[Rd] More efficient code?

2005-07-06 Thread Gavin Simpson
10.50 12.4 10.50 12.4 "residualMatrix" 10.32 12.2 0.22 0.3 "qr.coef" 6.26 7.4 0.42 0.5 "storage.mode<-" 3.26 3.9 0.36 0.4 ".Fortran" 2.78 3.3

[Rd] Interpretting R profiling output (was More efficient code?)

2005-07-08 Thread Gavin Simpson
On Wed, 2005-07-06 at 19:54 +0100, Gavin Simpson wrote: > Dear List, > I fixed up the code in coinertiaI to only return the bits I needed from La.svd() within the permutations - thus producing a 10% speed up. I am still a little unclear about the results from Rprof() (below). Do the t

[Rd] Follow-Up: R on FC4

2005-08-01 Thread Gavin Simpson
of a bad compilation of R-Devel on FC4 with gfortran? Both these compilations was using the svn-acquired sources from this afternoon: R-patched = revision 35098 R-Devel = revision 35098 HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson

Re: [Rd] Follow-Up: R on FC4

2005-08-01 Thread Gavin Simpson
On Mon, 2005-08-01 at 10:16 -0700, Thomas Lumley wrote: > On Mon, 1 Aug 2005, Gavin Simpson wrote: > > R-devel compiles without error (same set of flags as above) but fails > > make check-all in p-r-random-tests.R - the relevant section of p-r- > > rand

[Rd] deparse(substitute(x)) and S3 methods

2005-08-03 Thread Gavin Simpson
original call. Can anyone suggest a way round this problem? Thanks in advance, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL Department of

Re: [Rd] deparse(substitute(x)) and S3 methods

2005-08-03 Thread Gavin Simpson
On Wed, 2005-08-03 at 16:28 +0100, Gavin Simpson wrote: > Dear List, > > I have the following function: Thanks to Tony Plate (and his simple example - message to self: "follow the posting guide's advice next time!!!"), I realised that deparse (substitute( )) was ta

[Rd] problem using model.frame()

2005-08-16 Thread Gavin Simpson
a, data, na.action = na.fail) Y <- model.matrix(formula, mf) if (any(colnames(Y) == "(Intercept)")) { xint <- which(colnames(Y) == "(Intercept)") Y <- Y[, -xint, drop = FALSE] } } list(X = X, Y = Y)

Re: [Rd] problem using model.frame()

2005-08-16 Thread Gavin Simpson
al a manner as possible, so I'm fishing around for potential solutions. All the best, Gav > > On 8/16/05, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > Hi I'm having a problem with model.frame, encapsulated in this example: > > > > y1 <- matr

Re: [Rd] problem using model.frame()

2005-08-16 Thread Gavin Simpson
On Tue, 2005-08-16 at 12:35 -0400, Gabor Grothendieck wrote: > On 8/16/05, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > On Tue, 2005-08-16 at 11:25 -0400, Gabor Grothendieck wrote: > > > It can handle data frames like this: > > > > > > model.frame(y

Re: [Rd] problem using model.frame()

2005-08-17 Thread Gavin Simpson
On Wed, 2005-08-17 at 20:24 +0200, Martin Maechler wrote: > >>>>> "GS" == Gavin Simpson <[EMAIL PROTECTED]> > >>>>> on Tue, 16 Aug 2005 18:44:23 +0100 writes: > > GS> On Tue, 2005-08-16 at 12:35 -0400, Gabor Grothendiec

Re: [Rd] problem using model.frame()

2005-08-17 Thread Gavin Simpson
. So one data matrix plays the role of the response and one the predictor. Which is the reason for wanting to use a formula interface. Cheers, G > On 8/17/05, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > On Wed, 2005-08-17 at 20:24 +0200, Martin Maechler wrote: > > > >>

Re: [Rd] problem using model.frame()

