Re: [Rd] model.matrix() may be misleading for "lme" models

> I can't tell whether evaluating object$call$data in environment(object$formula) is a better or worse idea than parent.frame(). I have struggled with this a lot over the years. There is a bunch of wonky code in lme4, e.g. here , that t

Re: [Rd] numerical issue with t.test

To be more specific, this replicates the computations that t.test is doing (stripped of all the different cases that stats:::t.test.default handles) z <- err1-err2 se <- sqrt(var(z)/length(z)) mz <- mean(z) tstat <- mz/se 2*pt(tstat, df= length(z)-1, lower.tail = FALSE) On 2024-09-16 10:54 a

Re: [Rd] specials and ::

om effect' and 'nuisance variable' as synonyms ...) But taking the "train the users to do it right" path does also involve more discussion with users ("if your software knows what I should be doing why can't it just do it for me?") cheers Ben Bolk

Re: [Rd] CRAN package submission

Try the foghorn package for checking the status of your submission in the CRAN queue? On Mon, Aug 26, 2024, 4:46 AM jing hua zhao wrote: > Dear CRAN / All, > > I appeared not to receive any email notification after upload a package > update (to furnish the confirmation) -- is the system down? >

Re: [Rd] Strange Behavior in RNG

You could argue that the 'n' argument should be rounded rather than truncated, but this form of coercion from float to integer is common/standard (in C, for example). In any case, it's a long standing part of R and is very unlikely to be changed ... On Sat, Aug 17, 2024, 12:11 AM Jiefei Wang wrot

Re: [Rd] changes in R-devel and zero-extent objects in Rcpp

Thanks, that's very useful. AFAICT, in the problematic case we are doing some linear algebra with zero-column matrices that are mathematically well-defined (and whose base-R equivalents work correctly). It's maybe not surprising that Eigen/RcppEigen would do some weird stuff in this edge c

Re: [Rd] changes in R-devel and zero-extent objects in Rcpp

ed packages, but Rcpp could do better in detecting and handling this for client packages (avoiding a segfault). Best, Kevin On Sat, Jun 8, 2024, 3:06 PM Ben Bolker <mailto:bbol...@gmail.com>> wrote:     A change to R-devel (SVN r86629 or https://github.com/r-devel/r

[Rd] changes in R-devel and zero-extent objects in Rcpp

this problem should be resolved by changing R, Rcpp, or downstream Rcpp packages ... cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] confint Attempts to Use All Server CPUs by Default

Following up on this -- on my system, I have 69 packages installed that appear to provide something like a confint() method: h <- help.search("confint", agrep = FALSE) p <- sort(unique(h$matches$Package)) length(p) ## [1] 69 p [1] "bamlss" "bbmle" "binom" "brgl

Re: [Rd] [Non-DoD Source] Re: R for the US Air Force

at might qualify for lists A and B in your documentation specs, and they might be able to provide you with an Austrian tax receipt for list C ... cheers Ben Bolker On 2024-05-16 4:03 p.m., ADAMS, DOUGLAS L CIV USAF AFMC OO-ALC/OBWA via R-devel wrote: You described it well; I’m afraid t

Re: [Rd] [External] View() segfaulting ...

clean/make, so maybe give that a try. Best, luke On Wed, 24 Apr 2024, Ben Bolker wrote:  I'm using bleeding-edge R-devel, so maybe my build is weird. Can anyone else reproduce this?  View() seems to crash on just about anything. View(1:3) *** stack smashing detected ***: terminated Abort

Re: [Rd] View() segfaulting ...

As suggested by Josh Ulrich, here's what I get when running under valgrind. $ R -d valgrind ==218120== Memcheck, a memory error detector ==218120== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==218120== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2

[Rd] View() segfaulting ...

