Re: [Rd] readLines function with R >= 3.5.0

\n but I'm >> guessing that would likely be too slow. I am open to >> other workaround solutions. For the moment I have >> reverted back to R 3.4.4. >> >> Thanks for any suggestions. >> >> Jen. >> >>

Re: [Rd] Date class shows Inf as NA; this confuses the use of is.na()

> Joris Meys > on Sat, 9 Jun 2018 13:45:21 +0200 writes: > And now I've seen I copied the wrong part of ?is.na >> The default method for is.na applied to an atomic vector >> returns a > logical vector of the same length as its argument x, > containing TRUE for

Re: [Rd] Date class shows Inf as NA; this confuses the use of is.na()

> Emil Bode > on Tue, 12 Jun 2018 12:00:42 + writes: > I agree that calling it invalid is a bit confusing, but I’m not sure what the > wording should be, as the problem is that the conversion to POSIXlt is > failing. > The best solution would be to extend the whole

Re: [Rd] readLines function with R >= 3.5.0

>>>>> Ralf Stubner >>>>> on Tue, 29 May 2018 11:21:28 +0200 writes: > On 28.05.2018 16:38, Martin Maechler wrote: >> Then, I now do think this needs to be dealt with as a bug >> (but I'm not delving into fixing it!) > Ok. Ca

Re: [Rd] encoding argument of source() in 3.5.0

> peter dalgaard > on Sun, 3 Jun 2018 23:51:24 +0200 writes: > Looks like this actually comes from readLines(), nothing > to do with source() as such: In current R-devel (still): >> f <- file("http://home.versanet.de/~s-berman/source2.R;, encoding="UTF-8") >>

Re: [Rd] aic() component in GLM-family objects

> Ben Bolker > on Sun, 3 Jun 2018 17:33:18 -0400 writes: > Is it generally known/has it been previously discussed here that the > $aic() component in GLM-family objects (e.g. results of binomial(), > poisson(), etc.) does not as implemented actually return the AIC, but

Re: [Rd] readLines function with R >= 3.5.0

+ user_input <- readLines(stdin(), n=1) > + user_input <- as.numeric(user_input) > + print(user_input) > + } >> create_matrix() > Write the numbers of vertices: numeric(0) >> oh dear... yes, that is true .. >>>>>

Re: [Rd] readLines function with R >= 3.5.0

" if you additionally (the [Enter], i.e., EOL) you also "send" an EOF -- in Unix alikes via -D The same happens if you use 'Rscript ' I'm not the expert here, but am close to sure that we (R core) did not intend this change, when fixing other somewhat subtle bugs in Rscr

Re: [Rd] readLines function with R >= 3.5.0

>>>>> Martin Maechler >>>>> on Mon, 28 May 2018 10:28:01 +0200 writes: >>>>> Ralf Stubner >>>>> on Fri, 25 May 2018 19:18:58 +0200 writes: >> Dear all, I would like to draw you attention to this >> questi

Re: [Rd] issue with model.frame()

> Berry, Charles > on Tue, 1 May 2018 16:43:18 + writes: >> On May 1, 2018, at 6:11 AM, Therneau, Terry M., Ph.D. via R-devel wrote: >> >> A user sent me an example where coxph fails, and the root of the failure is a case

Re: [Rd] extendrange(): suggested improvement

if(!missing(r) && length(r) != 2) stop("'r' must be a \"range\", hence of length 2") f <- if(length(f) == 1L) c(-f,f) else c(-f[1L], f[2L]) r + f * diff(r) } PS: /* I hope the tidy faction will at some time be convinced that using if() as a *func

Re: [Rd] possible internal (un)tar bug

> Gábor Csárdi > on Tue, 1 May 2018 12:05:32 + writes: > This is a not too old R-devel on Linux, it already fails > in R 3.4.4, and on macOS as well. and fails in considerably older R versions, too. Basically untar() seems to fail on a

Re: [Rd] possible internal (un)tar bug

>>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Tue, 1 May 2018 16:14:43 +0200 writes: >>>>> Gábor Csárdi <csardi.ga...@gmail.com> >>>>> on Tue, 1 May 2018 12:05:32 + writes: >> This is a

Re: [Rd] possible internal (un)tar bug

TLDR: Use gzfile(), not file() .. and you have no problems. >>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Tue, 1 May 2018 16:39:57 +0200 writes: >>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>&g

Re: [Rd] download.file does not process gz files correctly (truncates them?)

