[Rd] complex NA's match(), etc: not back-compatible change proposal

NA NaN 1 [12,] NaN+NaNi NaN NaN 2 > --- Note that 'mz <- match(z, z)' and hence the last column of the matrix above are very different in current R, distinguishing most kinds of NA / NaN against the documentation (and the real/numeric case). Martin Maechler R Core

[Rd] recursion problem using do.call(rbind, list(..,,..))

d2(r, mL.410[[i]]) + }) user system elapsed 0.083 0.000 0.083 > dim(r) [1] 16405 > This should help Ben (the OP of the Matrix bug), and may be something like that should also guide on how to re-write the methods:::rbind() / methods:::cbind() in a non-recursive fashion ? Thank you for your thoughts. Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Is it possible to increase MAX_NUM_DLLS in future R releases?

te if the MAX_NUM_DLLS can be increased. > Thanks, > Qin >> On May 4, 2016, at 9:17 AM, Martin Morgan <martin.mor...@roswellpark.org> wrote: >> >> >> >> On 05/04/2016 05:15 AM, Prof Brian Ripley wrote: >>> On 04

Re: [Rd] Regression in match() in R 3.3.0 when matching strings with different character encodings

> http://developer.r-project.org/blosxom.cgi/R-devel/NEWS > Thank you for your report. I hope the benefits of this speedup will > eventually outweigh this unfortunate bug in my PR16491. I'm pretty sure that your hope will be fulfilled. > Regards

Re: [Rd] Is it possible to increase MAX_NUM_DLLS in future R releases?

the R sources (development trunk in subversion at https://svn.r-project.org/R/trunk/ ) are very welcome! Martin Maechler ETH Zurich & R Core Team __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [R-pkg-devel] using printf() in C code (package 'powell')

Warnings(.) etc. This will definitely not go away with R 3.3.0 or any later version of R. But then maintainer("powell") is still active, and his e-mail address at your fingertips,..., right ? --> I've BCC'ed Sundar, so he is informed. With best regards, Martin M

Re: [Rd] Typo in NEWS file for R-devel

> Erich Neuwirth > on Sun, 1 May 2016 23:40:40 +0200 writes: > From the first page of the NEWS file: (2016-04-29 r70564) > isSymmetrix(m) is much faster for large asymmetric > matrices m via pre-tests and a new option tol1 (with which >

Re: [Rd] paths for install and libraries?

> Dalthorp, Daniel > on Thu, 28 Apr 2016 16:41:28 -0700 writes: > I've written a fairly elaborate package (called "eoa") > that relies on functions from several other packages. I've > built the package into a zip file on Windows using > Hadley's

Re: [Rd] residual standard "error"

for sigma(). > —rjp Thank you, Randall! I only saw that part now and fixed it in the sources a few minutes ago. Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] S3 dispatch for S4 subclasses only works if variable "extends" is accessible from global environment

> Michael Lawrence > on Tue, 19 Apr 2016 05:34:41 -0700 writes: > Not sure why R_has_methods_attached() exists. Maybe Martin could shed > some light on that. It was to support (via 'classgets' in attrib.c) a very fast class(.) <- "" for S4

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

he complex the eigen vectors are even less determined, i.e. you could multiply them by any unit length complex number (of which only two are available in the real case: +/- 1). Martin > > From: R-devel <r-devel-boun...@r-project.org> on

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

> William Dunlap via R-devel > on Mon, 4 Apr 2016 12:26:38 -0700 writes: >> If I recall correctly, some eigen vectors had their >> direction flipped (negative values became positive and >> vice versa). Did you notice anything of this kind when

Re: [Rd] [PATCH] fix CHECK_this_length in sprintf.c

such bugs. Martin > Cheers, > Matt > On Thu, Apr 7, 2016 at 6:46 AM, Martin Maechler <maech...@stat.math.ethz.ch> > wrote: >> >>>>> Matthew Fowles Kulukundis <matt.fow...@gmail.com> >> >>>>>