I'm using bleeding-edge R-devel, so maybe my build is weird. Can anyone else reproduce this? View() seems to crash on just about anything. View(1:3) *** stack smashing detected ***: terminated Aborted (core dumped) If I debug(View) I get to the last line of code with nothing obviously l

Re: [Rd] read.csv

Tangentially, your code will be more efficient if you add the data files to a *list* one by one and then apply bind_rows or do.call(rbind,...) after you have accumulated all of the information (see chapter 2 of the _R Inferno_). This may or may not be practically important in your particular

Re: [Rd] VPAT OR Accessibility Conformance Report Request

There was a recent thread here started by someone asking a similar question. https://stat.ethz.ch/pipermail/r-devel/2024-January/083120.html You should probably start by going through all of that thread, but the bottom line is that: * R is in fact very accessible to people with a wide r

Re: [Rd] ADA Compliance

ithout a mouse, which should improve accessibility for users with neuromuscular conditions. cheers Ben Bolker On 2024-01-12 2:50 p.m., Hunter, Zayne via R-devel wrote: Hello, I am working with Ball State University to obtain a license of R. As part of our requirements for obtainin

Re: [Rd] Base R wilcox.test gives incorrect answers, has been fixed in DescTools, solution can likely be ported to Base R

.@r-project.org briefly explaining why, and a volunteer will add you to R’s Bugzilla members. (On the other hand, I think that posting to this list was a good idea in any case, as it is more visible than the bugs list and may spark some useful discussion.) cheers Ben Bolker On 2023-12

[Rd] option to silence/quieten stats::confint.glm ?

would the best name for the argument be? (scan() has "quiet") pos <- tail(search(), 1) ## base package tt <- lapply(c(lsf.str(pos = pos)), \(x) names(formals(x))) |> unlist() |> table() > tt[["quiet"]] [1] 4 > tt[["silent"]]

Re: [Rd] Minor bug with stats::isoreg

Thanks! Submitted as https://bugs.r-project.org/show_bug.cgi?id=18603 On 2023-09-27 4:49 p.m., Travers Ching wrote: Hello, I'd like to file a small bug report. I searched and didn't find a duplicate report. Calling isoreg with an Inf value causes a segmentation fault, tested on R 4.3.1 and

Re: [Rd] NROW and NCOL on NULL

This is certainly worth discussing, but there's always a heavy burden of back-compatibility; how much better would it be for NCOL and NROW to both return zero, vs. the amount of old code that would be broken? Furthermore, the reason for this behaviour is justified as consistency with the

Re: [Rd] A demonstrated shortcoming of the R package management system

elies on a Makefile rule that caches the current installed version of TMB: https://github.com/glmmTMB/glmmTMB/blob/d9ee7b043281341429381faa19b5e53cb5a378c3/glmmTMB/R/utils.R#L209-L295 cheers Ben Bolker On 2023-08-06 5:05 p.m., Dirk Eddelbuettel wrote: CRAN, by relying on the pow

[Rd] question about an R idiom: eval()ing a quoted block

In a few places in the R source code, such as the $initialize element of `family` objects, and in the body of power.t.test() (possibly other power.* functions), sets of instructions that will need to be run later are encapsulated by saving them as an expression and later applying eval(), rath

Re: [Rd] restoring LANGUAGE env variable within an R session

g the   main problem of PR#18055. introduced in R 4.2.0. Best, Sebastian Meyer Am 26.06.23 um 15:15 schrieb Ben Bolker:     I was playing around with the setting of the LANGUAGE variable and am wondering whether I'm missing something obvious about resetting the value to its orig

Re: [Rd] restoring LANGUAGE env variable within an R session

That's reasonable, but I'm wondering why it works the *first* time it's called in a session. Is this just undefined behaviour (so I shouldn't be surprised whatever happens)? Again, $ Rscript -e 'sqrt(-1); Sys.setenv(LANGUAGE="es"); sqrt(-1)' [1] NaN Warning message: In sqrt(-1) : NaNs produc

[Rd] restoring LANGUAGE env variable within an R session

I was playing around with the setting of the LANGUAGE variable and am wondering whether I'm missing something obvious about resetting the value to its original state once it's been set. I seem to be able to reset the language for warnings/errors once, but not to change it a second time (or r