2005-08-18 Thread Gavin Simpson
On Thu, 2005-08-18 at 07:57 +0300, Jari Oksanen wrote: > On 18 Aug 2005, at 1:49, Gavin Simpson wrote: > > > On Wed, 2005-08-17 at 20:24 +0200, Martin Maechler wrote: > >>>>>>> "GS" == Gavin Simpson <[EMAIL PROTECTED]> > >>>>>

Re: [Rd] problem using model.frame()

2005-08-19 Thread Gavin Simpson
code back to accepting y1 ~ ., data = y2 and leave it to throw an error for the rhs being a data frame case. Once again, thank you for helping me work through this dilemma. All the best, Gav > On 8/18/05, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > On Thu, 2005-08-18 at 07:

Re: [Rd] loadings() generic in R alpha

2005-09-16 Thread Gavin Simpson
casual about speciying what generic > > functions should return in the past, and have got bitten as a result. > > For example, can it be assumed that loadings() returns a matrix?) > > > > __ > R-devel@r-project.org maili

Re: [Rd] Lists and data frames (PR#8143)

2005-09-19 Thread Gavin Simpson
as explained on page 26 of said manual. If it was intentional, then IMHO it is not the most clear example of extending a list - the [[x]] notation is what I would expect to have to use - after reading page 26 of course... HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

Re: [Rd] Lists and data frames (PR#8143)

2005-09-19 Thread Gavin Simpson
On Mon, 2005-09-19 at 16:39 +0200, Uwe Ligges wrote: > Gavin Simpson wrote: > > > On Mon, 2005-09-19 at 15:34 +0200, [EMAIL PROTECTED] wrote: > > > >>Full_Name: Frank Wagner > >>Version: R 2.1.1 > >>OS: Windows > >>Submission from: (NULL

Re: [Rd] looks in liblapack.a not liblapack.so

2005-09-19 Thread Gavin Simpson
it. > > It might have been better to do this in the next release, rather than as > an update to FC4, but there you go. Better install lapack-devel > manually. Yep, and the same with BLAS - which just caused me to spend half a day wondering why R wasn't being configured with BLAS(generic) anymore when trying out R2.2.0

[Rd] Documenting newly created generic versions of non-generic base R functions

2005-10-10 Thread Gavin Simpson
hi-jack methodology? Cheers Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk UCL

[Rd] Packages that require other packages - How?

2005-11-09 Thread Gavin Simpson
I have listed this package in the Depends field in my DESCRIPTION. What do I need to do to have the package that my package depends on be attached when I call library or require to attach my package? Apologies for being dense... Thanks, G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

Re: [Rd] write.csv

2005-11-24 Thread Gavin Simpson
csv(iris, row.names = FALSE) > write.csv(iris, row.names = TRUE) As I didn't specify a filename as the file argument, the results are displayed at the console. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T]

[Rd] Building a windows binary of a package on Linux

2005-11-30 Thread Gavin Simpson
of R and Windows package binaries that contain C, C++, Fortran code that needs to be compiled. Thanks, Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565

Re: [Rd] Building a windows binary of a package on Linux

2005-11-30 Thread Gavin Simpson
On Wed, 2005-11-30 at 10:46 -0500, Duncan Murdoch wrote: > On 11/30/2005 9:33 AM, Gavin Simpson wrote: > > Dear List, > > > > Can I build a binary package (.zip) for Windows on my Linux machine from > > my package sources? There is no C, C++, Fortran code involved, j

Re: [Rd] Building a windows binary of a package on Linux

2005-11-30 Thread Gavin Simpson
On Wed, 2005-11-30 at 11:08 -0500, Duncan Murdoch wrote: > On 11/30/2005 11:02 AM, Gavin Simpson wrote: > > On Wed, 2005-11-30 at 10:46 -0500, Duncan Murdoch wrote: > >> On 11/30/2005 9:33 AM, Gavin Simpson wrote: > >> > Dear List, > >> > > >> &

[Rd] \dQuote{} in \code{} not processed

2005-11-30 Thread Gavin Simpson
Under development (unstable) (2005-11-30 r36557) Cheers, G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] gavi

Re: [Rd] \dQuote{} in \code{} not processed

2005-11-30 Thread Gavin Simpson
On Thu, 2005-12-01 at 07:14 +, Prof Brian Ripley wrote: > On Wed, 30 Nov 2005, Gavin Simpson wrote: > > > Just wondering if this is the expected behaviour. > > Yes. The only command processed inside \code is \link (plus support for > \example and \usage which go throug

[Rd] Bug in xy.coords() or documentation error?

