nnot

Re: [Rd] Documentation of option 'help.ports' not in help(options)

2010-11-05 Thread Martin Maechler
Henrik Bengtsson h...@stat.berkeley.edu on Wed, 27 Oct 2010 12:54:15 -0700 writes: FYI, the option 'help.ports' is not document under help(options). Should it? yes, for completeness' sake; I've added it besides the other help.foobar options. It is documented under

Re: [Rd] S4 package warning

2010-11-12 Thread Martin Maechler
Robin Hankin rk...@cam.ac.uk on Wed, 10 Nov 2010 09:53:30 + writes: Hello everyone. R-2.12.0, suse linux 11.3. I am debugging a package that uses S4 methods and R CMD check gives the following warning: Warning in methods::findMethods(g, env) : non-generic

Re: [Rd] package matrix dummy.cpp

2010-11-29 Thread Martin Maechler
should not be needed just because of dummy.cpp in Matrix; and hence I've removed it for the next version of Matrix. However, as said above, I strongly believe your OS / R setup should be amended in such a way that you can also easily install packages with C++ code. Best regards, Martin Maechler

[Rd] RFC: sapply() limitation from vector to matrix, but not further

2010-12-01 Thread Martin Maechler
, the default would be 'ARRAY = TRUE', but of course, given the long-standing different behavior, it seem much too risky, and my proposal includes remaining back-compatible with default ARRAY = FALSE. Martin Maechler, ETH Zurich __ R-devel@r-project.org

Re: [Rd] [Rcpp-devel] GPL and R Community Policies (Rcpp)

2010-12-02 Thread Martin Maechler
but not insignificant fraction of the R community. -- Thanks to all contributors ... and that should be *it*. Martin Maechler, ETH Zurich (Administrator of the R-devel mailing list) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [Rd] 0.5 != integrate(dnorm,0,20000) = 0

2010-12-07 Thread Martin Maechler
of subdivisions to be used in addition to the already present 'subdivisions = 100' (= the maximum number of subintervals.) Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] minor problem in strsplit help file

2010-12-27 Thread Martin Maechler
PatB == Patrick Burns pbu...@pburns.seanet.com on Fri, 24 Dec 2010 10:27:23 + writes: PatB The 'extended' argument to 'strsplit' has been PatB removed, but it is still mentioned in the argument PatB items in the help file for 'fixed' and 'perl'. Indeed; thank you Pat! I've

Re: [Rd] RFC: sapply() limitation from vector to matrix, but not further

2010-12-27 Thread Martin Maechler
Finally finding time to come back to this. Remember that I've started the thread by proposing a version of sapply() which does not just stop with making a matrix() from the lapply() result, but instead --- only when the new argument ARRAY = TRUE is set --- may return an array() of any

Re: [Rd] RFC: sapply() limitation from vector to matrix, but not further

2010-12-28 Thread Martin Maechler
Gabor Grothendieck ggrothendi...@gmail.com on Mon, 27 Dec 2010 17:06:25 -0500 writes: On Wed, Dec 1, 2010 at 3:39 AM, Martin Maechler maech...@stat.math.ethz.ch wrote: My proposal -- implemented and make check tested -- is to add an optional argument  'ARRAY' which

Re: [Rd] RFC: sapply() limitation from vector to matrix, but not further

2010-12-28 Thread Martin Maechler
On Tue, Dec 28, 2010 at 19:14, Tony Plate tpl...@acm.org wrote: The abind() function from the abind package is an alternative here -- it can take a list argument, which makes it easy to use with the result of lapply().  It's also able take direction about which dimension to join on. x -

Re: [Rd] aperm() should retain class of input object

2010-12-29 Thread Martin Maechler
with your proposal and would indeed implement it (for R-devel aka R 2.13.0 to be) unless someone has good arguments for something else. {{well, my version *would* keep the 'perm = NULL' default for both default and table methods.}} Martin Maechler, ETH Zurich The .table method does work

Re: [Rd] RFC: sapply() limitation from vector to matrix, but not further

2011-01-03 Thread Martin Maechler
Martin Maechler maech...@stat.math.ethz.ch on Tue, 28 Dec 2010 20:06:07 +0100 writes: On Tue, Dec 28, 2010 at 19:14, Tony Plate tpl...@acm.org wrote: The abind() function from the abind package is an alternative here -- it can take a list argument, which makes