Re: [Rd] [PATCH] fix CHECK_this_length in sprintf.c

> Matthew Fowles Kulukundis > on Tue, 5 Apr 2016 11:17:30 -0400 writes: > All~ > CHECK_this_length macro expands to multiple statements making it unsafe to > use in a single line `if` statement (as is happening near line 335). This > fixes the

Re: [Rd] documentation / warning when passing a vector as lower/upper bound in stats::integrate()

> Baptiste Auguie > on Tue, 29 Mar 2016 19:31:02 +1300 writes: > Dear R-dev list, > I wonder if stats::integrate shouldn't warn the user when a numeric vector > of length > 1 is passed as lower or upper bounds. If a vector is passed, > only

Re: [Rd] reg-tests-1a fails with r70391

> Hiroyuki Kawakatsu > on Wed, 30 Mar 2016 09:27:16 +0100 writes: > Hi, This may be a `transitional' bug but I am reporting a > make check fail with R-devel r70391 in > reg-tests-1a.Rout. The tail of reg-tests-1a.Rout.fail is >> ##

Re: [Rd] body(NULL) <- something; ditto formals() -- should not work

>>>>> Hervé Pagès <hpa...@fredhutch.org> >>>>> on Tue, 29 Mar 2016 12:19:12 -0700 writes: > Hi, > On 03/07/2016 09:26 AM, Martin Maechler wrote: >> I'm proposing to signal an error (from R >= 3.3.0) in such &g

Re: [Rd] summary( prcomp(*, tol = .) ) -- and 'rank.'

; have big matrices. >>> >>> (Note that there are awesome methods for actually only >>> computing a small number of PCs (unlike your code which >>> uses svn which gets all of them); these are available in >>> various CRAN packages).

[Rd] summary( prcomp(*, tol = .) ) -- and 'rank.'

ng? I think I would want to see (possibly in addition) proportions with respect to the full variance and not just to the variance of those few components selected. Opinions? Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Regression in strptime

>>>>> Mick Jordan <mick.jor...@oracle.com> >>>>> on Tue, 15 Mar 2016 19:50:48 -0700 writes: > On 3/15/16 3:52 AM, Martin Maechler wrote: >>>>>>> peter dalgaard <pda...@gmail.com> >>>>>>

Re: [Rd] Regression in strptime

* release. Thank you -- and others, please! -- in advance for doing it next time, i.e., *now*: The R web page https://www.r-project.org/ (for a few weeks) has the news o R version 3.3.0 (Supposedly Educational) prerelease versions will appear starting Monday 2016-03-14. Final release is scheduled for T

[Rd] body(NULL) <- something; ditto formals() -- should not work

proposal is that the underlying C code will signal an error when such replacement functions would create a function out of "something not a function". Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] as.vector in R-devel loaded 3/3/2016

> Morgan, Martin > on Fri, 4 Mar 2016 12:36:25 + writes: > I see as below, where getGeneric and getMethod imply a different signature; the signature is mode="any" for both cases in R version 3.2.3 Patched (2016-01-28 r70038)I don't know how to

Re: [Rd] as.vector in R-devel loaded 3/3/2016

> peter dalgaard > on Fri, 4 Mar 2016 09:21:48 +0100 writes: > Er, until _what_ is fixed? > I see no anomalies with the version in R-pre: Indeed. The problem ... I also have stumbled over .. is that I'm sure Jeff is accidentally loading a different version

Re: [Rd] [patch] Support many columns in model.matrix

ix ? yes, and basically call R level Matrix::sparse.model.matrix() [[ or even just mention the latter on the help page for model.matrix() ]]. Thank you, Karl > On Mon, Feb 29, 2016 at 10:01 AM, Martin Maechler > <maech...@stat.math.ethz.ch> wrote: >>>>>>> Karl

Re: [R-pkg-devel] Is it possible to protect a word from the spell checker?