> Tomas Kalibera > on Fri, 4 May 2018 08:34:03 +0200 writes: > On 05/03/2018 11:14 PM, Henrik Bengtsson wrote: >> Also, as mentioned in my >> https://stat.ethz.ch/pipermail/r-devel/2012-August/064739.html, >> when not specifying the mode

Re: [Rd] Another issue with Sys.timezone

>>>>> Stephen Berman <stephen.ber...@gmx.net> >>>>> on Thu, 19 Oct 2017 17:12:50 +0200 writes: > On Wed, 18 Oct 2017 18:09:41 +0200 Martin Maechler <maech...@stat.math.ethz.ch> wrote: >>>>>>> Martin Maechler <maech

Re: [Rd] range function with finite=T and logical parameters

> Lukas Stadler > on Mon, 23 Oct 2017 15:56:55 +0200 writes: > Hi! > I was wondering about the behavior of the range function wrt. logical NAs: >> range(c(0L, 1L, NA), finite=T) > [1] 0 1 >> range(c(F, T, NA), finite=T) > [1] NA NA

Re: [Rd] Fixed BLAS tests for external BLAS library

mentations where it sometimes seems, some are only interested in speed, rather than correctness. Martin Maechler ETH Zurich > On 01/04/2018 09:23 PM, Simon Guest wrote: >> Hi Tomas, >> >> Thanks for your reply. >> >> I find your response

Re: [Rd] Inconsistent rank in qr()

> Serguei Sokol > on Mon, 22 Jan 2018 17:57:47 +0100 writes: > Le 22/01/2018 à 17:40, Keith O'Hara a écrit : >> This behavior is noted in the qr documentation, no? >> >> rank - the rank of x as computed by the decomposition(*): always full

Re: [Rd] withTimeout bug, it does not work properly with nlme anymore

h exhibits the problem and shows the problem indeed does not happen in nlminb() -- which I wrongly assumed for a while -- but indeed in nlme's call to own .C() code. I am looking into fixing this (making it interruptable // detect the infinite loop). My guess is that it only happens in degenerate cas

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

> Henrik Bengtsson > on Thu, 25 Jan 2018 09:30:42 -0800 writes: > Just following up on this old thread since matrixStats 0.53.0 is now > out, which supports this use case: >> x <- rep(TRUE, times = 2^31) >> y <- sum(x) >> y > [1]

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

o, in the end, at least for now, we do not quite go all they way but overflow a bit earlier,... but do potentially gain a bit of speed, notably with the ITERATE_BY_REGION(..) macros (which I did not show above). Will hopefully become available in R-devel real soon now. Martin > Cheers, &g

Re: [Rd] as.list method for by Objects

>>>>> Michael Lawrence <lawrence.mich...@gene.com> >>>>> on Thu, 1 Feb 2018 06:12:20 -0800 writes: > On Thu, Feb 1, 2018 at 1:21 AM, Martin Maechler <maech...@stat.math.ethz.ch> > wrote: >> >>>>> Michael Lawr

Re: [Rd] as.list method for by Objects

>>>>> Henrik Bengtsson <henrik.bengts...@gmail.com> >>>>> on Thu, 1 Feb 2018 10:26:23 -0800 writes: > On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler > <maech...@stat.math.ethz.ch> wrote: >>>>>>> Michael Lawre

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

>>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Thu, 1 Feb 2018 16:34:04 +0100 writes: > >>>>> Hervé Pagès <hpa...@fredhutch.org> > >>>>> on Tue, 30 Jan 2018 13:30:18 -0800 writes: > > >

Re: [Rd] as.list method for by Objects

> Michael Lawrence > on Tue, 30 Jan 2018 10:37:38 -0800 writes: > I agree that it would make sense for the object to have c("by", "list") as > its class attribute, since the object is known to behave as a list. Well, but that (list behavior)

