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] 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

[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] 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] 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] 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] 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

[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

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 Eddelbue

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] 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

[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] R compilation on old(ish) CentOS

Thanks -- yes, I can confirm that it installs OK after erasing and checking out SVN from scratch. On 4/30/21 9:40 PM, Henrik Bengtsson wrote: Ben, it's most like what Peter says. I can confirm it works; I just installed https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz on

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

[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] 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

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] 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] 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] 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

[Rd] undefined subclass warning

guess there are class structures that are evaluated at install time and stored in the package environment ... Any more explanations would be welcome. cheers Ben __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

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] 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] 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] 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] 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] 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

[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()}

[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] 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

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

",] as.matrix(b)["A1",] illustrates the difference. thanks Ben On 1/14/22 9:19 PM, Steve Martin wrote: I don't think this is a bug in the documentation. The help page for `?[.data.frame` has the following in the last paragraph of the details: Both [ and [[ extraction metho

[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] 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 >   

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] 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

[Rd] Question on non-blocking socket

ore focused on using non-blocking sockets in general. Is it allowed to execute a read and a receive command immediately after each other or must a short waiting loop be built in. I'm asking this because I'm running into the same problems in a C++ project as I

Re: [Rd] Question on non-blocking socket

Hi Op 15-02-2023 om 14:38 schreef Tomas Kalibera: On 2/15/23 01:24, Ben Engbers wrote: Hi, December 27, 2021 I started a thread asking for help troubleshooting non-blocking sockets. .. I have two questions. The first is where I can find R documentation on proper use of non-blocking

Re: [Rd] Question on non-blocking socket

mp;read_set); }; return done; }; Inserting this call was essential in solving my problem. Ben Op 15-02-2023 om 17:17 schreef Tomas Kalibera: In the example you are waiting only for a single byte. But if the response may be longer, one needs to take into account in the client that not all bytes

[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] 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] 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] 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

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

ch/r-source/commit/fd50cf2047b636e496551bcefd6bfa505f93f168> but it's still widely used in new code ... But I agree that adding appropriate warnings/links to the documentation couldn't hurt. cheers Ben On 2023-03-26 12:41 p.m., Duncan Murdoch wrote: On 26/03/2023 11:54 a.m., J C Nash wrote: A tangential ema

[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] 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] 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] 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'

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

[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] restoring LANGUAGE env variable within an R session

en") > sqrt(-1) [1] NaN Warning message: In sqrt(-1) : NaNs produced On 2023-06-26 9:38 a.m., Dirk Eddelbuettel wrote: Ben, POSIX level / glibc level variables are set at process start and AGAIK cannot really be altered after start. They clearly work when set _before_ calling sqrt(-1

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

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

I missing something? cheers Ben https://github.com/r-devel/r-svn/blob/eac72e66a4d2c2aba50867bd80643b978febf5a3/src/library/stats/R/power.R#L38-L52 https://github.com/r-devel/r-svn/blob/master/src/library/stats/R/family.R#L166-L171 __ R-devel@r-p

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

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] 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

[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] 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

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] 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] 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

[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] 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

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

A clean build solves it for me too. Thank you! (I need to add this to my "have you tried turning it off and back on again?" list ...) Ben On 2024-04-25 8:07 a.m., luke-tier...@uiowa.edu wrote: I saw it also on some of my Ubuntu builds, but the issue went away after a make

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] 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

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

perhaps R-core doesn't want to guarantee that these operations give identical answers, in which case Rcpp will have to change the way it does things ... cheers Ben On 2024-06-08 6:39 p.m., Kevin Ushey wrote: IMHO, this should be changed in both Rcpp and downstream packages: 1. Rcpp c

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

this edge case. I'll see if I can come up with some pure RcppEigen/Eigen examples to illustrate the problem ... cheers Ben On 2024-06-10 10:12 a.m., Mikael Jagan wrote: The ASan output is:     > reference binding to misaligned address 0x0001 for type 'const do