> Hana Sevcikova > on Tue, 1 Mar 2016 11:45:34 -0800 writes: > If it's in the DESCRIPTION file put the word into quotes. > Hana Indeed, thank you Hana! To add - embarrassingly I've only learned this about a week ago - they need to be *single* quotes (as used

Re: [Rd] Data frame printing buglet when multiple empty column names

> Hadley Wickham > on Tue, 1 Mar 2016 09:12:00 -0600 writes: > This is admittedly minor, and you shouldn't have repeated names in a > data frame anyway, but: > df <- data.frame(1:3, 1:3, 1:3) > # Ok > setNames(df, c("x", "y", "")) > #

Re: [Rd] [patch] Support many columns in model.matrix

inally got around to provide model.matrix(, sparse = TRUE) which would then produce a Matrix-package sparse matrix. Even for this somewhat small case, a sparse matrix is a factor of 13.5 x smaller : > s1 <- object.size(mff); s2 <- object.size(M <- Matrix::Matrix(mff)); > as.vector( s1/s2 ) [1] 13.47043 I'm happy to collaborate with you on adding such a (C level) interface to sparse matrices for this case. Martin Maechler __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] iconv to UTF-16 encoding produces error due to embedded nulls (write.table with fileEncoding param)

patch only related to the iconv() problem not allowing 'raw' (instead of character) argument x. ... and it is > 5.5 years old, for an iconv() version that was less featureful than today. Rather, current iconv(x) allows x to be a list of raw entries. >> Are there chances to fix this pr

[Rd] Deprecating old pkgDepends(), package.dependencies() in tools

e of the deprecated functions and hence will get a warning, and find it hard to replace that use by a combination of available.packages() and package_dependencies() {note the "_"}, please ask here, as we may have overlooked edge cases. This should make this part of tools-package functionality easier

Re: [R-pkg-devel] Development Testers?

indeed quite focused (with a somewhat different focus). And yes, for the specific, I'd strongly recommend R-SIG-HPC (in addition, i.e., with the very rare case of sensible cross posting). Best regards, Martin -- Martin Maechler ETH Zurich and R Core Team > Regards, Charles > On F

Re: [Rd] inconsistency in treatment of USE.NAMES argument

> Hervé Pagès > on Mon, 8 Feb 2016 10:48:50 -0800 writes: > Hi, > Both vapply() and sapply() support the 'USE.NAMES' argument. According > to the man page: > USE.NAMES: logical; if ‘TRUE’ and if ‘X’ is character, use ‘X’ as >‘names’ for

Re: [R-pkg-devel] S3 length method behavior

> Barry Rowlingson > on Tue, 2 Feb 2016 17:23:46 + writes: > On Tue, Feb 2, 2016 at 3:28 PM, Hadley Wickham wrote: >> I've found that it's a very bad idea to provide length or names >> methods for just this reason.

Re: [Rd] More problems with building R on a musl platform

AP> Any more information I can give to help debug this? Maybe just privately, to confirm my suspicion above: Send me privately the result of 'f1' from that R script. Martin AP> On Mon, Feb 1, 2016 at 3:49 PM, Martin Maechler AP> <maech...@stat.math.ethz.ch> wrote: >

Re: [Rd] Best way for rgl's .onLoad to fail?

> "BH" == Bryan Hanson > on Sun, 31 Jan 2016 09:50:46 -0500 writes: BH> I think the 2nd option will be more palatable to BH> inexperienced users, but both do state the important BH> detail. Bryan >> On Jan 30, 2016, at 4:11 PM, Duncan Murdoch

Re: [Rd] Wrong config check for __libc_stack_end

> Alba Pompeo > on Fri, 29 Jan 2016 08:23:26 -0200 writes: > Here is my log from 'make check' using an Intel i5 64-bit > processor - http://pastebin.com/raw/N6SYAuFX Here is > Isaac's log from 'make check' using an Intel Atom 32-bit > processor -

Re: [Rd] In plot.ts, las=1 applies to ylab with multiple series and not to axis labels

blems in our checks). > Thanks to all the developers who have made R such a great > contribution to humanity. Thank you for the flowers! Martin Maechler > Best Wishes, > Spencer Graves > sessionInfo() > R version 3.2.3 (2015-12-10) > Pla

Re: [Rd] More problems with building R on a musl platform

bit more work on your system libraries (or possibly on our configuration) side before you should bundle R with your Alpine Linux. I'd call it "unsafe" for now. Martin -- Martin Maechler, ETH Zurich and R Core Team. >>>> On Feb 1, 2016, at 4:16 AM, Mar

Re: [Rd] More Capability for Capabilities

> Paul Grosu > on Thu, 28 Jan 2016 07:53:13 -0500 writes: > Hi Dario, > Here are another couple of other fun functions you can utilize besides the > ones Dirk recommended :) > extSoftVersion() > grSoftVersion() > Below is an example:

Re: [Rd] as.data.frame and illegal row.names argument (bug in package:DoE.wrapper?)