Re: [Rd] why does [A-Z] include 'T' in an Estonian locale?

quot;[A-Ø]", "Å") [1] TRUE grepl("[A-Ø]", "Æ") [1] TRUE So for character ranges, the order is Å,Æ,Ø (which is how they'd collate in Swedish, except that Swedish uses diacriticals rather than Æ and Ø). Sys.setlocale("LC_ALL", "sv_SE

Re: [Rd] infelicity in `na.print = ""` for numeric columns of data frames/formatting numeric values

On 2023-06-05 9:27 a.m., Martin Maechler wrote: Ben Bolker on Sat, 3 Jun 2023 13:06:41 -0400 writes: > format(c(1:2, NA)) gives the last value as "NA" rather than > preserving it as NA, even if na.encode = FALSE (which does the > 'expected'

[Rd] infelicity in `na.print = ""` for numeric columns of data frames/formatting numeric values

you look carefully enough), but IMO it violates the principle of least surprise https://en.wikipedia.org/wiki/Principle_of_least_astonishment , so I would call it at least an 'infelicity' (sensu Bill Venables) Is there any chance that this design decision could be revisited?

Re: [Rd] why does [A-Z] include 'T' in an Estonian locale?

wrote: On 5/30/23 17:45, Ben Bolker wrote: Inspired by this old Stack Overflow question https://stackoverflow.com/questions/19765610/when-does-locale-affect-rs-regular-expressions I was wondering why this is TRUE: Sys.setlocale("LC_ALL", "et_EE") grepl("[A-Z]", &

[Rd] why does [A-Z] include 'T' in an Estonian locale?

Inspired by this old Stack Overflow question https://stackoverflow.com/questions/19765610/when-does-locale-affect-rs-regular-expressions I was wondering why this is TRUE: Sys.setlocale("LC_ALL", "et_EE") grepl("[A-Z]", "T") TRE's documentation at

Re: [Rd] Query: Could documentation include modernized references?

For one point of evidence about how much people pay attention to the documentation about what's outdated: Brian Ripley added a comment to nlminb.Rd in 2013 saying that the function was "for historical compatibility"

Re: [Rd] use Ctrl-W to close View() window?

ebian Linux FWIW. Cheers, Johannes Am Freitag, 17. März 2023, 23:16:49 CET schrieb Ben Bolker: I might be the last person in the world who's using View() outside of RStudio, but does anyone have a sense of how hard it would be to enable closing such a window (when in focus) with a s

[Rd] use Ctrl-W to close View() window?

base?   Or maybe this can already be enabled somehow?   cheers    Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] transform.data.frame() ignores unnamed arguments when no named argument is provided

For what it's worth I think the increased emphasis on classed errors should help with this (i.e., it will be easier to filter out errors you know are false positives/irrelevant for your use case). On Fri, Mar 3, 2023 at 12:17 PM Antoine Fabri wrote: > > Let me expand a bit, I might have expres

[Rd] uniroot violates bounds?

, I think (?) that the 'trace' argument only produces any output if the 'extendInt' option is enabled? Inspired by https://stackoverflow.com/questions/75494696/solving-a-system-of-non-linear-equations-with-only-one-unknown/75494955#75494955 cheers Ben Bolker

Re: [Rd] Linking to Intel's MKL on Windows

ums/en-US/home?forum%20=ropen I might tweet at @revodavid (David Smith) to see if there's any more information available about the MRO release schedule ... good luck, Ben Bolker On 2022-10-01 12:00 p.m., Viechtbauer, Wolfgang (NP) wrote: Hi Christine, MKL is a closed-sourc

Re: [Rd] Problem with accessibility in R 4.2.0 and 4.2.1.

