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 Aborted (c

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

[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

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

On 2024-04-18 9:41 a.m., Uwe Ligges wrote: On 18.04.2024 15:35, Ben Bolker wrote:     Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN has apparently just caught up to checking.  What's a little frustrating (to me) is that the dependence of prediction on ffbase is *very

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

*in the opposite direction* -- i.e. if A Enhances B, it's not entirely clear why the disappearance of B should matter at all ...) On 2024-04-18 9:35 a.m., Ben Bolker wrote:    Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN has apparently just caught up to checking.  What's

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

a given body of data. ~ John Tukey /// <https://www.inbo.be> Op do 18 apr 2024 om 15:25 schreef Ben Bolker <mailto:bbol...@gmail.com>>:    Thank you! (I know about package_dependencies() but ran into precisely the same problem and didn't want to re-imp

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

is not available on CRAN, however. On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker <mailto:bbol...@gmail.com>> wrote:    The 'dotwhisker' package was archived on CRAN: from https://cran.r-project.org/web/packages/dotwhisker/index.html <https://cran.r-project.org/web/pa

[R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

The 'dotwhisker' package was archived on CRAN: from https://cran.r-project.org/web/packages/dotwhisker/index.html Package ‘dotwhisker’ was removed from the CRAN repository ... Archived on 2024-04-12 as requires archived package 'prediction'. However, I can't for the life of

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: [R-pkg-devel] Avoid Possibly misspelled words in DESCRIPTION

AFAICT isn't actually mentioned anywhere in the docs ...) What do you mean by "already inserted these words in the WORDLIST"? cheers Ben Bolker On 2024-04-12 9:18 a.m., Gabriel Constantino Blain wrote: Hello, When I apply the devtools::check_win_devel() to my package it shows the

Re: [R-pkg-devel] Package vulnerabilities

FWIW there is a repo for R advisories. https://github.com/RConsortium/r-advisory-database with a front-end here https://osv.dev/list?ecosystem=CRAN= At present all of the *reported* vulnerabilities seem to be caused by problems with underlying/bundled libraries ... On 2024-04-03 4:37

Re: [R-pkg-devel] help diagnosing win-builder failures

++), but there is not enough information to give a conclusive diagnosis. On Sun, 17 Mar 2024 14:01:33 -0400 Ben Bolker wrote: 2. an ERROR running tests, where the output ends with a cryptic Anova: .. (please try to refrain from snarky comments about not using testthat ...) Pardon my ignorance

[R-pkg-devel] help diagnosing win-builder failures

...) Full log is here, at least for a little while: https://win-builder.r-project.org/9I5WG5R8WJg3/00check.log We could admit defeat and throw ourselves on the CRAN-maintainers' mercy, but we would like to resolve these if we can. cheers Ben Bolker __

[R-pkg-devel] confusion over spellchecking

I am working on a package and can't seem to get rid of a NOTE about Possibly misspelled words in DESCRIPTION: glmmTMB (10:88) lme (10:82) on win-builder. I have set export _R_CHECK_CRAN_INCOMING_USE_ASPELL_=TRUE locally, and have tried to set up the .aspell defaults as specified by

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

Re: [R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

https://github.com/r-lib/revdepcheck does the 'step 3 twice' part. I have had a few issues with it but overall it's been very helpful. https://github.com/HenrikBengtsson/revdepcheck.extras may also be useful. On 2024-01-30 10:56 a.m.,

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

Are you sure the issue that CRAN has is the library sizes, and not the issues flagged by the "LTO" platform ? https://www.stats.ox.ac.uk/pub/bdr/LTO/rar.out I would check with CRAN for clarification before you spend a lot of time trying

Re: [Rd] ADA Compliance

t 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 obtaining new

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

now what the warning looks like, but the ?tar help page discusses the issues. Duncan Murdoch On 12/12/2023 3:10 p.m., Ben Bolker wrote:    FWIW the R-windows FAQ says: Yet another complication is a 260 character limit on the length of the entire path name imposed by Windows. The limit applies

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

e R source tree. It would be helpful to have the exact wording of the NOTE/WARNING (?) that is thrown ... (I know I could make my own mini-package with a long path length in it somewhere but ...) cheers Ben Bolker On 2023-12-12 2:57 p.m., Simon Urbanek wrote: Justin, now that you clarif

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 ?