> William Dunlap via R-devel > on Wed, 13 Jan 2016 13:46:05 -0800 writes: > as.data.frame methods behave inconsistently when they are given a row.name > argument of the wrong length. The matrix method silently ignores row.names > if it has the wrong length and

Re: [Rd] as.data.frame and illegal row.names argument (bug in package:DoE.wrapper?)

two (potential) bugs: - one in R [not reporting erronous as.data.frame() usage] - one in DoE.wrapper I'm going to look into the R one, which is indeed in the as.data.frame.vector() method, as you've noted. -- Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Small inaccuracy in the Writing R Extensions manual

> Duncan Murdoch > on Tue, 12 Jan 2016 07:32:05 -0500 writes: > On 11/01/2016 11:59 PM, Berwin A Turlach wrote: >> G'day all, >> >> In Chapter 1.4 (Writing package vignettes) the Writing R >> Extensions manual states: >> >> By

Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.

>>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Sat, 12 Dec 2015 10:32:51 +0100 writes: >>>>> John Chambers <j...@r-project.org> >>>>> on Fri, 11 Dec 2015 10:11:05 -0800 writes: >> Somehow, the

Re: [Bioc-devel] [Rd] For integer vectors, `as(x, "numeric")` has no effect.

>>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Sat, 12 Dec 2015 10:32:51 +0100 writes: >>>>> John Chambers <j...@r-project.org> >>>>> on Fri, 11 Dec 2015 10:11:05 -0800 writes: >> Somehow, the

Re: [Rd] array() ignores illegal non-list dimnames

> William Dunlap via R-devel > on Thu, 17 Dec 2015 14:40:18 -0800 writes: > Is there a reason that array() silently ignores dimnames > that are not a list but matrix() gives an error? >> str(matrix(11:14, 2, 2, dimnames=c("Rows","Cols"))) >

Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.

uot;integer", "double"} { class - subclasses } 2) as(1L, "numeric") continues to return 1L .. since integer is one case of "numeric" 3) as(1L, "double") newly returns 1.0 {and in fact would be

Re: [Bioc-devel] [Rd] For integer vectors, `as(x, "numeric")` has no effect.

>>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Tue, 8 Dec 2015 15:25:21 +0100 writes: >>>>> John Chambers <j...@r-project.org> >>>>> on Mon, 7 Dec 2015 16:05:59 -0800 writes: >> We do nee

Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.

>>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Tue, 8 Dec 2015 15:25:21 +0100 writes: >>>>> John Chambers <j...@r-project.org> >>>>> on Mon, 7 Dec 2015 16:05:59 -0800 writes: >> We do nee

Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.

> John Chambers > on Mon, 7 Dec 2015 16:05:59 -0800 writes: > We do need an explicit method here, I think. > The issue is that as() uses methods for the generic function coerce() but cannot use inheritance in the usual way (if it did, you would be

Re: [Rd] Outdated information in regex.Rd

> Mikko Korpela > on Wed, 18 Nov 2015 11:35:14 +0200 writes: > The NEWS for R-devel has the following item: >> The previously included versions of zlib, bzip2, xz and PCRE have >> been removed, so suitable external (usually system) versions are

Re: [Rd] rank(, ties.method="last")

43:02 +0200 writes: >> Den 2015-10-21 kl. 07:24, skrev Suharto Anggono Suharto Anggono via R-devel: >>> Marius Hofert-4-- >>>> Den 2015-10-09 kl. 12:14, skrev Martin Maechler: >>>> I think so: the code above doe