Re: [Rd] as.list method for by Objects

> Michael Lawrence > on Tue, 30 Jan 2018 15:57:42 -0800 writes: > I just meant that the minimal contract for as.list() appears to be that it > returns a VECSXP. To the user, we might say that is.list() will always > return TRUE. Indeed. I

Re: [Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y

> Gabriel Becker > on Wed, 21 Feb 2018 07:11:44 -0800 writes: > Hi all, > For the record this approach isnt 100% backwards compatible, because > names(mergeddf) will e incompatibly different. Thatx why i claimed > bakcwards compatable-ish

Re: [Rd] Problem with R_registerRoutines

> > on Fri, 23 Feb 2018 15:43:43 + writes: > Thanks a lot for your answer Jeroen! > I should have mentioned that I had actually only checked with the win-builder, as I did not have R-devel installed on my computer. > But based on your

Re: [Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y

I commit.. Martin > Best, > Scott > On 22 February 2018 at 22:31, Martin Maechler <maech...@stat.math.ethz.ch> > wrote: >> >>>>> Gabriel Becker <gmbec...@ucdavis.edu> >> >>>>> on Wed, 21 Feb 2018

Re: [Rd] Rscript failing with h5 reveals bugs in h5 (and 'R CMD check')

> Duncan Murdoch > on Wed, 27 Dec 2017 06:13:12 -0500 writes: > On 26/12/2017 9:40 AM, Dirk Eddelbuettel wrote: >> >> On 26 December 2017 at 22:14, Sun Yijiang wrote: | Thanks >> for the solution. Now I know the work-arounds, but still

Re: [Rd] R CMD check warning about compiler warning flags

e modules and svn - niceties just such that the server would run minimal services and hence would be minimally vulnerable. The times have changed though and I will look into adding WebSVN to svn.r-project.org as one of the first things in 2018. Martin Maechler >> >>> And

Re: [Rd] possible bug in plot.intervals.lmList

tely is a buglet in package 'nlme' (maintained by R Core, currently). I've committed a bug fix (and related "cleanup cosmetics") to the nlme package sources which are maintained in subversion / svn at https://svn.r-project.org/R-packages/trunk/nlme/ Thank you for your precise and reproduc

Re: [Rd] apply with zero-row matrix

> David Hugh-Jones > on Mon, 30 Jul 2018 10:12:24 +0100 writes: > Hi Martin, Fair enough for R functions in general. But the > behaviour of apply violates the expectation that apply(m, > 1, fun) calls fun n times when m has n rows. That seems > pretty basic. Well,

Re: [Rd] Code Optimization: print.data.frame + as.data.frame(head(x, n = options("max.print")))

> Juan Telleria Ruiz de Aguirre > on Tue, 31 Jul 2018 08:19:33 +0200 writes: > I polished a little bit more the function: > * Used: getOption("max.print") > * Added comment at the end: cat('[ reached getOption("max.print") -- > omitted ', omitted,' rows ]') > I

Re: [Rd] Suggestion for updating `p.adjust` with new method (BKY 2006)

> Xiaoqing Claire Rong-Mullins > on Mon, 23 Jul 2018 12:03:55 -0400 writes: > Dear R contributors, > I suggest adding a new method to `p.adjust` ("Adjust P-values for Multiple > Comparisons", > https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html).

Re: [Rd] odd behavior of names

Component: Windows GUI / Window specific Reporter: kevinushey .. gmail .. His minimal REPREX was even much simpler: > list(a = 1, b = 2) $`a` [1] 1 $b [1] 2 Thank you, Bill, for the nice extra example. Martin Maechler ETH Zurich and R Core Team > >

Re: [Rd] apply with zero-row matrix

ile that makes sense for high-level R functions that do a lot of things, this would really be a bad idea in general : This would make all of these basic functions larger {more to maintain} and slightly slower for all non-zero cases just to make them slightl

Re: [Rd] withTimeout bug, it does not work properly with nlme anymore

>>>>> Martin Maechler >>>>> on Tue, 30 Jan 2018 15:17:50 +0100 writes: (a bit more than 6 months ago) >>>>> Ramiro Barrantes >>>>> on Mon, 27 Nov 2017 21:02:52 + writes: >> Hello, I was relying on withTimeout (f

Re: [Rd] vctrs: a type system for the tidyverse

> Hadley Wickham > on Wed, 8 Aug 2018 09:34:42 -0500 writes: Method dispatch for `vec_c()` is quite simple because associativity and commutativity mean that we can determine the output type only by considering a pair of inputs at a time. To this

Re: [Rd] image() method for Matrix fails on empty matrices (?)