Re: [Rd] Minimum of an ordered factor

2011-01-05 Thread Martin Maechler
..) But your code is fine, even nice, in most parts, and I will add (most of) it (and some documentation) to R-devel unless we get contradicting comments : Any comments appreciated. (still) Thank you, Thorn! With regards, Martin Maechler, ETH Zurich

Re: [Rd] Minimum of an ordered factor

2011-01-07 Thread Martin Maechler
TTLAM == Thaler, Thorn, LAUSANNE, Applied Mathematics thorn.tha...@rdls.nestle.com on Thu, 6 Jan 2011 15:37:01 +0100 writes: TTLAM Kurt Hornik writes if (!all(sapply(args, is.ordered)) || !all(sapply(level.list, identical, y = level.set))) { I think it would be

Re: [Rd] Minimum of an ordered factor

2011-01-07 Thread Martin Maechler
Thaler,Thorn,LAUSANNE,Applied Mathematics thorn.tha...@rdls.nestle.com on Fri, 7 Jan 2011 13:35:16 +0100 writes: Martin Maechler writes I have now committed the amended proposal (rev 53925); thank you for the feedbacks.. I had a look at it and there is a typo

Re: [Rd] plotmath indices: suggested addition to help file

2011-01-21 Thread Martin Maechler
Thank you, Claudia, CB == Claudia Beleites cbelei...@units.it on Thu, 20 Jan 2011 14:05:41 +0100 writes: CB Dear all, I just stumbled over the fact that subsetting CB by square bracket will only output the first given CB index. I guess the rest is thrown away by the CADDR in

Re: [Rd] plotmath indices: suggested addition to help file

2011-01-21 Thread Martin Maechler
PE == Peter Ehlers ehl...@ucalgary.ca on Fri, 21 Jan 2011 06:17:20 -0800 writes: PE On 2011-01-21 02:27, Martin Maechler wrote: Thank you, Claudia, CB == Claudia Beleitescbelei...@units.it on Thu, 20 Jan 2011 14:05:41 +0100 writes: CB Dear all, I just

Re: [Rd] help with S4 objects: trying to use a link-glm as a class in an object definition

2011-01-29 Thread Martin Maechler
(a,item=make.link(probit)) } b - fa() b An object of class a Slot item: $linkfun function (mu) Martin Maechler, ETH Zurich fa - function() { + new(a,item=make.link(probit)) + } fa() Error in validObject(.Object) : invalid class a object: undefined class

[Rd] patch dendrogram.R from stats [was: Re: dendrogram plot does not draw long labels ?]

2011-01-29 Thread Martin Maechler
box is well visible. I was searching a bit and did not find mentioned on ?par or ?clip that clipping happens device dependently, but I vaguely recall to have seen it stated.. However the patch is a good idea, anyway, and it will be in R 2.13.x.. Thanks again, Martin Maechler Best, Tobias

[Rd] [.raster bug {was str() on raster objects fails ..}

2011-02-01 Thread Martin Maechler
Henrik Bengtsson h...@biostat.ucsf.edu on Mon, 31 Jan 2011 11:16:59 -0800 writes: Hi, str() on raster objects fails for certain dimensions. For example: str(as.raster(0, nrow=1, ncol=100)) 'raster' chr [1, 1:100] #00 #00 #00 #00 ...

Re: [Rd] [.raster bug {was str() on raster objects fails ..}

2011-02-02 Thread Martin Maechler
On Wed, Feb 2, 2011 at 02:16, Paul Murrell p.murr...@auckland.ac.nz wrote: Hi On 2/02/2011 2:03 p.m., Henrik Bengtsson wrote: On Tue, Feb 1, 2011 at 4:46 PM, Paul Murrellp.murr...@auckland.ac.nz  wrote: Hi On 1/02/2011 9:22 p.m., Martin Maechler wrote: Henrik Bengtssonh

Re: [Rd] [.raster bug {was str() on raster objects fails ..}

2011-02-02 Thread Martin Maechler
., Martin Maechler wrote: Henrik Bengtssonh...@biostat.ucsf.edu     on Mon, 31 Jan 2011 11:16:59 -0800 writes:        Hi, str() on raster objects fails for certain dimensions.  For        example:        str(as.raster(0, nrow=1, ncol=100)) 'raster' chr [1, 1:100]        #00 #00 #00