There was a long apparently related thread back in May: https://stat.ethz.ch/pipermail/r-devel/2022-May/081708.html but that problem was supposedly patched in 4.2.1 ... On 2022-09-22 9:48 a.m., Andrew Hart via R-devel wrote: Hi. I'm having an issue with R 4.2.1 on Windows but I'm not sure if

Re: [Rd] Writing in R // R 4.2.0 on Windows doesn't work with Dasher

mailto:murdoch.dun...@gmail.com>> wrote:     On 15/05/2022 2:44 p.m., Ben Bolker wrote: >     I don't know if there's a good up-to-date list anywhere of > editors/IDEs that handle R nicely, but it would include at least: > >     Atom >   

[Rd] model.weights and model.offset: request for adjustment

ward compatibility with tibbles, but in this case [[-indexing would seem to be better practice in any case. Might a patch be accepted ... ? cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] partial matching of row names in [-indexing

t sw["C", ] # partially matches sw[match("C", row.names(sw)), ] # no exact match Whether this is good behaviour or not is a different question, but the documentation seems clear enough (to me, at least). Best, Steve On Fri, 14 Jan 2022 at 20:40, Ben Bolker wrote:

[Rd] partial matching of row names in [-indexing

People are often surprised that row-indexing a data frame by [ + character does partial matching (and annoyed that there is no way to turn it off: https://stackoverflow.com/questions/18033501/warning-when-partial-matching-rownames https://stackoverflow.com/questions/34233235/r-returning-p

[Rd] documentation patch for as.formula → reformulate

- as.formula(paste("y ~ ", paste(xnam, collapse= "+" which could arguably be better done as reformulate(xname, response = "y") I've attached a documentation patch that adds the alternative version and a \seealso{} link. Happy to submit to r-bugzilla

[Rd] trivial typo in NEWS file

Index: doc/NEWS.Rd === --- doc/NEWS.Rd (revision 81435) +++ doc/NEWS.Rd (working copy) @@ -425,7 +425,7 @@ data frames with default row names (Thanks to Charlie Gao's \PR{18179}). - \item \code{txtProgresBar()}

Re: [Rd] Why does lm() with the subset argument give a different answer than subsetting in advance?

I agree that it seems non-intuitive (I can't think of a design reason for it to look this way), but I'd like to stress that it's *not* an information leak; the predictions of the model are independent of the parameterization, which is all this issue affects. In a worst case there might be som

Re: [Rd] plogis (and other p* functions), vectorized lower.tail

On 12/9/21 10:03 AM, Martin Maechler wrote: Matthias Gondan on Wed, 8 Dec 2021 19:37:09 +0100 writes: > Dear R developers, > I have seen that plogis silently ignores vector elements of lower.tail, and also of 'log'. This is indeed the case for all d*, p*, q* functions. Yes,

Re: [Rd] stats::fft produces inconsistent results

Nice! On 10/21/21 4:26 PM, Dipterix Wang wrote: Thank you for such detailed and plain explanation. It is much clearer to me now w.r.t. the R internal memory management and how PROTECT should be used. Also after diving into the documentation of FFTW3 library, I think I found why the data wa

Re: [Rd] stats::fft produces inconsistent results

This is a long shot, but here's a plausible scenario: as part of its pipeline, ravetools::mvfftw computes the mean of the input vector **and then centers it to a mean of zero** (intentionally or accidentally?) because variables are passed to compiled code by reference (someone can feel

Re: [Rd] Question about quantile fuzz and GPL license

On 9/14/21 9:22 AM, Abel AOUN wrote: Hello, I'm currently working on Python numpy package to develop linear interpolation methods for quantiles. Currently, numpy only support the type 7 of Hyndman & Fan and I did the implementation for the 8 other methods to do as much as R ::quantile. As

Re: [Rd] Issues with drop.terms

cal Models in S" (Becker/Chambers white book), *or* the source code itself, I would love some pointers ... Ben Bolker On 8/23/21 10:36 AM, Therneau, Terry M., Ph.D. via R-devel wrote: This is a follow-up to my earlier note on [.terms.   Based on a couple days' work getting the su

Re: [Rd] Feature request: Change default library path on Windows

;) is to compose & submit a wishlist request to the R bug tracker ... It might also be worth reaching out to/double-checking with Jeroen Ooms (Rtools maintainer and Windows infrastructure expert; I don't know if he has any more formal association with R-core/CRAN ?) cheers Ben Bo