> Ben Bolker > on Sat, 18 Aug 2018 17:51:38 -0400 writes: > Reasonably easy to avoid, but maybe an edge case that > should be handled? Haven't looked yet to see how easy it > would be to fix ... Am I missing something? No, I don't think so. "Of course", we would

Re: [Rd] Should there be a confint.mlm ?

7 > y1:x1 -0.5100 0.2868 > y1:x2 -2.7554 0.8736 > y2:(Intercept) -0.6980 2.2182 > y2:x1 -0.6162 0.5879 > y2:x2 -3.9724 1.5114 > ``` I'm looking into a relatively small patch to confint.lm() *instead* of the confint.ml

Re: [Rd] Library lib.loc Option Ignored for Dependencies

> Benjamin Tyner > on Fri, 20 Jul 2018 19:42:09 -0400 writes: > Here's a trick/workaround; if lib.loc is the path to your > library, then prior to calling library(), >> environment(.libPaths)$.lib.loc <- lib.loc Well, that is quite a "trick" -- and potentially a pretty

Re: [Rd] problem with display of complex number

TL;DR : It's more complicated and needs more discussion (which I start below) > Hi, > > 1e10+5i > [1] 1e+10+0e+00i > > Im(1e10+5i) > [1] 5 > > maybe little better... > > --- R-3.5.1.orig/src/main/complex.c2018-03-26 07:02:25.0 +0900 > +++ R-3.5.1/src/main/complex.c

Re: [Rd] Library lib.loc Option Ignored for Dependencies

quietly = quietly) instead of the current code which uses lib.loc = NULL equivalently to lib.loc = .libPaths() Others / ideas? Reproducible examples with small fake packages? Martin > On 07/21/2018 12:34 PM, Martin Maechler wrote: >>>>>>> Benjamin Tyner >

Re: [Rd] Tiny bug in lm()?

> Brett Presnell > on Sun, 24 Jun 2018 13:57:04 +0100 writes: > I meant ncol(y) of course. > Brett Presnell writes: >> I suppose that this never affects anything, but in line >> 57 of lm.R, where the coefficients are defined for an >> empty model, when y is a

Re: [Rd] ROBUSTNESS: x || y and x && y to give warning/error if length(x) != 1 or length(y) != 1

ne after checking isNumber(): so then we know we have an atomic and can use XLENGTH() } The 0-length case I don't think we should change as I do find NA (is logical!) to be an appropriate logical answer. Martin Maechler ETH Zurich and R Core team. > Cheers Joris > -- > Jo

Re: [Rd] Segfault when performing match on POSIXlt object

> I think this could be a bug, since even if that match > operation makes no sense, the R session is not supposed to > crash with segmentation fault, but rather throw an > exception. Definitely. It is a bug. > Thanks in advance Thank you for reporting!

Re: [Rd] Segfault when performing match on POSIXlt object

>>>>> Martin Maechler on Fri, 31 Aug 2018 16:00:07 +0200 writes: >>>>> Marco Giuliano on Fri, 31 Aug 2018 08:53:02 +0200 writes: >> Hi All, I found a possible unexpected behavior when >> performing match/%in% on POSIXlt objects,

Re: [Rd] config.status: error: cannot find input file: `po/Makefile.in'

> Matt Dowle > on Wed, 5 Sep 2018 19:25:33 -0700 writes: > Hi, > Does anyone else see the following or is it just me? It usually works > fine. I checked latest R-devel commits and couldn't see anything very > recently changed or fixed w.r.t. po/ or Makefile. >