Re: [Rd] rank(, ties.method="last")

>>>>> Henric Winell <nilsson.hen...@gmail.com> >>>>> on Wed, 21 Oct 2015 13:43:02 +0200 writes: > Den 2015-10-21 kl. 07:24, skrev Suharto Anggono Suharto Anggono via R-devel: >> Marius Hofert-4-- >&g

Re: [Rd] R 3.2.2 64 bit compilation error on AIX

>>>>> Vinh Nguyen <vinhdi...@gmail.com> >>>>> on Fri, 9 Oct 2015 06:35:01 -0700 writes: > On Oct 8, 2015 11:36 PM, "Martin Maechler" > <maech...@stat.math.ethz.ch> wrote: >> >> >>>>> Vi

Re: [Rd] identical(..., ignore.environment=TRUE)

> Duncan Murdoch > on Mon, 12 Oct 2015 19:31:11 -0400 writes: > On 12/10/2015 9:51 AM, Ben Bolker wrote: >> Duncan Murdoch gmail.com> writes: >> BB> > It seems odd/inconvenient to me that the > "ignore.environment" argument

Re: [Rd] identical(..., ignore.environment=TRUE)

check-all' ) [Yes, I think I know why they probably won't come from you, Bill, unfortunately ..] Martin > Bill Dunlap > TIBCO Software > wdunlap tibco.com > On Tue, Oct 13, 2015 at 8:39 AM, Martin Maechler <maech...@stat.math.ethz.ch > > wrote: > > >>>

Re: [Rd] rank(, ties.method="last")

se names(y) <- nm[!nas] > y > } > ## MWE > x <- c(10, 11, 11, 12, 12, 13) > rank(x, ties.method="first") > rank2(x, ties.method="last") Indeed, this makes sense to me, and is easy enough to document and maintain, and preferable to asking useRs to us

Re: [Rd] R 3.2.2 64 bit compilation error on AIX

ctually, I think we (R Core) should just apply that patch to the R/src/extras/tre/ sources. But this does not seem to be related to your original problem where compilation stopped during tools package building, or does it ? Martin Maechler, ETH Zurich > -- Vinh > On Thu, Oct 8,

Re: [Rd] Unexpected failure when calling new() with unnamed arg and

etc. Martin > Cheers, > Josh > On Thu, May 14, 2015 at 8:13 AM, Hervé Pagès > <hpa...@fredhutch.org> wrote: >> Thanks Martin for looking into this. H. >> >> >> On 05/13/2015 03:57 AM, Martin Maechler wr

Re: [Rd] Should as.complex(NaN) -> NA?

whereas e.g., complex(re = Inf, im = NaN) considered as one of the infinitely many complex infinities by at least some of the C library implementations. --- I have found that match(), unique(), and duplicated() still behave pretty pecularly --- I'd say bugously --- even after the 69410

Re: [Rd] R-devel_2015-09-14 throws an error in reg-packages test

> Jeroen Ooms > on Wed, 16 Sep 2015 22:56:19 +0200 writes: > On Wed, Sep 16, 2015 at 9:32 PM, Avraham Adler wrote: >> When running make check, I get the following error: >> >> running code in 'reg-packages.R'

Re: [R-pkg-devel] Return Value of By Function

ling list for such questions ! Please ask on different list (or forum), e.g., on R-help. Martin Maechler __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [Rd] No new daily R-devel tarball since r69202?

> Rainer Hurling > on Sun, 6 Sep 2015 08:40:13 +0200 writes: > Am 05.09.2015 um 19:09 schrieb peter dalgaard: >> >>> On 05 Sep 2015, at 13:54 , Rainer Hurling >>> wrote: >>> >>> Am 05.09.2015 um 10:18 schrieb peter

Re: [Rd] Issues with libcurl + HTTP status codes (eg. 403, 404)

DM == Duncan Murdoch murdoch.dun...@gmail.com on Wed, 26 Aug 2015 19:07:23 -0400 writes: DM On 26/08/2015 6:04 PM, Jeroen Ooms wrote: On Tue, Aug 25, 2015 at 10:33 PM, Martin Morgan mtmor...@fredhutch.org wrote: actually I don't know that it does -- it addresses the

Re: [Rd] match()/%in% with language objects?