2006-01-21 Thread Gavin Simpson
em i686, linux-gnu status Patched major2 minor2.1 year 2006 month01 day 18 svn rev 37123 language R > sessionInfo() R version 2.2.1, 2006-01-18, i686-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics"

Re: [Rd] Bug in xy.coords() or documentation error?

2006-01-21 Thread Gavin Simpson
f: x, y: the x and y coordinates of a set of points. Alternatively, a single object 'x' can be provided if 'y = NULL' is also supplied. 'object' might not be correct here - is a formula an 'object'? Cheers, Gav > > On 1/

Re: [Rd] Bug in xy.coords() or documentation error?

2006-01-21 Thread Gavin Simpson
On Sat, 2006-01-21 at 13:39 -0500, Gabor Grothendieck wrote: > I think the docs have been changed for the next vesion > of R. Not in R Version 2.3.0 Under development (unstable) (2006-01-18 r37123) downloaded today. G > > On 1/21/06, Gavin Simpson <[EMAIL PROTECTED]> wrote: &

Re: [Rd] Bug in xy.coords() or documentation error?

2006-01-21 Thread Gavin Simpson
On Sat, 2006-01-21 at 14:07 -0500, Duncan Murdoch wrote: > On 1/21/2006 1:21 PM, Gavin Simpson wrote: > > On Sat, 2006-01-21 at 13:12 -0500, Gabor Grothendieck wrote: > >> This was discussed just recently. This is a design > >> error but the maintainers claim there ar

[Rd] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

2020-03-24 Thread Gavin Simpson
the resulting reported bug on the RedHat Bugzilla: https://bugzilla.redhat.com/show_bug.cgi?id=1815128 Beyond switching to `type = 'Xlib'`, has anyone worked around this issue on a Fedora 31 or later system? Thanks in advance Gavin -- Gavin Simpson, PhD _

Re: [Rd] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

2020-03-25 Thread Gavin Simpson
Thanks Iñaki, that worked a treat. Gavin On Wed, 25 Mar 2020 at 04:28, Iñaki Ucar wrote: > > On Wed, 25 Mar 2020 at 01:14, Gavin Simpson wrote: > > > > Dear list > > > > On Fedora 31 the pango library has recently updated to version >= 1.44 > > an

Re: [Rd] Tips for debugging: R CMD check examples

2010-06-30 Thread Gavin Simpson
(i.e. drop into a debugger on error). HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk

Re: [Rd] One possible cause for incorrect symbols in X11() output

2010-08-19 Thread Gavin Simpson
uot;q" symbol being used in Evince etc in place of pch == 1. Am I inserting this incorrectly? Many thanks, G > > (This workaround was culled from > https://bugs.launchpad.net/ubuntu/+source/fontconfig/+bug/551977 > ) > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20

Re: [Rd] One possible cause for incorrect symbols in X11() output

2010-08-19 Thread Gavin Simpson
; > Standard Symbols L > > > > > ZapfDingbats > Dingbats > > > > > On Thu, 19 Aug 2010, Gavin Simpson wrote: > > > On Thu, 2010-08-19 at 07:55 +0100, Prof Brian Ripley wrote: > >> There have been spasmodic r

Re: [Rd] How do you make a formal "feature" request?

2010-08-21 Thread Gavin Simpson
eration or tell me how to do it. > > Thanks. > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

Re: [Rd] No RTFM?