Re: [Rd] Better error message in loadNamespace

. Otherwise you’re also welcome > to take it from here. I'll do that for you in any case. Martin Maechler ETH Zurich > With best wishes Thomas Lin Pedersen __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Fwd: Re: [EXTERNAL] Re: backquotes and term.labels

ne formulas and partition >> them into bits >> needs its own terms function? This does not look like a good solution to >> me. >> >> On 03/07/2018 07:39 AM, Ben Bolker wrote: >>> >>> I knew I had seen this bef

Re: [Rd] importing namespaces from base packages

r loaded nor attached (e.g., when R runs with only base, say, and suddenly encounters an S4 object), and there still are situations where 'methods' needs to be in the search() path and not just loaded, but these cases should be unrelated to the above DESCRIPTION-Imports vs NAMESPACE-Imports correspondence. Martin Maechler ETH Zurich & R Core Team __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] importing namespaces from base packages

>>>>> Adrian Dușa <dusa.adr...@unibuc.ro> >>>>> on Tue, 13 Mar 2018 09:17:08 +0200 writes: > On Mon, Mar 12, 2018 at 2:18 PM, Martin Maechler <maech...@stat.math.ethz.ch> > wrote: >> [...] >> Is that so? Not

Re: [Rd] Bug report - duplicate row names with as.data.frame()

ior which entails that as.data.frame.*(x) (and similar coercions to data frames) should typically _handle_ invalid row names rather than signal errors. Feedback is welcome ! ((though I will be slow in replying, going basicaly off work for my early-starting weekend in the Alps)) Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Base R examples that write to current working directory

> Henrik Bengtsson > on Fri, 30 Mar 2018 10:14:04 -0700 writes: > So, the proposal would then be to write to tempdir(), > correct? If so, I see three alternatives: > 1. explicitly use file.path(tempdir(), filename), or > tempfile()

Re: [Rd] Base R examples that write to current working directory

=17403#c4 : 3) prompt() and promptData() [and possibly other prompt*()] : I did not apply your proposed changes here, see the R-bugzilla for reasoning. Still one may want to propose changing the default behavior from using the getwd() working directory to tempdir() instead.

Re: [Rd] Fwd: suggested patch for messages

> Ben Bolker > on Fri, 13 Apr 2018 14:42:10 -0400 writes: > Any follow-up/comments on this? If I don't hear back I'll submit to > r-bugs so it doesn't get lost ... > (Don't see any changes in QC.R in the last few days ... >

Re: [Rd] odd assignInNamespace / setGeneric interaction

> Michael Lawrence > on Wed, 18 Apr 2018 14:16:37 -0700 writes: > Hi Bill, > Ideally, your coworker would just make an alias (or shortcut or > whatever) for R that passed --no-save to R. I'll try to look into this > though. > Michael

Re: [Rd] packageDate() segfaults, if used without argument

> Rainer Hurling > on Sun, 15 Apr 2018 11:01:59 +0200 writes: > Out of curiosity, I played a bit with the new function > packageDate() from April, 4th. All works fine, except > using it without any argument. In this case, it > segfaults: Thank you,

[Rd] Spam to R-* list posters

> Serguei Sokol > on Thu, 19 Apr 2018 13:29:54 +0200 writes: [...] > Thanks Tomas for this detailed explanation. > I would like also to signal a problem with the list. It must be > corrupted in some way because beside the Tomas' 

Re: [Rd] Minor glitch in optim()

thod == c("L-BFGS-B","Brent"))) { > warning("bounds can only be used with method L-BFGS-B (or Brent)") > method <- "L-BFGS-B" > } > Best, JN I aim to go for the first line if((any(lower > -Inf)) || any(upper < Inf)) w

Re: [Rd] R 3.5.0 fails its regression test suite on Linux/x86_64

rkaround the issue, and as Dirk has mentioned, Debian etc have adopted a more robust procedure for packaging both R without rec.pkg. and the rec.pkg.s (and then bundle the two in yet another). Best, Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Suggesting patch to link DOIs against secure resolver

> Katrin Leinweber > on Sun, 25 Mar 2018 19:04:34 +0200 writes: > Dear Madams and Sirs, > because the DOI foundation recommends a new, secure resolver [1], I > wanted to suggest the attached patch. It > a) updates a static DOI link