William Dunlap wdun...@tibco.com on Tue, 25 Aug 2015 09:47:23 -0700 writes: match(x,table) and x%in%table work when x and table are lists of language objects or expressions. E.g., expression(quote(1+2), quote(log2(16))) %in% expression(3, quote(1+2), c(4L,5L,6L,7L))

Re: [Rd] enableJIT in Rprofile leads to 'not a proper evaluation environment' on startup

in R-devel .. will be fixed in R 3.2.2 patched next week.. but is most probably not making it into R 3.2.2 which has been in code freeze, to be released tomorrow(!). Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch

Re: [Rd] Weird issue when iterating through dates

(Resend: was meant for R-devel, not just Joshua) On Wed, Aug 12, 2015 at 10:55 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: I am not sure if this is a bug or not. I would argue that this isn't a bug, not even in the documentation of for (even though it might be clearer). ?for says that

Re: [R-pkg-devel] Visible bindings and reference classes

with that. So there must be something peculiar in your package leading to the - warnings. Maybe you should look into the source code of such other CRAN packages to see how they do it differently than you. Best regards, Martin Martin Maechler, ETH Zurich After some googling, I came across the page

Re: [Rd] all.equal: possible mismatch between behaviour and documentation

precise) scaled by the mean absolute value of those finite entries of \code{target} where it differs from \code{current} or yet another version which is both precise and understandable ? Martin Maechler, ETH Zurich All the best, Jon __ R

Re: [Rd] Improvements (?) in stats::poly and stats::polym.

MM == Martin Maechler maech...@stat.math.ethz.ch on Fri, 17 Jul 2015 18:00:28 +0200 writes: MM Dear Keith, keith.jew...@campdenbri.co.uk on Thu, 16 Jul 2015 08:58:11 + writes: Dear R Core Team, Last week I made a post to the R-help mailing list “predict.poly

Re: [Rd] Improvements (?) in stats::poly and stats::polym.

Dear Keith, keith.jew...@campdenbri.co.uk on Thu, 16 Jul 2015 08:58:11 + writes: Dear R Core Team, Last week I made a post to the R-help mailing list “predict.poly for multivariate data” https://stat.ethz.ch/pipermail/r-help/2015-July/430311.html but it has

Re: [Rd] Building r-devel fails on Ubuntu (old and new as well)

Gábor Csárdi csardi.ga...@gmail.com on Thu, 16 Jul 2015 07:18:00 -0400 writes: ... making array.d from array.c array.c:33:23: fatal error: duplicate.h: No such file or directory compilation terminated. ...

Re: [Rd] Lack of protection bug in current R release candidate

-trivial like this. We'd be *very* happy to get such problems during alpha or beta testing phase (or even before). Martin Maechler __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Lack of protection bug in current R release candidate

a regression test. Thank you once more, Radford! Martin Maechler __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [R-pkg-devel] apparent S3 methods note in R CMD check

wrote: Dear Martin, Thank you for addressing this issue. Introducing a nonS3method() directive in NAMESPACE seems a reasonable solution. It could replace export() for functions with .s in their names. Best, John On Fri, 12 Jun 2015 09:55:18 +0200 Martin Maechler maech...@stat.math.ethz.ch

Re: [Rd] RFC: Declaring foo.bar as nonS3method() ?!

, Jun 12, 2015 at 6:52 AM, Kurt Hornik kurt.hor...@wu.ac.at wrote: Duncan Murdoch writes: On 12/06/2015 7:16 AM, Kurt Hornik wrote: Duncan Murdoch writes: On 12/06/2015 4:12 AM, Martin Maechler wrote: This is a topic ' apparent S3 methods note in R CMD check

Re: [R-pkg-devel] use of `dev.new` across platforms in RStudio

Alex Chubaty alex.chub...@gmail.com on Fri, 12 Jun 2015 14:41:56 -0700 writes: Dear list members, Use of platform-specific code to open new plot devices (e.g., `quartz`, `x11`) is discouraged in favour of using `dev.new`; however, this does not work in RStudio. A

[Rd] RFC: Declaring foo.bar as nonS3method() ?!