2010-08-23 Thread Gavin Simpson
list for comments/suggestions. IIRC this was how the original guide was produced. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, Londo

Re: [Rd] Decision tree and factor variables

2010-08-26 Thread Gavin Simpson
decision tree. > > Any idea on how I should handle the problem? > Thanks. Wrong list. R-Devel is for discussion pertaining to development of and with R. You need R-Help. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44

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

2010-12-01 Thread Gavin Simpson
mp; Software Consulting > > GKX Group, GKX Associates Inc. > > tel: 1-877-GKX-GROUP > > email: ggrothendieck at gmail.com > > > > [[alternative HTML version deleted]] > > ______ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailm

Re: [Rd] Reordering entries in package manual PDF's

2010-12-01 Thread Gavin Simpson
R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e]

Re: [Rd] possible bug in chron packages

2010-12-08 Thread Gavin Simpson
he object returned by `chron` never gets stored or used on the object returned form `dates`. G > I would expect the outcome of both functions to be the same, or am I > overlooking something? > > Kind regards > Joris > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~

Re: [Rd] License statement

2010-12-23 Thread Gavin Simpson
ALAND > > Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 > > Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018 > > > > Director of Consulting, Department of Statistics > > > > ______ > > R-devel@r-project.o

[Rd] Minor typo in influence.measures.Rd ?

2011-01-27 Thread Gavin Simpson
mial)) signif(cooks.distance(lmI), 3)# ~= Ci in Table 3, p.184 ### Both are against the R svn trunk, r54122, and are attached, but may not make it through the mailing list filters. All the best, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpso

Re: [Rd] terribly annoying bug with POSIXlt : one o'clock is midnight?

2011-02-04 Thread Gavin Simpson
"1970-01-01 01:00:00 BST" > as.POSIXlt(0,origin="1970-01-01", tz = "GMT") [1] "1970-01-01 GMT" > as.POSIXlt(0,origin="1970-01-01 00:00:00") [1] "1970-01-01 01:00:00 BST" > as.POSIXlt(0,origin="1970-01-01 00:00:00", tz = &

[Rd] rebuilding vignettes in 2.13-0-alpha fails if name of source dir is not package name

2011-03-26 Thread Gavin Simpson
Calls: buildVignettes -> pkgVignettes Execution halted * checking PDF version of manual ... OK WARNING: There were 3 warnings, see ‘/home/gavin/work/R/packages/analogue/analogue_check/pkg.Rcheck/00check.log’ for details -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

[Rd] Bug in tools::compactPDF() in 2.13-0-alpha

2011-03-27 Thread Gavin Simpson
LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets [7] methods base Thanks, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr.

Re: [Rd] Bug in tools::compactPDF() in 2.13-0-alpha

2011-03-27 Thread Gavin Simpson
On Sun, 2011-03-27 at 09:00 -0400, Duncan Murdoch wrote: > On 11-03-27 8:48 AM, Gavin Simpson wrote: > > Dear List, > > > > There seems to be an bug in compactPDF() or at least an inconsistency > > with the documented behaviour. > > Thanks, looks easy to fix.

[Rd] Inconsistency between rowMeans documentation and reality?

2011-04-05 Thread Gavin Simpson
e packages: [1] stats graphics grDevices utils datasets methods [7] base loaded via a namespace (and not attached): [1] tools_2.13.0 Thanks, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECR

Re: [Rd] Inconsistency between rowMeans documentation and reality?

2011-04-11 Thread Gavin Simpson
oise. G >As they are written for speed, they blur over some of the subtleties >of ‘NaN’ and ‘NA’. > > So, given that (and that real NA is a specific NaN) I think it is > perfectly reasonable to claim they are consistent with mean. > > On Tue, 5 Apr 2011, Gavin Si

[Rd] methods() not listing some S3 plot methods...?

2011-08-26 Thread Gavin Simpson
ched base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 loaded via a namespace (and not attached): [1] grid_2.14.0lattice_0.19-33Matrix_0.9996875-3 nlme_3.1-102 [5] tools_2.14.0 -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

Re: [Rd] methods() not listing some S3 plot methods...?