Re: [Rd] [.raster bug {was str() on raster objects fails ..}

2011-02-07 Thread Martin Maechler
Martin Maechler wrote: On Wed, Feb 2, 2011 at 23:30, Simon Urbaneksimon.urba...@r-project.org wrote: On Feb 1, 2011, at 8:16 PM, Paul Murrell wrote: Hi On 2/02/2011 2:03 p.m., Henrik Bengtsson wrote: On Tue, Feb 1, 2011 at 4:46 PM, Paul Murrellp.murr

Re: [Rd] print(...,digits=2) behavior

2011-02-07 Thread Martin Maechler
- function(v, dig=2) { ## Purpose: Add names to vector if it hasn't ## Author: Martin Maechler, Date: 16 Jul 97, 08:49 names(v) - formatC(v, w=1, dig=dig) v } do.sci - function(v, nam.dig = 3, digits = getOption('digits')) { ## Purpose: Call scientific(.) and do some more

Re: [Rd] axTicks.Rd documentation bug

2011-02-07 Thread Martin Maechler
... Thanks a lot, Ben! I've also added the new example .. though slightly modified. Notably I'm a tiny bit disappointed ;-) that you were not aware of the existence of the extendrange() function ... Martin Maechler __ R-devel@r-project.org

Re: [Rd] request for patch in drop1 (add.R)

2011-02-23 Thread Martin Maechler
Ben Bolker bbol...@gmail.com on Wed, 23 Feb 2011 09:14:37 -0500 writes: By changing three lines in drop1 from access based on $ to access based on standard accessor methods (terms() and residuals()), it becomes *much* easier to extend drop1 to work with other model

Re: [Rd] request for patch in drop1 (add.R)

2011-02-24 Thread Martin Maechler
authors to write nobs() methods for their models will be probably worth doing, as soon as 2.13.0 hits the roads.. Martin On Wed, 23 Feb 2011, Martin Maechler wrote: Ben Bolker bbol...@gmail.com on Wed, 23 Feb 2011 09:14:37 -0500 writes: By changing three lines

Re: [Rd] Standardized Pearson residuals

2011-03-17 Thread Martin Maechler
peter dalgaard pda...@gmail.com on Thu, 17 Mar 2011 15:45:01 +0100 writes: On Mar 16, 2011, at 23:34 , John Maindonald wrote: One can easily test for the binary case and not give the statistic in that case. Warning if expected cell counts 5 would be another

Re: [Rd] texi2dvi / egrep issue shows (a.o.) up in R-alpha

2011-03-22 Thread Martin Maechler
Tobias Verbeke tobias.verb...@openanalytics.eu on Mon, 21 Mar 2011 23:45:33 +0100 writes: L.S. I noticed weird tools::texi2dvi behaviour on R-alpha when specifying an absolute path to the .tex file. The same phenomenon also appears to occur on R-2.12.2, so maybe the

Re: [Rd] R-alpha typo in ?replicate ?

2011-03-22 Thread Martin Maechler
Thank you, Ben. I'm committing the fixes. Martin Ben Bolker bbol...@gmail.com on Mon, 21 Mar 2011 23:09:29 -0400 writes: simplify: logical or character string; should the result be simplified to a vector, matrix or higher dimensional array if possible? The default,

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-28 Thread Martin Maechler
Douglas Bates ba...@stat.wisc.edu on Mon, 28 Mar 2011 09:24:39 -0500 writes: Can you provide the output from sessionInfo() so we can know the platform? Also, did you configure R with --enable-strict-barrier or set the C compilation flag -DTESTING_WRITE_BARRIER? I

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Martin Maechler
HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL Douglas Bates wrote: I isolated the problem and tested then committed a fix. I am going to ask Martin to upload the new release as I have gotten out of sync with some of his

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Martin Maechler
Martin Maechler maech...@stat.math.ethz.ch on Thu, 7 Apr 2011 12:24:32 +0200 writes: HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7 Apr 2011 07:51:44 +0100 writes: HL Douglas Bates wrote: I isolated the problem and tested then committed a fix. I am going