, and for that reason, I'm cross posting this (as one of the famous exceptions that accompany real-life rules!!) to R-devel. and actually I did *not* cross post, but have now moved the relevant part of the thread to R-devel. Martin Maechler, ETH Zurich

Re: [Rd] RFC: Declaring foo.bar as nonS3method() ?!

functions that can't easily be changed. Hadley On Fri, Jun 12, 2015 at 6:52 AM, Kurt Hornik kurt.hor...@wu.ac.at wrote: Duncan Murdoch writes: On 12/06/2015 7:16 AM, Kurt Hornik wrote: Duncan Murdoch writes: On 12/06/2015 4:12 AM, Martin Maechler wrote

[Rd] Nabble gibberish on R-devel: please stop it (Re: S3 internal ...)

should be able to subscribe to a mailing list and deal with mail filtering etc... Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Fix for bug in arima function

Patrick Perry ppe...@stern.nyu.edu on Wed, 27 May 2015 23:19:09 -0400 writes: {@PP, you forgot this part:} peter dalgaard pda...@gmail.com on Thu, 21 May 2015 14:36:03 +0200 writes: I suspect that what we really need is fitI - lm(x ~ xreg - 1, na.action =

Re: [Rd] building with tcltk on Ubuntu 14.04

Ben Bolker bbol...@gmail.com on Tue, 26 May 2015 11:13:41 -0400 writes: False alarm. Completely wiping out my build directory followed by ../R-devel/configure --with-tcl-config=/usr/lib/tclConfig.sh - --with-tk-config=/usr/lib/tkConfig.sh; make seems to work. (My

Re: [Rd] MetaCran website v1.0.0-alpha

Hi Gábor, just to you : Gábor Csárdi csardi.ga...@gmail.com on Tue, 26 May 2015 14:16:00 -0400 writes: On Tue, May 26, 2015 at 2:10 PM, Gabriel Becker gmbec...@ucdavis.edu wrote: [...] Well, sort of. I mean if the package is being actively developed not on

Re: [Rd] Fix for bug in arima function

the initialization for the optimization routine. The proposed fix leaves the deliberate part of the patch unchanged (it preserves the value of init0). I can confirm this... a change introduced in R 3.0.2. I'm about to commit changes ... after also adding a proper regression test. Martin Maechler

[Rd] The R Foundation announces new mailing list 'R-package-devel'

. Please read the description of the mailing list here https://stat.ethz.ch/mailman/listinfo/r-package-devel or below, subscribe and start using it! For the R foundation, Martin Maechler, Secretary General --- About R-package-devel (from above URL): - This list

Re: [Rd] Fix for bug in arima function

peter dalgaard pda...@gmail.com on Thu, 21 May 2015 11:03:05 +0200 writes: On 21 May 2015, at 10:35 , Martin Maechler maech...@lynne.stat.math.ethz.ch wrote: I noticed that the 3.2.1 release cycle is about to start. Is there any chance that this fix will make

Re: [Rd] Probably a bug in the dendextend package

Tal Galili tal.gal...@gmail.com on Mon, 18 May 2015 23:01:44 +0300 writes: The problem: === Once a dendrogram has a branch with both a line type AND a color (which is a character color), the plot.dendrogram function will not plot and return an error. If the

[Rd] \alias{} -- rather \concept{} for conceptual links to help pages

() and hence ??topic will find. The other advantage of \concept{} is that you can use short phrases, i.e., \concept{all variable combinations} would be possible here. (Better wording proposals for this specific case are welcome! -- maybe privately). Martin Maechler, ETH Zurich On Sun, May 17

Re: [Rd] Unexpected failure when calling new() with unnamed arg and

in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : B is not eligible to be the data part of another class (must be a basic class or a virtual class with no slots) So, I am not yet committing my changes to R-devel. Hopefully more on this, later today. Martin Maechler, ETH Zurich Thanks, H

Re: [Rd] Why is the diag function so slow (for extraction)?