[Rd] undefined subclass warning

A colleague recently submitted a paper to JSS and was advised to address the following warning which occurs when their package (https://CRAN.R-project.org/package=pcoxtime) is loaded: Warning message: In .recacheSubclasses(def@className, def, env) : undefined subclass "numericVector" of

Re: [Rd] dgTMatrix Segmentation Fault

Nice! On 6/9/21 9:00 PM, Dario Strbenac via R-devel wrote: Good day, Thanks to handy hints from Martin Morgan, I ran R under gdb and checked for any numeric overflow. We pinpointed the cause: (gdb) info locals i = 0 j = 10738 m = 20 n = 5 ans = 0x5b332790 aa = 0x5b3327c0 Th

Re: [Rd] How to get utf8 string using R externals

Might the new UCRT build help? https://developer.r-project.org/Blog/public/2021/03/12/windows/utf-8-toolchain-and-cran-package-checks/ On 6/2/21 5:36 PM, Ben Bolker wrote: On 6/2/21 5:31 PM, Duncan Murdoch wrote: On 02/06/2021 4:33 p.m., xiaoyan yu wrote: I have a R Script Predict.R

Re: [Rd] How to get utf8 string using R externals

On 6/2/21 5:31 PM, Duncan Murdoch wrote: On 02/06/2021 4:33 p.m., xiaoyan yu wrote: I have a R Script Predict.R: set.seed(42) C <- seq(1:1000) A <- rep(seq(1:200),5) E <- (seq(1:1000) * (0.8 + (0.4*runif(50, 0, 1 L <- ifelse(runif(1000)>.5,1,0) df <- data.fra

Re: [Rd] {splines} package gone missing?

splines is 'recommended' ( not sure about capitalization), not "base' On Thu, May 20, 2021, 7:02 AM Randall Pruim wrote: > Thanks. I actually sort of checked for this: > > > row.names(installed.packages(priority = "base")) > [1] "base" "compiler" "datasets" "graphics" "grDevices" "grid

Re: [Rd] Add to Documentation of atan2.

ther* taken from system libraries or is defined at line 489. On my system (Ubuntu), 'man 3 catan' gives documentation on the function, and says "The real part of y is chosen in the interval [-pi/2,pi/2]" - but that _could_ be system-dependent. cheers Ben Bolker On

[Rd] base R pipe documentation

s a little weird, but it would be helpful in this case ...) I know I could go back to the mailing list discussion at https://hypatia.math.ethz.ch/pipermail/r-devel/2020-December/080173.html and try to figure it out for myself ... cheers Ben Bolker __

Re: [Rd] Testing R build when using --without-recommended-packages?

Sorry if this has been pointed out already, but some relevant text from https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Suggested-packages > Note that someone wanting to run the examples/tests/vignettes may not have a suggested package available (and it may not even be possib

Re: [Rd] R compilation on old(ish) CentOS

er-Dalgaards-iMac:R pd$ grep newsock src/main/connections.c con = R_newsock(host, port, server, serverfd, open, timeout, options); but your file seems to have lost the ", options" bit somehow. Also, mine is line 3488, not 3477. Maybe you have an old file getting in the way? - Peter On 2

[Rd] R compilation on old(ish) CentOS

o] Error 1 Any suggestions for a quick fix/diagnosis? cheers Ben Bolker $ gcc --version gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39) $ lsb_release -a LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:lan

Re: [Rd] Possible bug in predict.lm when x is a poly

Any particular reason you're using I() around your poly()? That looks weird to me ... and it works fine if you don't do that ... {AND, I think your result is *incorrect* when you have 3 observations in your response}. Basically, you have managed to short-circuit the (admittedly) obscure

Re: [Rd] boneheaded BLAS questions

For what it's worth I eventually got it to build in a hacky way (had to add -lopenblaslib manually). FWIW I *did* RTFM, several times, but for whatever reason the standard recipes are not working for me ... thanks! Ben Bolker On 3/18/21 7:52 AM, Dirk Eddelbuettel wrote: On 18