Re: [Rd] Function 'factor' issues

> - For remapping, use > f <- match(xlevs, nlevs)[f] > instead of > f <- match(xlevs[f], nlevs) > (I have mentioned it). > - Remap only if length(nlevs) differs from length(xlevs) . > [snip] >

Re: [Rd] names lost in functions from packages installed by R-devel r74500

tion, if you define foo in the globalenv, and call it, the JIT kicks in pretty quickly and you can see that 'foo' is byte compiled as well, but it still does not break. This is pretty important, so thank you very much for the nice reproducible report! Martin Maechler ETH Zurich --- *) R-devel CMD INSTA

Re: [Rd] [FORGED] recordPlot/replayPlot not working with saveRDS/readRDS

> Paul Murrell > on Tue, 3 Apr 2018 09:41:56 +1200 writes: > Hi What you are doing "wrong" is loading a recordedplot > into the same session that it was created in. The > saveRDS()/readRDS() works if you save in one R session and > then read

Re: [Rd] names lost in functions from packages installed by R-devel r74500

>>>>> Martin Maechler <maech...@stat.math.ethz.ch> >>>>> on Tue, 3 Apr 2018 17:03:02 +0200 writes: >>>>> Francois Rousset <francois.rous...@umontpellier.fr> >>>>> on Tue, 3 Apr 2018 16:38:42 +0200 writes:

Re: [Rd] Inappropriate parens fix for Logic.Rd

> Suharto Anggono Suharto Anggono via R-devel > on Sat, 17 Mar 2018 11:53:28 + writes: > Logic.Rd has been changed again in r74377. After change:   > \item{x, y}{raw or logical or \sQuote{number-like} vectors > (i.e., of     types

Re: [Rd] trivial typo in man/pretty.Rd

> Ben Bolker > on Mon, 19 Mar 2018 11:57:34 -0400 writes: > patch against recent SVN ... > as far as I can tell this trivial typo has been there for 20 years: >

Re: [Rd] [R-pkg-devel] Warning: rBind is deprecated

your packages: a) replace cBind() by cbind() and rBind() by rbind() b) Ensure that your package depends on at least R 3.2.0, i.e. possibly add a 'Depends: R (>= 3.2.0)' to your DESCRIPTION file. Of course feel free to comment / ask privately or here {R-devel only} if necessary. Wit

Re: [Rd] Unclosed parenthesis in grep.Rd

> Hugh Parsonage > on Mon, 5 Mar 2018 13:39:24 +1100 writes: > Lines 129-131: \code{grep(value = FALSE)} returns a vector > of the indices of the elements of \code{x} that yielded a > match (or not, for \code{invert = TRUE}. This will be an >

Re: [Rd] scale.default gives an incorrect error message when is.numeric() fails on a dgeMatrix

e its authors have been saying (for rather more than 5 years I think) that one should really use require("glmnet") instead. Your point is still valid that it would be easy to enhance base :: scale.default() so it'd work in more cases. Thank you for that. I do plan to consider such a change in R-devel (planned to become R 3.5.0 in April). Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Redundant code in 'split.default' in R devel

> Suharto Anggono via R-devel > on Fri, 5 Oct 2018 17:13:30 + writes: > After r75387, function 'split.default' in R devel still has this part that no > longer has effect. > lf <- levels(f) > y <- vector("list", length(lf)) > names(y) <- lf Indeed --> removed

[Rd] methods(class = class()) - improve for |cl.| > 1 ?

all this works fine with S4 classes: There the full inheritance is used and all methods are found. Still, would it make sense to improve the underlying .S3methods() ? I assume it will break *some* overzealous package checks out there when .S3methods() and hence methods() would return *more* in s

Re: [Rd] small bug in formatC?

it is one, is in .format.zeros: > .format.zeros("0.000", "xx") > Error in strrep(" ", nc - i1) : invalid 'times' value > > R version 3.5.1. > > David Thank you, David. Yes, this looks like a bug / wrong assumption in .format.zeros(). I will have