[Rd] Certificates are not trusted

ched until the next successful transaction. You can delete cached packages by running ‘dnf clean packages’. Error: GPG check failed Translated with DeepL.com (free version) How can I renew or update the certificates? Ben Engbers __ R-devel@r-

Re: [Rd] Certificates are not trusted

I checked the installed versions from R-CRAN-kernlab and R-CRAN-tseries R-CRAN-kernlab = 0.9.32 R-CRAN-tseries = 0.10.56 . Updating these packages fails because of incorrect installation Op 15-08-2024 om 14:57 schreef Ben Engbers: Hi, The GPG keys intended for repository ‘Copr repo for cran

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] 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] 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] 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

[Rd] load/unload segfault puzzle

te the problem by (1) minimizing the amount of package-exercising code run between loading and unloading; (2) trying to create a minimal version of the package. In the meantime if anyone can think of any shortcuts or clever diagnostics I would love to hear about it ... thanks Ben Bolker --2

Re: [Rd] load/unload segfault puzzle

Ben Bolker gmail.com> writes: > > > Dear r-devel readers, > > I have a pretty deep problem with package loading and unloading in > the development version of the lme4 package > <https://github.com/lme4/lme4>; it's not boiled down to a properly &

Re: [Rd] load/unload segfault puzzle

On 13-06-12 07:09 PM, Duncan Murdoch wrote: > On 13-06-12 1:47 PM, Ben Bolker wrote: >> Ben Bolker gmail.com> writes: >> >>> >>> >>>Dear r-devel readers, >>> >>>I have a pretty deep problem with package loading and unloadin

[Rd] problem with eval(..., parent.frame(1L)) when package is not loaded

littering our code with lme4:: to make sure that the function gets looked for in the right place (ugh). See also https://github.com/lme4/lme4/issues/50 . Any ideas appreciated. Ben Bolker -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux)

Re: [Rd] problem with eval(..., parent.frame(1L)) when package is not loaded

Duncan Murdoch gmail.com> writes: > [snip] > > The other choice is to use the explicit ::, i.e. > > mc[[1]] <- quote(lmer::lFormula) > > This would be the solution I'd prefer, but you seem to have some > prejudice against :: . > I just thought that the whole point of using the machinery

Re: [Rd] problem with eval(..., parent.frame(1L)) when package is not loaded

On 13-06-28 01:56 PM, Duncan Murdoch wrote: > On 28/06/2013 12:42 PM, Ben Bolker wrote: >> Duncan Murdoch gmail.com> writes: >> >> > >> >> [snip] >> > >> > The other choice is to use the explicit ::, i.e. >> > >> > mc[[1

Re: [Rd] problem with eval(..., parent.frame(1L)) when package is not loaded

ous call, without uglifying the call in the process)? I read your e-mail about making the comparison with S3 method dispatch, but to be honest I don't understand it very well -- don't know if those particular techniques are applicable here ... ? Ben > > > On Fri, Jun 28,

[Rd] robustbase compilation problem: probably boneheaded? maybe 32-bit?

; Can anyone confirm/enlighten me? cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] SweaveParseOptions, quoted commas, and knitr vignettes

one of the hard parts is that I can't actually reproduce the error myself -- I don't know if it's specific to Windows, or to not having knitr installed, or both ...) Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] SweaveParseOptions, quoted commas, and knitr vignettes

installed, which can > be more helpful for the users to realize the real problem. I like the third option here. It might be nice if this were documented in the "Writing R extensions" manual, although I guess I shouldn't complain until I volunteer to write a documentation p

Re: [Rd] On the mechanics of function evaluation and argument matching

Brian Rowe muxspace.com> writes: > > Thanks for the lead. Given the example in ?missing though, > wouldn't it be safer to explicitly define a > default value of NULL: > > myplot <- function(x, y=NULL) { > if(is.null(y)) { > y <- x > x <- 1:length(y) > } > plot(x, y) > } > [sni

[Rd] Building R with Cairo

er pkg-config knows about cairo... yes > checking whether cairo is >= 1.2 and works... no Does anyone have perspective on what flags/tests to run in debugging this? Many thanks in advance for your perspective, and apologies for socializing such a minor problem; I am so very close, but have

[Rd] proposal for new FAQ entry?