2011-08-26 Thread Gavin Simpson
On Fri, 2011-08-26 at 07:06 -0700, Martin Morgan wrote: > On 08/26/2011 04:44 AM, Gavin Simpson wrote: > > Dear List, > > > > This may be related to this email thread initiated by Ben Bolker last > > month: https://stat.ethz.ch/pipermail/r-devel/2011-July/061630.htm

Re: [Rd] NEWS.md support on CRAN

2015-06-04 Thread Gavin Simpson
gt;>>> those), so I'd suggest putting your news into a vignette > instead > > of a > > >> | >>>> news file. Put in a token news file that points to the > vignette > > so > > >> | >>>> users can find it. > > >> | >>> > > >> | >>>> Duncan Murdoch > > >> | >>> > > >> | >>>> __ > > >> | >>>> R-devel@r-project.org mailing list > > >> | >>>> https://stat.ethz.ch/mailman/listinfo/r-devel > > >> | >> > > >> | >> [[alternative HTML version deleted]] > > >> | >> > > >> | >> __ > > >> | >> R-devel@r-project.org mailing list > > >> | >> https://stat.ethz.ch/mailman/listinfo/r-devel > > >> | > > >> | > -- > > >> | > Peter Dalgaard, Professor, > > >> | > Center for Statistics, Copenhagen Business School > > >> | > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > > >> | > Phone: (+45)38153501 > > >> | > Email: pd@cbs.dk Priv: pda...@gmail.com > > >> | > > >> | > __ > > >> | > R-devel@r-project.org mailing list > > >> | > https://stat.ethz.ch/mailman/listinfo/r-devel > > >> | > > >> | __ > > >> | R-devel@r-project.org mailing list > > >> | https://stat.ethz.ch/mailman/listinfo/r-devel > > >> > > > > > __ > > > R-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] NEWS.md support on CRAN

2015-06-04 Thread Gavin Simpson
is not as simple as plain text. G On 4 June 2015 at 11:09, Prof Brian Ripley wrote: > On 04/06/2015 17:00, Gavin Simpson wrote: > ... > >> 1. Markdown was designed to be as readable as possible in plain text >> format >> (i.e. the sources, not the rendered file). Ther

Re: [Rd] NEWS.md support on CRAN

2015-06-04 Thread Gavin Simpson
On 4 June 2015 at 11:16, Duncan Murdoch wrote: > On 04/06/2015 1:09 PM, Prof Brian Ripley wrote: > >> On 04/06/2015 17:00, Gavin Simpson wrote: >> ... >> > 1. Markdown was designed to be as readable as possible in plain text >> format >> > (i.e. th

Re: [Rd] NEWS.md support on CRAN

2015-06-05 Thread Gavin Simpson
the NEWS: > > - a plain text NEWS file; following the GNU recommendations > - NEWS.Rd > - NEWS.md > > Would it not be more elegant to have e.g. roxygen2 generate NEWS.Rd? > (perhaps it is already possible, I'm not sure of that). I don't maintain > CRAN,

Re: [Rd] Request: making cutree S3 in R?

2015-06-08 Thread Gavin Simpson
e HTML version deleted]] > > __________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Update CRAN submission process

2016-05-27 Thread Gavin Simpson
Patrick Perry > Assistant Professor > NYU Stern School of Business > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Gavin Simpson, PhD ___

[Rd] Accessing the formals() of a non-exported method without :::?

2013-08-23 Thread Gavin Simpson
to get the formal arguments of a non-exported S3 method? Thanks. G -- Gavin Simpson __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Accessing the formals() of a non-exported method without :::?

2013-08-23 Thread Gavin Simpson
> On Aug 23, 2013, at 11:15, Gavin Simpson wrote: > >> Dear List, >> >> I'm in the process of making tweaks to my various R packages following >> changes in r-devel for package checks. I'm wondering about the one use >> of ::: in one of my packages. I a

[Rd] Correct NAMESPACE approach when writing an S3 method for a generic in another package

2013-08-23 Thread Gavin Simpson
possible I could get rid of both of these from Depends if I can solve the above issue. Thanks in advance. Gavin -- Gavin Simpson __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Accessing the formals() of a non-exported method without :::?