Re: [Rd] disappearing paragraphs in html rendering of text from Rd macros

rexes/blob/master/disappearingParagraphs/a.html > and R-3.5.1patched: > https://github.com/GeoBosh/reprexes/blob/master/disappearingParagraphs/a351.html > [..] > Georgi Boshnakov Thank you. I can reproduce what you report, thanks to your 'reprex', and will hav

Re: [Rd] Rmpfr: build vector sequentially -- c(.) not working

vec <- c(vec, mpfr(i^2, 88)) } works fine. In the next version of Rmpfr, both as(NULL, "mpfr") mpfr(NULL) will also give the 'mNUL' above. I hope you enjoy using Rmpfr! Best regards, Martin Martin Maechler ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Seg fault stats::runmed

oducibly in R 3.4.3, R3.4.4 (Ubuntu 14.04/Ubuntu 16.04) and also in the latest development version (we call "R-devel"). THank you very much, Hilmar! I will have a look, to ensure missing values (incl NaN) are handled propertly. Martin -- Martin Maechler ETH Zurich and R Core T

Re: [Rd] Improvement to documentation in dput.Rd

> Korpela Mikko (MML) > on Sat, 29 Sep 2018 06:49:25 + writes: > If the "Matrix" package is attached, 'example(dget)' > fails: >> library(Matrix) example(dget) dget> fil <- tempfile() dget> ## Write an ASCII version of function mean to our temp dget>

Re: [Rd] Suggested Patch: Adding commas to list of packages after R CMD check

> Duncan Murdoch > on Tue, 18 Sep 2018 16:23:47 -0400 writes: > On 18/09/2018 2:16 PM, Marcel Ramos wrote: > > Dear R-devs, > > > > > > Scenario: > > > > When checking a package via `R CMD check package_tar.ball`, required / > > suggested packages may be missing. R subsequently

Re: [Rd] Segfault when performing match on POSIXlt object

> Marco Giuliano > on Fri, 31 Aug 2018 16:50:56 +0200 writes: > Hi Martin, should I file a formal bug report somewhere or > you've already done it ? No, I haven't, and as I may not address this bug further myself (in the near future), it may be best if you file a formal

Re: [Rd] compairing doubles

g behind a new operator which does not allow to take into account that there are quite a few versions of near-equality --- only partly) mirrored by the existence of extra arguments of all.equal() --- only encourages simplified thinking about the underlying subtle issue

Re: [Rd] A different error in sample()

> Wolfgang Huber > on Thu, 20 Sep 2018 08:47:47 +0200 writes: > FWIW, I suspect this is related to the function > R_unif_index that was introduced in src/main/RNG.c around > revision 72356, or the way this function is used in > do_sample in src/main/random.c. Yes, it

Re: [Rd] Possible bug, max argument in print.default(), on R-3.5.1-patched

> peter dalgaard > on Mon, 24 Sep 2018 10:16:07 +0200 writes: > Not in print.default(), but in print.data.frame(), which > is now doing its own max= handling but not passing max to > print.default (maechler, r75122 --- was this really for > r-patched? -pd Yes,

Re: [Rd] as.vector() broken on a matrix or array of type "list"

> Hervé Pagès > on Tue, 25 Sep 2018 23:27:19 -0700 writes: > Hi, Unlike on an atomic matrix, as.vector() doesn't drop > the "dim" attribute of matrix or array of type "list": >m <- matrix(list(), nrow=2, ncol=3) >m ># [,1] [,2] [,3] ># [1,] NULL NULL

Re: [Rd] segfault issue with parallel::mclapply and download.file() on Mac OS X

> Seth Russell > on Wed, 19 Sep 2018 15:19:48 -0600 writes: > I have an lapply function call that I want to parallelize. Below is a very > simplified version of the code: > url_base <- "https://cloud.r-project.org/src/contrib/; > files <- c("A3_1.0.0.tar.gz",

Re: [Rd] A different error in sample()

>>>>> Martin Maechler >>>>> on Thu, 20 Sep 2018 09:20:46 +0200 writes: >>>>> Wolfgang Huber >>>>> on Thu, 20 Sep 2018 08:47:47 +0200 writes: >> FWIW, I suspect this is related to the function >> R_unif_