"Why did read.table stop reading my file" is a pretty FAQ, e.g. http://thread.gmane.org/gmane.comp.lang.r.general/297406/focus=297409 (I could come up with a lot more examples if someone wanted). The answer is typically "check for spurious comment characters and unmatched quotation marks" Does

[Rd] trivial typo in "writing r extensions"

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 "followed" on line 423 of R-exts.texi should probably be "followed by" (or you could say "'followed' on line 423 should probably followed by &

[Rd] model.frame(), model.matrix(), and derived predictor variables

ve considered trying to write some kind of 'augmented' model frame, that would contain the equivalent of setdiff(all.vars(formula),model.frame(m)) [i.e. all input variables that appeared in the formula but not in the model frame ...]. thanks Ben Bolker

Re: [Rd] model.frame(), model.matrix(), and derived predictor variables

Bump: just trying one more time to see if anyone had thoughts on this (so far it's just ...) Original Message Subject: model.frame(), model.matrix(), and derived predictor variables Date: Sat, 17 Aug 2013 12:19:58 -0400 From: Ben Bolker To: r-de...@stat.math.et

[Rd] possible tweaking of family()$simulate?

elpful for me, I don't know if there is latent demand out there ... thoughts? Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Minimum requirements for package submission

t it in inst/vignetteData) and then 'fake' the twitter call: add a non-eval'd but echo'd chunk that appears to run the command, and an eval'd but non-echo'd chunk that loads the results of having run the command. Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] model.frame(), model.matrix(), and derived predictor variables

On 13-08-28 05:43 PM, Gabriel Becker wrote: > Ben, > > It works for me ... >> x = rpois(100, 5) + 1 >> y = rnorm(100, x) >> d = data.frame(x,y) >> m <- lm(y~log(x),d) >> update(m,data=model.frame(m)) > > Call: > lm(formula = y ~ log(x), dat

Re: [Rd] FOSS licence with BuildVignettes: false

Uwe Ligges statistik.tu-dortmund.de> writes: > > Setting > > BuildVignettes: false > > is fine if it is possible to build the vignettes, and the latter is > checked in CRAN incoming checks (but not the daily checks). > > Uwe Ligges Hmmm. I was told by the CRAN maintainers on Aug 7 that

Re: [Rd] declaring package dependencies

wer (which surely must be a reasonable tradeoff for fewer human resources!), *if* having the auto-filter made people sloppier about checking before submitting. Do you happen to remember what the technical difficulty was? If I were a CRAN maintainer (thank goodness I'm not!), overcoming it

Re: [Rd] (no subject)

lme4 could import from, but that seems tricky to do without making fairly major architectural changes. Ben Bolker > > For the record, you're referring to R-devel thread 'Correct NAMESPACE > > approach when writing an S3 method for a generic in another package' > > st

[Rd] type="message" possibility for capture.output() ?

As far as I can tell, there's no built-in way to get capture.output() to capture messages (stderr) instead of stdout ... suggested, fairly trivial, patch below. f <- function() { message("abc") cat("def\n") } x <- capture.output(f()) ## prints 'abc' x ## value: "def" source("~/R/r-dev

[Rd] version comparison puzzle

Can anyone explain what I'm missing here? max(pp1 <- package_version(c("0.9911.3","1.0.4","1.0.5"))) ## [1] ‘1.0.4’ max(pp2 <- package_version(c("1.0.3","1.0.4","1.0.5"))) ## [1] ‘1.0.5’ I've looked at ?package_version , to no avail. Since max() goes to .Primitive("max") I'm having tr

[Rd] Q-Q plot scaling in plot.lm(); bug or thinko?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I've been looking fairly carefully at the Q-Q plots produced by plot.lm() and am having difficulty understanding why plot.lm() is doing what it's doing, specifically scaling the standardized residuals by the prior weights. Can anyone explain this to m

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