2013-08-23 Thread Gavin Simpson
By "...I had forgotten that a package can refer to any of *its own packages*" I of course meant "...I had forgotten that a package can refer to any of *its own functions*" Guess I should call it a night... G On 23 August 2013 21:49, Gavin Simpson wrote: > T

Re: [Rd] Correct NAMESPACE approach when writing an S3 method for a generic in another package

2013-08-26 Thread Gavin Simpson
port an imported object, but it has to be done via an > explicit export(), cf. "It is possible to export variables from a > namespace which it has imported from other namespaces: this has to be > done explicitly and not via exportPattern" [Writing R Extensions]. > > /H

Re: [Rd] Correct NAMESPACE approach when writing an S3 method for a generic in another package

2013-08-26 Thread Gavin Simpson
lling `foo()` will result in an error. As long as the package containing the definition of the generic is not attached, there is no function `foo()` and hence the user gets an error. G On 26 August 2013 13:12, Paul Gilbert wrote: > > > On 13-08-26 12:04 PM, Gavin Simpson wrote: >>

Re: [Rd] ‘:::’ call

2013-08-28 Thread Gavin Simpson
__ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Gavin Simpson, PhD __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] [RFC] A case for freezing CRAN

2014-03-19 Thread Gavin Simpson
t requires extra work by >>>> the >>>> third party, rather than extra work by the CRAN team. I don't think the >>>> total amount of work required is much different. I'm very unsympathetic >>>> to >>>> proposals to dump work on others. >>>> >>> >>> I am merely trying to discuss a technical issue in an attempt to improve >>> reliability of our software and reproducibility of papers created with R. >>> >>> [[alternative HTML version deleted]] >>> >>> __ >>> R-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > > -- > Carl Boettiger > UC Santa Cruz > http://carlboettiger.info/ > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Gavin Simpson, PhD __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] [RFC] A case for freezing CRAN

2014-03-19 Thread Gavin Simpson
lieve that it would be more effective and would > ultimately benefit the entire R community (and not just the BioC > community) if this problem was addressed upstream. > > > H. > >> >> Best, >> -- >> Joshua Ulrich | about.me/joshuaulrich >> FOSS Tradi

Re: [Rd] [RFC] A case for freezing CRAN

2014-03-19 Thread Gavin Simpson
versions" isn't good enough in your eyes? Is it the lack of CRAN > provided binaries or the fact that the user has to proactively set up their > environment to replicate that of published results? > > In your XML example, it seems the problem was that the reproducer didn'

[Rd] Bug in tools:::.check_package_depends ?

2014-05-19 Thread Gavin Simpson
_suggests, check_incoming) : object 'bad3' not found Thanks in advance Gavin -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] A bug in princomp(), perhaps?

2014-05-30 Thread Gavin Simpson
t; > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000

Re: [Rd] A bug in princomp(), perhaps?

2014-05-30 Thread Gavin Simpson
ugh to remove the rows of `x’ with NAs. This is my main point. > > > > Ravi > > > > *From:* Gavin Simpson [mailto:ucfa...@gmail.com] > *Sent:* Friday, May 30, 2014 10:46 AM > *To:* Ravi Varadhan > *Cc:* peter dalgaard; r-devel@r-project.org > > *Subject:* R

Re: [Rd] R CMD check for the R code from vignettes

2014-06-02 Thread Gavin Simpson
ntaining some quality assurance, >>> which >>> I think of as an aid but not a debugging aid. >>> >>> I believe the CRAN maintainers have intentionally, and successfully, made >>> disabling the running of tangled code more trouble than it is generally >>> worth. Effectively, a package should have tangle code that runs without >>> errors. >>> >>> (Of course, I could be wrong about all this, it has happened before.) >>> >>> Paul >>> >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R CMD check for the R code from vignettes

2014-06-02 Thread Gavin Simpson
On 2 June 2014 15:59, Duncan Murdoch wrote: > On 03/06/2014, 4:12 AM, Gavin Simpson wrote: > >> On 2 June 2014 11:44, Duncan Murdoch > <mailto:murdoch.dun...@gmail.com>> wrote: >> >> > Several of us have told you the real harm: it means that use