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-07 Thread Martin Maechler
HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 07 Apr 2011 19:31:35 +0100 writes: HL Martin Maechler wrote: Martin Maechler maech...@stat.math.ethz.ch on Thu, 7 Apr 2011 12:24:32 +0200 writes: HL == Hin-Tak Leung ht...@users.sourceforge.net on Thu, 7

Re: [Rd] R CMD build now removes empty dirs

2011-04-11 Thread Martin Maechler
/ !) Thanks for the heads up about NEWS.html. It's finally current again, and hopefully remains so: It got outdated accidentally, as it was removed from the default 'make' target, and now needs an extra make call. Martin Maechler, ETH Zurich __ R-devel@r

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-11 Thread Martin Maechler
Fantastic. Thanks a lot, Luke! I can close the thread just to say the finalit wasn't Matrix after all! ;-) On Fri, Apr 8, 2011 at 20:48, luke-tier...@uiowa.edu wrote: Fixed in R-devel by 55385 and R-2-113-branch by 55386. The problem was a call to install() in the C srouce code

Re: [Rd] R CMD build --resave-data

2011-04-13 Thread Martin Maechler
Hervé Pagès hpa...@fhcrc.org on Tue, 12 Apr 2011 22:21:58 -0700 writes: On 11-04-12 07:06 PM, Simon Urbanek wrote: On Apr 12, 2011, at 8:53 PM, Hervé Pagès wrote: Hi Uwe, On 11-04-11 08:13 AM, Uwe Ligges wrote: On 11.04.2011 02:47,

Re: [Rd] Dangerous Bug with IF function of R

2011-04-19 Thread Martin Maechler
salmajj salm...@softhome.net on Mon, 18 Apr 2011 11:11:28 -0700 (PDT) writes: Thanks a lot Petr it works!!! of course .. You know for someone who is used to work with matlab it is not so obvious:) well, what do you mean with that? I'm intrigued. After such a blatantly wrong

Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code

2011-04-23 Thread Martin Maechler
Simon Urbanek simon.urba...@r-project.org on Thu, 21 Apr 2011 10:57:19 -0400 writes: On Apr 21, 2011, at 10:52 AM, Sean Robert McGuffee wrote: Thanks, That's great, but I don't know how to determine what foo is. It's the name of your package. How do I declare

Re: [Rd] An update of the Distribustions man page

2011-04-23 Thread Martin Maechler
. Suggestions are welcome. Kind regards Christophe Thank you for the suggestion, Christophe! Martin Maechler, ETH Zurich -- Christophe DUTANG Ph. D. student at ISFA, Lyon, France __ R-devel@r-project.org mailing list https

Re: [Rd] request for R-exts addition

2011-04-29 Thread Martin Maechler
or even better a patch towards a current version of the manual Rsource/doc/manual/R-exts.texi from subversion, a nightly tarball, or simply https://svn.r-project.org/R/trunk/doc/manual/R-exts.texi With many thanks in advance, Martin Maechler, ETH Zurich

Re: [Rd] median and data frames

2011-04-29 Thread Martin Maechler
Paul Johnson pauljoh...@gmail.com on Thu, 28 Apr 2011 00:20:27 -0500 writes: On Wed, Apr 27, 2011 at 12:44 PM, Patrick Burns pbu...@pburns.seanet.com wrote: Here are some data frames: df3.2 - data.frame(1:3, 7:9) df4.2 - data.frame(1:4, 7:10) df3.3 -

Re: [Rd] Kendall's tau code

2011-04-30 Thread Martin Maechler
(*, method=kendall) I'll eventually want a C version, not the least because we may look into dealing with NA 's in the same -- flexible -- way that they are handled currently via the 'use = ...' argument. I may contact you privately for more. Thanks again, Martin Maechler, ETH Zurich (and R

Re: [Rd] R CMD check and Suggests Packages

2011-05-03 Thread Martin Maechler
Hervé Pagès hpa...@fhcrc.org on Mon, 02 May 2011 11:55:08 -0700 writes: Hi, On 11-04-28 07:00 PM, Dario Strbenac wrote: Hello, In my description file, I have an example data package in Suggests: that I've deleted from my library to test what the user who

Re: [Rd] Add See Also: missing to help('exists')?