Re: [Rd] boneheaded BLAS questions

Thanks. I know it's supposed to Just Work (and I definitely appreciate all the work that's gone into making it Just Work 99% of the time!). I tried --with-lapack, no joy. Will try to decipher the rules file tomorrow ... cheers Ben On 3/17/21 10:25 PM, Dirk Eddelbuettel wrote: B

[Rd] boneheaded BLAS questions

I've been going around in circles trying to get BLAS-switching working on a current r-devel, I'm sure I'm doing something dumb. Any ideas about what I might be doing wrong, or suggestions for further diagnosis, would be welcome! tl;dr I am compiling R-devel with (to the best of my knowle

[Rd] fragility of MASS::boxcox

Is there anything to be done about this (other than the old "don't use names for your objects that are the same as built-in R functions") ? cheers Ben Bolker library(MASS) m1 <- lm(height~age, data=Loblolly) boxcox(m1) attr <- Loblolly m3 <- update(m1, data=attr

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

eral positions where you have a partial match). "Non-uniquely partially matching", perhaps? -pd On 13 Mar 2021, at 01:50 , Ben Bolker wrote: ll. 17-18 of src/library/base/man/pmatch.Rd says "the value to be returned at non-matching or multiply partially matching positions".

[Rd] trivial typo in src/library/base/man/pmatch.Rd

ll. 17-18 of src/library/base/man/pmatch.Rd says "the value to be returned at non-matching or multiply partially matching positions". I think "multiply" should be "multiple" there? Can submit an actual patch if that would be more useful. __ R-dev

Re: [Rd] installing from source

Kevin Ushey pointed out to me privately that he submitted a bug report and a patch for this about a month ago, which Kurt Hornik put in R-devel (c79477): https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17973 On 12/28/20 4:35 AM, Martin Maechler wrote: Ben Bolker on Sun, 27 Dec

[Rd] installing from source

below with \\' solve the problem? I'm happy to post this (with a patch if my fix seems appropriate) on r-bugzilla. cheers Ben Bolker line 1672 of src/library/tools/R/install.R : cmd <- paste0("tools:::.test_load_package('", pkg_name, "', "

Re: [Rd] R crashes when using huge data sets with character string variables

On Windows you can use memory.limit. https://stackoverflow.com/questions/12582793/limiting-memory-usage-in-r-under-linux Not sure how much that helps. On 12/12/20 6:19 PM, Arne Henningsen wrote: When working with a huge data set with character string variables, I experienced that various

Re: [Rd] the pipe |> and line breaks in pipelines

Definitely support the idea that if this kind of trickery is going to happen that it be confined to some particular IDE/environment or some particular submission protocol. I don't want it to happen in my ESS session please ... I'd rather deal with the parentheses. On 12/9/20 3:45 PM, Timothy

Re: [Rd] the pipe |> and line breaks in pipelines

FWIW there is previous discussion of this in a twitter thread from May: https://twitter.com/bolkerb/status/1258542150620332039 at the end I suggested defining something like .__END <- identity() as a pipe-ender. On 12/9/20 2:58 PM, Kevin Ushey wrote: I agree with Duncan that the right solu

[Rd] undocumented 'offset' argument in src/library/grDevices/man/adjustcolor.Rd

The 'offset' argument description is blank ... maybe 'additive adjustment to each of the (red, green, blue, alpha) values defining the colors, after adjustment by the corresponding \code{.f} factor' ...? This is the relevant code: x <- col2rgb(col, alpha = TRUE)/255 x[] <- pmax(0, p

Re: [Rd] return (x+1) * 1000

OK, you're way ahead of me. If this is in the QA tools, I guess I don't really see the need to change the parser and/or the language to flag it immediately? On Fri, Nov 20, 2020 at 7:43 PM Duncan Murdoch wrote: > > On 20/11/2020 7:01 p.m., Ben Bolker wrote: > >I may