What 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: [R-pkg-devel] NOTE: Examples with CPU time > 2.5 times elapsed time

Wow. On Mon, Dec 4, 2023, 5:43 PM Ivan Krylov wrote: > Dear Artur, > > You've got a well-written package. There are some parts I wasn't able > to understand (e.g. changing the class of a variable by reference using > SET_CLASS and later changing it back), but there are no obvious places > where

Re: [R-pkg-devel] Question regarding finding the source file location without R-packages outside of R-Studio

Not sure, but I think the 'here' package might do what you want. It's tidyverse-affiliated but pretty stable On Thu, Nov 23, 2023, 2:39 PM Tony Wilkes wrote: > Hi everyone, > > I have a question. I hope it's not a stupid question. > > Suppose you'd want to perform version control and project

Re: [R-pkg-devel] Check warning around sprintf: Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system

You may also be able to use Rprintf ? https://teuder.github.io/rcpp4everyone_en/060_printing_massages.html On 2023-11-18 8:07 p.m., Iris Simmons wrote: Yes, the reason for the error is the use of sprintf. You can instead use snprintf where n is the maximum number of bytes to write, including

Re: [R-pkg-devel] What happened to mlr3proba on CRAN?

ect.org/src/contrib/Archive/mlr3proba/mlr3proba_0.4.9.tar.gz if you want to follow up with them ... cheers Ben Bolker On 2023-10-08 5:28 p.m., Dr. Franz Király wrote: Dear all, can someone explain to me what exactly happened to mlr3proba on CRAN? https://cran.r-project.org/web/packages/m

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

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: [R-pkg-devel] Suppressing compiler warnings?

This also doesn't answer your question, but: A trick that the TMB package uses to help users is to suggest that they add "CXXFLAGS += -Wno-ignored-attributes" to their `.R/Makevars` file. This means that *they* don't have to see useless warnings when compiling code. In your case I don't

[R-pkg-devel] status of "possibly invalid URL/403 error" NOTEs?

I have a package whose documentation includes the reference \doi{10.1137/18M1186411} which redirects here: https://epubs.siam.org/doi/10.1137/18M1186411 Running R CMD check --as-cran on the package gives Found the following (possibly) invalid URLs: URL:

Re: [R-pkg-devel] LICENSE file in an R package for CRAN submission

11:15 a.m., Ben Bolker wrote:    You have two choices: * put LICENSE in your .Rbuildignore file so that it shows up on Github but is excluded from the package * follow the instructions in https://cran.r-project.org/doc/manuals/R-exts.html#Licensing to refer to LICENSE in your DESCRIPTION f

Re: [R-pkg-devel] LICENSE file in an R package for CRAN submission

You have two choices: * put LICENSE in your .Rbuildignore file so that it shows up on Github but is excluded from the package * follow the instructions in https://cran.r-project.org/doc/manuals/R-exts.html#Licensing to refer to LICENSE in your DESCRIPTION file. However, CRAN generally

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

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 powerful

[R-pkg-devel] "Version contains leading zeroes" note: clarity

<https://github.com/r-devel/r-svn/blob/0252cdbf14c73acd26ae2090df3c04aa6118b523/src/library/tools/R/check.R#L6009>: wouldn't that be more appropriate here?) cheers Ben Bolker __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Package PowerSDI NOTES

See also https://ropensci.org/blog/2022/01/21/ropensci-news-digest-january-2022/#to-quote-or-not-to-quote-non-existing-words-in-description https://stat.ethz.ch/R-manual/R-patched/library/utils/html/aspell-utils.html On 2023-07-18 3:11 p.m., Duncan Murdoch wrote: On 18/07/2023 12:37 p.m.,

[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(),

Re: [R-pkg-devel] Public URLs for help for versions of base packages

Nice! (I like "A longer description will go here eventually.") It would be cute/handy to have navigation links available for "go to this help page in the next (previous) version of R" (if it's not a huge pain) On 2023-06-30 11:10 a.m., David Hugh-Jones wrote: OK, so I took Jeff's hint

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

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 original state

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

[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

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' thing fo

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

lly 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? cheers Ben Bolker --

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

: 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: [R-pkg-devel] masked from 'package:utils':,, ?