2011-05-16 Thread Martin Maechler
... though quite disillusioned with a very vague hope that useRs would read the help page so thoroughly ... Martin Maechler, ETH Zurich SpGThanks, Spencer SpG On 5/14/2011 3:30 AM, David Winsemius wrote: On May 14, 2011, at 3:30 AM, utkarshsinghal wrote: Hi

Re: [Rd] (no subject)

2011-07-19 Thread Martin Maechler
code, instead of simply using the R packages 'gmp' and 'Rmpfr' and work with R code? -- Martin Maechler, ETH Zurich I have installed mpfr and gmp under the instructions of the following website http://pauillac.inria.fr/cdrom_a_graver/prog/pc/mpfr/eng.htm and I get no errors

Re: [Rd] short documentation suggestion for by --- reference simplify2array and ave

2011-07-21 Thread Martin Maechler
probably also be iw mentioned in the See also section of apply.) iw hope this helps. Yes, thank you. I did (something like) that. -- Martin Maechler, ETH Zurich iw /iaw Ivo Welch (ivo.we...@gmail.com) __ R-devel@r-project.org mailing

Re: [Rd] heatmap documentation typo

2011-07-21 Thread Martin Maechler
, not 'NULL'. An anonymous expert suggested that I should attach an svn diff file to this report, so I will. Not necessary. I've now committed the fix. Thank you, Jonathan, for the report. Martin Maechler, ETH Zurich

Re: [Rd] Same class name, different package

2011-07-25 Thread Martin Maechler
John Chambers j...@r-project.org on Sun, 24 Jul 2011 14:58:23 -0700 writes: A point that has come up a couple of times with the new test is that two classes from two packages may be the same class. Should that turn on duplicate classes? One situation where the answer

Re: [Rd] 'data.frame' method for base::rep()

2011-08-03 Thread Martin Maechler
yet another data.frame method .. Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] X11.options().

2011-08-08 Thread Martin Maechler
Hi Rolf, please excuse a short top-reply: As I see you are using an operating system (instead of Win..), can you try in the shell echo 'X11.options()$type' | R --vanilla --slave and does that really *not* report [1] cairo ?? (and BTW: Your subject had tolower(LL) instead of 11 )

Re: [Rd] X11.options().

2011-08-08 Thread Martin Maechler
Uwe Ligges lig...@statistik.tu-dortmund.de on Mon, 8 Aug 2011 21:38:06 +0200 writes: On 08.08.2011 10:20, Martin Maechler wrote: Hi Rolf, please excuse a short top-reply: As I see you are using an operating system (instead of Win..), can you try

Re: [Rd] matrix bands

2011-08-26 Thread Martin Maechler
be included in the Matrix package. well, see above and let us know if you see anything lacking in bandSparse(). Till now we haven't got much feedback about it, and there may well be room for improvement. Martin Maechler, ETH Zurich and co- maintainer(Matrix) I have included two versions

Re: [Rd] matrix bands

2011-08-26 Thread Martin Maechler
at it, further I'll look at your examples of getting ... and at the moment I'm still a bit curious why, i.e., to what end / in what application you need them [ rather than band(*,.,.) ]. We may e-talk about this off-public if you want. Martin On 2011-08-26 14:08, Martin Maechler wrote: Jeremy David

Re: [Rd] An example of very slow computation

2011-09-01 Thread Martin Maechler
) %*% v{A matrix, v vector, t scalar} and *still* numerically reliable. Martin Maechler, ETH Zurich Which is why I said it applies when the system is diagonalizable. It won't work for non-diagonalizable matrix A, because T (eigenvector matrix) is singular

Re: [Rd] repeatable segfault - on Mac

2011-09-08 Thread Martin Maechler
August). As this is calling LAPACK code, I guess that this is yet another case where the Mac version of optimized BLAS / LAPACK is playing wrongly. Martin Maechler David Winsemius On Sep 6, 2011, at 12:12 AM, robin hankin wrote: Hi. macosx 10.6.8 With R-2.13.1

Re: [Rd] repeatable segfault - on Mac

2011-09-08 Thread Martin Maechler
Simon Urbanek simon.urba...@r-project.org on Thu, 8 Sep 2011 09:33:23 -0400 writes: On Sep 8, 2011, at 4:01 AM, Martin Maechler wrote: David Winsemius dwinsem...@comcast.net on Tue, 6 Sep 2011 00:38:13 -0400 writes: I can reproduce: eigen(crossprod(matrix(1

Re: [Rd] should dir(all=TRUE) return . and ..?