Re: [Rd] return (x+1) * 1000

I may be unusual but I don't find these examples surprising at all/ I don't think I would make these mistakes (maybe it's easier to make that mistake if you're used to a language where 'return' is a keyword rather than a function? My two cents would be that it would make more sense to (1) wri

Re: [Rd] vignettes present in 2 folders or won't work

I take Duncan's point but would second the motion to have WRE clarify how static vignettes are supposed to work; it's a topic I am repeatedly confused about despite being an experienced package maintainer. If knowledgeable outsiders compiled a documentation patch would it be likely to be cons

[Rd] more Matrix weirdness

trix(0,nrow=3,ncol=10, dimnames=list(letters[1:3],LETTERS[1:10])) rr <- c("a","b","c") cc <- c("B","C","E") m <- Matrix(matrix(1:9,3,3)) x[rr,cc] <- m cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] M[cbind()] <- assignment with Matrix object loses attributes

antics. And str() excludes attributes, but attributes() includes slots. Highlighting the problems here... I think R should generate an error or a warning, if a user tries to assign attributes to S4 objects. In saying that, mixing OO design with numerical linear algebra is a gold mine... On

[Rd] M[cbind()] <- assignment with Matrix object loses attributes

unk")==12)) ## not OK attr(m1,"junk") ## NULL ## note I have to use the ugly stopifnot(isTRUE(...)) because a missing attribute returns NULL, an assignment to NULL returns NULL, and stopifnot(NULL) doesn't stop ...    cheers Ben Bolker _

Re: [Rd] qnbinom with small size is slow

tracker, so it will get more attention here; once the excitement has died down here (which might be almost immediately!), if no-one has already volunteered to post it to the bug tracker, request an account (as specified at https://www.r-project.org/bugs.html )   Thanks!    Ben Bolker For what

[Rd] trivial typo in ?Matrix::sparse.model.matrix.Rd

  "form" -> "from". Diff against latest SVN: Index: sparse.model.matrix.Rd === --- sparse.model.matrix.Rd    (revision 3336) +++ sparse.model.matrix.Rd    (working copy) @@ -4,7 +4,7 @@  \alias{fac2sparse}  \alias{fac2Sparse}  \descr

[Rd] closing R graphics windows?

   Does anyone have any idea how hard it would be/where to start if one wanted to hack/patch R to allow X11 graphics windows that had keyboard focus to be closed with standard keyboard shortcuts (e.g. Ctrl-W to close on Linux)?  Has this been suggested/tried before?    cheers     Ben

Re: [Rd] unstable corner of parameter space for qbeta?

On 2020-03-26 4:02 a.m., Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> on Wed, 25 Mar 2020 21:09:16 -0400 writes: > > > I've discovered an infelicity (I guess) in qbeta(): it's not a bug, > > since there

[Rd] unstable corner of parameter space for qbeta?

I've discovered an infelicity (I guess) in qbeta(): it's not a bug, since there's a clear warning about lack of convergence of the numerical algorithm ("full precision may not have been achieved"). I can work around this, but I'm curious why it happens and whether there's a better workaround -

Re: [Rd] help with rchk warnings on Rf_eval(Rf_lang2(...))

re a way I can use Shield() since this an Rcpp-based project anyway? Sorry for all the very basic questions, but I'm flying nearly blind here ... cheers Ben Bolker On 2020-03-23 4:01 p.m., Tomas Kalibera wrote: > On 3/23/20 8:39 PM, Ben Bolker wrote: >> Dear r-devel folk

[Rd] help with rchk warnings on Rf_eval(Rf_lang2(...))

orrections, pointers to further documentation, etc. would be most welcome ... Web searching for this stuff hasn't gotten me very far, and it seems to be deeper than most of the introductory material I can find (including the Rcpp vignettes) ... cheers Ben Bolker

Re: [Rd] survival bug?