[Rd] Inconsistent handling of data frames in min(), max(), and mean()

2014-08-21 Thread Gavin Simpson
n(as.matrix(df[, 1:2])) [1] 2.78366 > mean(df[,1:2]) [1] 2.78366 I just can't see the sense in having `mean` work the way it does now? Thanks, Gavin -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Inconsistent handling of data frames in min(), max(), and mean()

2014-08-22 Thread Gavin Simpson
l the Summary.data.frame methods as well. More comments in-line On 22 August 2014 02:23, Martin Maechler wrote: > >>>>> Gavin Simpson > >>>>> on Thu, 21 Aug 2014 12:32:31 -0600 writes: > > >> mean(df) > > [1] NA Warning messag

[Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
what is the ideal solution in the view of R Core given this change to R CMD check. Thanks in advance Gavin -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
nds. Or am I thinking about this in the wrong way? Thanks again Gavin > > Hadley > > > -- > http://had.co.nz/ > -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
On 27 August 2014 16:09, Dan Tenenbaum wrote: > - Original Message - > > From: "Gavin Simpson" > > To: "Hadley Wickham" > > Cc: r-devel@r-project.org > > Sent: Wednesday, August 27, 2014 3:01:53 PM > > Subject: Re: [Rd] Re R CMD che

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
an in DESCRIPTION. What I'm pushing back on is the notion that *no* packages should be in Depends. Cheers, G -- Gavin Simpson, PhD [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
On Aug 27, 2014 5:24 PM, "Hadley Wickham" > I'd say: Depends is a historical artefact from ye old days before > package namespaces. Apart from depending on a specific version of R, > you should basically never use depends. (The one exception is, as > mentioned in R-exts, if you're writing somethi

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Gavin Simpson
t;Data is not information. Information is not knowledge. And knowledge > is certainly not wisdom." > Clifford Stoll > > > > > On Thu, Aug 28, 2014 at 7:39 AM, Simon Urbanek > wrote: > > > > On Aug 27, 2014, at 6:01 PM, Gavin Simpson wrote: > > > &

Re: [Rd] Re R CMD check checking in development version of R

2014-08-28 Thread Gavin Simpson
e analysis, the case for Depends is not as strong. In that > case, the official wisdom, AFAIK, is that Depends is not warranted. > > ~G > > > On Thu, Aug 28, 2014 at 11:43 AM, Gavin Simpson wrote: > >> I fully agree. >> >> This is how I have come to understand Depen

Re: [Rd] timings for examples in R CMD check

2014-09-03 Thread Gavin Simpson
uce equivalent > check files. on their example checks. > > This behavior is on R 3.1.0, 3.1.1, and R-devel. > > I would assume from the documentation that there should be a way to get a > clean check, without the timing diffs. > > Advice appreciated, > > Brian > >

Re: [Rd] error code 1 from Lapack routine 'dsyevr'

2015-02-02 Thread Gavin Simpson
ject.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > [[alternative HTML version deleted]] > > ______ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Gavin Simpson, PhD [[

Re: [Rd] R_HOME default setting

2015-03-10 Thread Gavin Simpson
} > > Without success. > Any idea? > which file has the R_HOME setting? > Thanks > Karim > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://sta

Re: [Rd] readRDS and saveRDS

2011-10-18 Thread Gavin Simpson
all the code that would inevitably break. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w]

Re: [Rd] round() ignores missing arguments if it is used inside another function where some arguments are missing.

2011-11-18 Thread Gavin Simpson
C_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

Re: [Rd] package DESCRIPTION file and CRAN Task View entries?

2012-01-16 Thread Gavin Simpson
t; > > > > Jeff Hamann, PhD > PO Box 1421 > Corvallis, Oregon 97339-1421 > 541-754-2457 > jeff.hamann[at]forestinformatics[dot]com > jeff.d.hamann[at]gmail[dot]com > http://www.forestinformatics.com > http://en.wikipedia.org/wiki/Forest_informatics > >

Re: [Rd] requesting a new SIG mailing list

2012-02-16 Thread Gavin Simpson
es of 'R-sig-ecology' for the > > year 2011, and I could only found one single mail related to hydrology: > > > > https://stat.ethz.ch/pipermail/r-sig-ecology/2011-July/002274.html > > > > (in the same search I couldn't find any single reference to hydrology in the

[Rd] Controlling simplification in apply()?