   This is harmless and should be accepted by CRAN (if masking existing functions were illegal half of the tidyverse would be banned ...).  It's there because it needs to be defined in order to enable the ??? alias for findFn().  sos:::"?" (and experimentation) show that use of a single ? is

Re: [R-pkg-devel] Acknowledging small functions from another package

In fact Martin Maechler added this in 2021: https://github.com/wch/r-source/blob/trunk/src/library/utils/R/str.R#L19-L21 ## A pearl from ggplot2 et al. NB: often needs '(.)' :%||% ( ) ## *not exported* [should rather be in 'base' than exported here] `%||%` <- function(L,R)

[R-pkg-devel] new/slightly mysterious CRAN warnings

Submission of most recent version of lme4 threw a NOTE on CRAN's Debian platform that we had not seen when running "R CMD check --as-cran" with the most recent SVN checkout, nor when submitted to win-builder/R-devel. These are legitimate issues (all now fixed), but we were taken by surprise

Re: [R-pkg-devel] Replacing dplyr by stats functions

    If you use Depends: in your package I think this is unavoidable (but, I don't think these should be counted against you as warnings by CRAN - they're "Warnings" not "WARNINGs" :-) )    The only way I know of to avoid this would be to Import: rather than Depend:, and import only the

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?

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 standard ke

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

?   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: [R-pkg-devel] Checking timings of packages

I would try running them on https://win-builder.r-project.org/ . If the Windows timings are OK on that platform I think you can make a good case to CRAN that you've done your best ... On 2023-03-14 9:52 a.m., Chris Brien wrote: Dear list members. I have run into a problem with examples

[R-pkg-devel] URL timeout in win-builder check: suggestions?

of fluff (click through if you want to see), but I don't want it causing hiccups in my CRAN submission (i.e., I could take it out if necessary but would prefer not to ...) Suggestions? === * checking CRAN incoming feasibility ... NOTE Maintainer: 'Ben Bolker ' Found the following (possibly

[R-pkg-devel] FAIL output in CRAN checks?

forms() Error in curl::curl_fetch_memory(url, handle = handle) :   Peer certificate cannot be authenticated with given CA certificates: [builder.r-hub.io] SSL certificate problem: certificate has expired   I guess I could report that ...   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

Re: [R-pkg-devel] Package submission rejected as it fails checks on Debian

Not important (of course) but where does the 5000 kWh per tree number come from? Is that (dry weight) x (50% carbon per dry weight) / (carbon content of CO2 emissions per kWh) ? https://www.epa.gov/energy/greenhouse-gas-equivalencies-calculator#results If we say 200 watts x 15 minutes

[Rd] uniroot violates bounds?

hink (?) 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: [R-pkg-devel] CRAN Packages over 5 MB & Time Length for Manual Inspection

Out of curiosity, what was the recently added package? It looks like the previous version of your package from about a year ago is only a 1.2MB tarball. Also out of curiosity, what caused the increase? cheers Ben Bolker On 2023-01-29 1:53 p.m., EcoC2S - Irucka Embry wrote

Re: [R-pkg-devel] Pretest failed and I fail to find out what's the problem

Seems pretty mysterious to me! (No cryptic NOTEs anywhere in the logs, other than the inevitable "Note_to_CRAN_maintainers") I will be curious to see if anyone else finds something, but my guess is a hiccup on the CRAN end (i.e., you'll end up sending e-mail to the CRAN maintainers to

Re: [R-pkg-devel] Mysterious "invalid z limit"

On 2023-01-08 1:38 p.m., Spencer Graves wrote: On 1/8/23 11:36 AM, Kevin Coombes wrote: I have been using R-Forge for many years for package development. And I have been using GitLab for other projects almost as long. However, over the past few months, the R-Forge support seems to be

Re: [R-pkg-devel] How to reduce examples in a package that takes more than 5 seconds to run?