. cheers Ben Bolker On 2020-03-03 4:02 p.m., Gabriel Becker wrote: > Hi Terry, > > http://win-builder.r-project.org/ and the rhub build service (which can be > invoked by the rhub package) allow on demand checks in windows > environments, though for active debugging the iterat

Re: [Rd] dput()

I think Robin knows about FAQ 7.31/floating point (author of 'Brobdingnag', among other numerical packages). I agree that this is surprising (to me). To reframe this question: is there way to get an *exact* ASCII representation of a numeric value (i.e., guaranteeing the restored value is ide

Re: [Rd] specials issue, a heads up

In the long run, coming up with a way to parse specials in formulas that is both clean and robust is a good idea - annoying users are a little bit like CRAN maintainers in this respect. I think I would probably do this by testing identical(eval(extracted_head), survival::Surv) - but this has lots o

[Rd] trivial typo in man page Quote.Rd

Attn: someone on R-core: "ran" should be "can". Also, thanks for this feature! Index: Quotes.Rd === --- Quotes.Rd (revision 77845) +++ Quotes.Rd (working copy) @@ -74,7 +74,7 @@ Raw character constants are also availa

Re: [Rd] R 3.6.3 scheduled for February 29

Because it's the fifth recurrence of the date (29 February). https://en.wikipedia.org/wiki/The_Pirates_of_Penzance On Thu, Feb 6, 2020 at 3:32 PM Abby Spurdle wrote: > > Congratulations! > > > celebrate (beeR=TRUE, loud.music=FALSE, > nbeeRs=2L, > proportion.of.tech.talk=0.4) > > Why

Re: [Rd] [External] Re: rpois(9, 1e10)

Ugh, sounds like competing priorities. * maintain type consistency * minimize storage (= current version, since 3.0.0) * maximize utility for large lambda (= proposed change) * keep user interface, and code, simple (e.g., it would be easy enough to add a switch that provided user contro

Re: [Rd] as-cran issue

From R NEWS (changes in 3.6.0) Experimentally, setting environment variable _R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors if the variable is set to a ‘true’ value) when && or || encounter and use arguments of length more than one. On 2020-01-13 11:46 a.m., Therneau, Terry M., Ph.D.

Re: [Rd] Inconsistencies in wilcox.test

Your second issue seems like a more or less unavoidable floating-point computation issue. The paired test operates by computing differences between corresponding values of x and y. It's not impossible to try to detect "almost-ties" (by testing for differences less than, say, sqrt(.Machine$do

Re: [Rd] depending on orphaned packages?

On 2019-09-25 3:26 a.m., Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> on Tue, 24 Sep 2019 20:09:55 -0400 writes: > > > SuppDists is orphaned on CRAN (and has been since 2013). > > https://cran.r-project.org/web/checks/check_

[Rd] depending on orphaned packages?

ng call to statmod::rinvgauss ? Would a patch be considered? Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Underscores in package names

Ugh, but not *as* ambiguous as the proposed example (you can still split unambiguously on "_"; yes, you could split on "last _" in Gabriel's example, but ...) On 2019-08-09 4:17 p.m., Duncan Murdoch wrote: > On 09/08/2019 2:41 p.m., Gabriel Becker wrote: >> Note that this proposal would make my

Re: [Rd] Underscores in package names

Creeping code complexity ... I like to think that the cuteR names will have a Darwinian disadvantage in the long run. FWIW Hadley Wickham argues (rightly, I think) against mixed-case names: http://r-pkgs.had.co.nz/package.html#naming. I too am guilty of picking mixed-case package names in th

Re: [Rd] [External] Re: quiet namespace load is noisy

Does setting message=FALSE in the chunk options of the vignette help? Or less preferably, using supressMessages() ? On 2019-07-23 9:36 a.m., Lenth, Russell V wrote: > Lionel, > > Thanks for your response. I understand that method overriding can be a > serious issue, but as you say, this i

[Rd] trivial typos in man/switch.Rd

My colleague points out that these typos are probably still present because almost no-one has the stamina to read that far down in ?switch ... cheers Ben Bolker Index: switch.Rd === --- switch.Rd (revision 76766

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