Steve Bronder sbron...@stevebronder.com on Thu, 7 May 2015 11:49:49 -0400 writes: Is it possible to replace c() with .subset()? It would be possible, but I think entirely wrong. .subset() is documented to be an internal function not to be used lightly and more to the point it is

Re: [Rd] S4 method dispatch sometimes leads to incorrect when object loaded from file?

Martin Morgan mtmor...@fredhutch.org on Mon, 11 May 2015 10:18:07 -0700 writes: On 05/10/2015 08:19 AM, Martin Morgan wrote: Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class

Re: [Rd] Wrongly checked MD5 checksums in R 3.2.0's windows binary

Tal Galili tal.gal...@gmail.com on Sun, 10 May 2015 23:13:09 +0300 writes: Dear R-devel members, Several R user recently reported https://github.com/talgalili/installr/issues/30 (while using the installr http://cran.r-project.org/web/packages/installrpackage) that

Re: [Rd] PATCH: library(..., quietly=TRUE) still outputs Loading required package: ... (forgot to pass down 'quietly')

Henrik Bengtsson henrik.bengts...@ucsf.edu on Sat, 9 May 2015 13:57:12 -0700 writes: Calling library(..., quietly=TRUE) may still output: Loading required package: other pkg in some cases, e.g. library(R.utils, quietly=TRUE) Loading required package: R.methodsS3

Re: [Rd] Shouldn't vector indexing with negative out-of-range index give an error?

John, for the perspective and clarification! I'm committing a patch to the documentation now. Martin On May 5, 2015, at 7:01 AM, Martin Maechler maech...@lynne.stat.math.ethz.ch wrote: Henrik Bengtsson henrik.bengts...@ucsf.edu on Mon, 4 May 2015 12:20:44 -0700 writes

Re: [Rd] Shouldn't vector indexing with negative out-of-range index give an error?

Henrik Bengtsson henrik.bengts...@ucsf.edu on Mon, 4 May 2015 12:20:44 -0700 writes: In Section 'Indexing by vectors' of 'R Language Definition' (http://cran.r-project.org/doc/manuals/r-release/R-lang.html#Indexing-by-vectors) it says: Integer. All elements of i must

Re: [Rd] R CMD check and missing imports from base packages

(?) (*) IIUC, you suggested to use standard packages := packages which are attached by default in R, apart from package 'base' because that does come immediately after the imports anyway (and because you cannot explicity import from base). Martin Maechler ETH Zurich

Re: [Rd] dimnames returned by function apply

Martin Maechler maech...@lynne.stat.math.ethz.ch on Thu, 30 Apr 2015 18:23:58 +0200 writes: Fischer, Bernd b.fisc...@dkfz-heidelberg.de on Wed, 29 Apr 2015 20:22:44 +0200 writes: Dear all, I noticed that the dimnames returned by apply are different in the new release

Re: [Rd] dimnames returned by function apply

Thank you, Bernd, for the report! Martin Maechler, ETH Zurich X = array(1:8, dim=c(4,2)) dimnames(X) = list(c(A,B,C,D),c(S,T)) apply(X, 1, function(x) { c(X=x[1]*5,Y=x[2]*5) } ) A B C D S 5 10 15 20 T 25 30 35 40 sessionInfo() R version 3.2.0 (2015

Re: [Rd] --interactive and -f/-e

above is clearly not enough. Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Development version of R: Improved nchar(), nzchar() but changed API

Mark van der Loo mark.vander...@gmail.com on Mon, 27 Apr 2015 10:26:32 +0200 writes: Dear Martin, Does the work on nchar mean that bugs #16090 and #16091 will be resolved [1,2]? Thanks, Mark [1] https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16090 [2]

[Rd] Development version of R: Improved nchar(), nzchar() but changed API

see problems with R-devel (that you don't see with R 3.2.0), but you should become aware of the slightly changed semantics of nchar() and nzchar(). Longer term, the change should have made R more internally coherent, namely vectorized R functions preserving NA's by default. Martin Maechler, ETH

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