2011-09-23 Thread Martin Maechler
William Dunlap wdun...@tibco.com on Fri, 23 Sep 2011 15:49:43 + writes: dir(all=TRUE) returns the file names . and .. while dir(recursive=TRUE, all=TRUE, include.dirs=TRUE) does not. I always filter out the . and .. entries and was wondering if anyone would mind if

Re: [Rd] broken save(..., compress=xy)

2011-09-23 Thread Martin Maechler
Hervé Pagès hpa...@fhcrc.org on Fri, 23 Sep 2011 11:44:32 -0700 writes: On 11-09-23 11:02 AM, Sarah Goslee wrote: Hi, 2011/9/23 Hervé Pagèshpa...@fhcrc.org: Hi, With current R devel and R 2.13.1: aa=1:5 save(aa, file=aa.rda, compress=xy)

Re: [Rd] load.R patch suggestion

2011-09-28 Thread Martin Maechler
Ben Bolker bbol...@gmail.com on Thu, 15 Sep 2011 11:03:26 +0200 writes: Inspired by http://stackoverflow.com/questions/7487778/could-you-tell-me-what-this-error-means I wrote the following very small (one-line) patch which returns an *informative* error message when R

Re: [Rd] [R] are arithmetic comparison operators binary?

2009-02-24 Thread Martin Maechler
WK == Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no on Mon, 23 Feb 2009 19:29:31 +0100 writes: WK Martin Maechler wrote: WK == Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no on Mon, 23 Feb 2009 12:06:32 +0100 writes: Thank you, Wacek

Re: [Rd] [R] Semantics of sequences in R

2009-02-24 Thread Martin Maechler
WK == Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no on Tue, 24 Feb 2009 11:31:13 +0100 writes: WK Dimitris Rizopoulos wrote: in my opinion the point of the whole discussion could be summarized by the question, what is a design flaw? This is totally subjective, and

Re: [Rd] Unexpected side effect of the ::: operator on the value of isGeneric

2009-02-28 Thread Martin Maechler
Wolfi == Wolfgang Huber hu...@ebi.ac.uk on Wed, 25 Feb 2009 18:15:03 + writes: Wolfi Hi, Wolfi when running the following on a fresh R, Wolfi library(IRanges) Wolfi annotation Wolfi showMethods(annotation) Wolfi Biobase:::annotation Wolfi

Re: [Rd] Unexpected side effect of the ::: operator on the value of isGeneric

2009-03-02 Thread Martin Maechler
Wolfi == Wolfgang Huber hu...@ebi.ac.uk on Sat, 28 Feb 2009 18:01:19 + writes: Wolfi Dear Martin name masking is a separate issue, which I Wolfi do not want to explore here. Wolfi If one accepts the notion that unrelated generics of Wolfi the same name may exist in

Re: [Rd] array subsetting of S4 object that inherits from array

2009-03-06 Thread Martin Maechler
revert the mis-feature. So, the override is to use 2.8.1 patched (or newer). I'm sorry for my thinko that may also affect other R-S4-programmers [of course I hope not, but then there's Murphy's law]. Regards, Martin Maechler, ETH Zurich BB Regards, BB Brad Buchsbaum BB R

Re: [Rd] Putting demo shell scripts, text files, and RScript files with a package?

2009-03-18 Thread Martin Maechler
(scripts, ch01.R, package=MASS)) { which ends in an error: It's not made for source(); it might well be source()able if 'if(interactive()) ' where replaced by 'if(dev.interactive()) ' } Martin Maechler, ETH Zurich __ R-devel@r-project.org

Re: [Rd] suggestion/request: install.packages and unnecessary file modifications

2009-03-19 Thread Martin Maechler
Thank you, Mark, I've now committed (a version of) your suggestion to R-devel (destined to become R 2.9.0 on April 17). Martin Maechler, ETH Zurich mark.braving...@csiro.au on Tue, 10 Mar 2009 21:52:30 +1100 writes: Dear R-devel When 'install.packages' runs, it updates all

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