Re: [Rd] Objectsize function visiting every element for alt-rep strings

> Travers Ching > on Tue, 15 Jan 2019 12:50:45 -0800 writes: > I have a toy alt-rep string package that generates > randomly seeded strings. example: library(altstringisode) > x <- altrandomStrings(1e8) head(x) [1] > "2PN0bdwPY7CA8M06zVKEkhHgZVgtV1" >

Re: [Rd] long-standing documentation bug in ?anova.lme

, at least 'foreign', 'mgcv' and 'cluster' are also maintained there. Thank you for the question: I do think "we" should add the corresponding svn URL to the respective DESCRIPTION file. OTOH, 'Matrix' has moved to R-forge a while ago .. and I'm currently also

Re: [Rd] trivial typo in src/library/base/man/LongVectors.Rd

> Ben Bolker > on Wed, 12 Dec 2018 14:45:10 -0500 writes: > Line 23: > "In theory up they can to" > should be > "In theory they can be up to" > or (slightly more formally) > "In theory they can contain up to" > cheers > Ben Bolker Thank you, Ben!

[Rd] R is missing log1p(z) etc for complex numbers z.

Working on my 'Bessel' package, I've re-detected today, that indeed even C99 standard GLIBC does not contain, a complex number version of log1p() Further missing in current R, are, basically these > z <- 1 + 2i > log1p(z) Error in log1p(z) : unimplemented complex function > expm1(z) Error

Re: [Rd] formula(model.frame(..)) is misleading

> William Dunlap via R-devel > on Thu, 20 Dec 2018 15:09:56 -0800 writes: > When formula() is applied to the output of model.frame() > it ignores the formula in the model.frame's 'terms' > attribute: >> d <- data.frame(A=log(1:6), B=LETTERS[rep(1:2,c(2,4))], >>

Re: [Rd] formula(model.frame(..)) is misleading

the class of model frames, so as far as I can see, one > can’t know whether problems will arise before trying it. > I hope that helps, John > - > John Fox, Professor Emeritus McMaster University > Hamilton, Ontario, Canada Web:

Re: [Rd] formula(model.frame(..)) is misleading

> William Dunlap via R-devel > on Fri, 21 Dec 2018 13:34:16 -0800 writes: > I don't have a copy of SV4 (or SV3, where model.frame was > introduced), but S+ 8.3 (based on SV4) puts the class > "model.frame" on model.frame()'s return value but has no > methods (in the

Re: [Rd] Documentation examples for lm and glm

> David Hugh-Jones > on Sat, 15 Dec 2018 08:47:28 +0100 writes: > I would argue examples should encourage good > practice. Beginners ought to learn to keep data in data > frames and not to overuse attach(). Note there's no attach() there in any of these examples! >

Re: [Rd] patch to support custom HTTP headers in download.file() and url()

> Gábor Csárdi > on Tue, 4 Dec 2018 21:23:20 + writes: > The patch below adds support for custom HTTP headers in > download.file() and url(). > My main motivation for this is performing basic http > authentication. Some web sites do not support embedding >

Re: [Rd] Bug report: Function ppois(0:20, lambda=0.9) does not generate a non-decreasing result.

> Serguei Sokol > on Tue, 4 Dec 2018 11:46:32 +0100 writes: > Le 04/12/2018 à 11:27, Iñaki Ucar a écrit : >> On Tue, 4 Dec 2018 at 11:12, wrote: >>> function ppois is a function calculate the CDF of Poisson distribution, it should generate a non-decreasing result, but

Re: [Rd] Dead link in documentation of ?timezones

> Michael Chirico > on Fri, 7 Dec 2018 10:36:37 +0800 writes: > This link is referenced in ?timezones and appears to have been > moved/removed. Is there a replacement? > http://www.twinsun.com/tz/tz-link.htm Yes, already in the sources (*) of R at

Re: [Rd] Unexpected argument-matching when some are missing

> Michael Lawrence > on Fri, 30 Nov 2018 08:24:31 -0800 writes: > Argument matching is by name first, then the still missing > arguments are filled positionally. Unnamed missing > arguments are thus left missing. Does that help? Thank you, Michael! Unfortunately, it may

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