2012-02-20 Thread Gavin Simpson
there was I'd be happy to provide a first stab and contribute updated documentation. All the best, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pe

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

2012-03-21 Thread Gavin Simpson
with environments. > > > > -- > > 4dpiecharts.com > > > > ______ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > __ > R-devel@r-project.org mai

Re: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}

2012-10-19 Thread Gavin Simpson
> versioned path. > | > | > > | > | > FWIW, defaulting to a versioned path is (to this no-longer-bemused > user) as > | > | > much a permenent R bug (on Windoze) as the default installation into > a path > | > | > with spaces. > | > | > > | > | > Dirk > | > | > >

[Rd] Trouble building package using R in development

2013-01-16 Thread Gavin Simpson
uilt before R 3.0.0: please re-install it ERROR: lazy loading failed for package ‘analogue’ * removing ‘/tmp/Rtmpctxbtv/Rinst30e3f762569/analogue’ --- ERROR: package installation failed Can anyone suggest where to go from here? TIA Gavin -- %~%~%~%~%

Re: [Rd] Trouble building package using R in development

2013-01-16 Thread Gavin Simpson
here a bug here? All the best, Gavin [1] http://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Checking-and-building-packages On Wed, 2013-01-16 at 16:05 +0100, Gavin Simpson wrote: > Dear List, > > I'm having considerable trouble setting up my environment (Linux, Fedora > 1

[Rd] R CMD check not reading R_LIBS from ~/.R/check.Renviron

2013-01-16 Thread Gavin Simpson
[7] base -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT.

Re: [Rd] Trouble building package using R in development

2013-01-16 Thread Gavin Simpson
dant, although my experience from several hours working this through today suggests there is a difference between R --vanilla CMD check and R CMD check. G > Hadley > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522

[Rd] Improve aggregate.default ...?

2009-05-09 Thread Gavin Simpson
vectors > res$`dat$A` [1] 0.4269715 0.5479352 0.5091543 0.4926412 Is there a way of coming up with a better way to name the aggregated variable? Would a change of this kind be something R Core would consider making to aggregate.default if a good solution is found? Thanks in advance, G --

Re: [Rd] Improve aggregate.default ...?

2009-05-09 Thread Gavin Simpson
using `$`, prefering with(), I don't run the risk of non syntactic names being produced. I was really looking for ideas for improving aggregate.default in general. The solution I posted has its own infelicities... Cheers, G > > On Sat, May 9, 2009 at 8:14 AM, Gavin Simpson wrote: &g

Re: [Rd] Bug in base function sample ( ) (PR#13727)

2009-05-29 Thread Gavin Simpson
t; length(ggtrack) > hist(ggtrack) > > > Highest Regards, > Michael Chajewski > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [

[Rd] Bug in print.Arima and patch

2009-06-05 Thread Gavin Simpson
x$var.coef)) { ses <- rep(0, length(coef)) ses[x$mask] <- round(sqrt(diag(x$var.coef)), digits = digits) coef <- matrix(coef, 1L, dimnames = list(NULL, names(coef))) HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~

Re: [Rd] Bug in print.Arima and patch

2009-06-05 Thread Gavin Simpson
And the same is attached, that implements your suggested change rather than the one I sent earlier. Cheers, G > > On Fri, 5 Jun 2009, Gavin Simpson wrote: > > > Dear List, > > > > A posting to R-Help exposed this problem with the print method for > > objects

[Rd] Problem using model.frame with argument subset in own function

2009-08-08 Thread Gavin Simpson
Perhaps the question should be, how do I modify foo() to allow it to have a formal subset argument, passed to model.frame? Any other suggestions gratefully accepted. Thanks in advance, G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (

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