On 2022-12-15 9:57 a.m., Brian G. Peterson wrote: On 12/15/22 08:34, Ismail Otoakhia wrote: The R package 'ardl.nardl' has some examples that take more than 5 seconds to run. I was advised by the CRAN team to reduce the run time to less than 5 seconds. How can this be achieved? - you

Re: [R-pkg-devel] Issue handling datetimes: possible differences between computers

Right now as.POSIXlt.Date() is just function (x, ...) .Internal(Date2POSIXlt(x)) How expensive would it be to throw a warning when '...' is provided by the user/discarded ?? Alternately, perhaps the documentation could be amended, although I'm not quite sure what to suggest. (The sentence

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

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-source commercial pr

Re: [R-pkg-devel] Found the following (possibly) invalid URLs:

I get a 404. On 2022-09-29 4:50 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel wrote: In testing a new version of one of my package on win builder, I get the following: Found the following (possibly) invalid URLs: . . . URL:

Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.

the NOTE definitely seems like something CRAN would object to, so you should fix it before resubmitting ...) good luck, Ben Bolker On 9/22/22 4:15 PM, Carsten Croonenbroeck wrote: Hi Lluís, thanks for the clarification. And kudos to your detective flair. I’m serious about that, as I would

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

Re: [R-pkg-devel] Warning... unable to translate 'Ekstrm' to a wide string; Error... input string 1 is invalid

 The help pages are at https://github.com/wch/r-source/blob/trunk/src/library/base/man/iconv.Rd or the equivalent at https://github.com/r-devel/r-svn or https://svn.r-project.org/R/trunk/src/library/base/man/iconv.Rd   they still have \x examples in them, but maybe the use of \x is not

Re: [R-pkg-devel] DOI / URL issues in package vignettes

On 2022-05-18 6:56 a.m., Ivan Krylov wrote: В Wed, 18 May 2022 12:06:03 +1000 Joshua Wiley пишет: curl -I -L https://doi.org/10.1037/met434 gives the below on my system, which (I think?) means you get the expected redirect for a DOI and then a 403 forbidden error. On the

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

om>> 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 >     Sublime Text >     VS Code    

[R-pkg-devel] nit-picking about CRAN repository policy

ey refine their 'noSuggests' test so that it conforms to the wording in the CRP, or that they change the CRP wording to something stricter like > Any package listed in ‘Suggests’ or ‘Enhances’ should be used conditionally in examples, tests, and vignettes. ? cheers

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

ty 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

;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: Peop

[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

[Rd] documentation patch for as.formula → reformulate

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 if reques

[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

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

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: [R-pkg-devel] Using \donttest with R >= 4.0.0

(This crossed with Martin Ondrus's reply). In the past few years CRAN screeners have gotten more strict about \dontrun{}; a first-round screening often comes back requesting that \dontrun{}, and commented-out examples, not be used.

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

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

Re: [R-pkg-devel] [Tagged] Re: multithreading in packages

FWIW there is some machinery in the glmmTMB package for querying, setting, etc. the number of OpenMP threads. https://github.com/glmmTMB/glmmTMB/search?q=omp On 10/9/21 11:45 AM, Vladimir Dergachev wrote: On Sat, 9 Oct 2021, Jeff Newmiller wrote: Keep in mind that by embedding this

Re: [R-pkg-devel] [External] Formula modeling

There's a Formula package on CRAN that's designed for this use case. lme4 and nlme don't use it, but implement their own formula manipulation machinery. (The cleanest version of this machinery is actually in glmmTMB at

Re: [R-pkg-devel] Internet resources and Errors

I think you're not supposed to stop(). You should just proceed with the other tests (skipping any tests/examples that depend on access to the inaccessible internet resources, or values derived from the failing call, to work) Does that help? On 9/24/21 10:49 AM, Roy Mendelssohn - NOAA

Re: [R-pkg-devel] Solaris segfaults

hurdle I encountered last time I tried, it was probably some weird idiosyncratic thing. For the record I haven't tried valgrind recently, but the CRAN versions of the valgrind tests weren't throwing any errors ... https://cran.r-project.org/web/checks/check_issue_kinds.html thanks Ben Bolk

[R-pkg-devel] Solaris segfaults

ithub.com/glmmTMB/glmmTMB/issues/732 (with some red herrings) if anyone is interested. cheers Ben Bolker __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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: [R-pkg-devel] (no subject)

cieve more mails. *Best regards,* *Krishan Gupta* *PhD scholar, the Sengupta Laboratory* [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel chee

Re: [Rd] Issues with drop.terms

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 survival package to wo

Re: [R-pkg-devel] Solaris Support

.] So, at least as far as publicly viewable policies go, the CRAN maintainers would be able to ask you to make "all reasonable efforts". (In my opinion, figuring out how to make your package work properly with ODS 12.6 would take more than a "reasonable" effort, but .. ??

Re: [R-pkg-devel] Expired Incoming Package

That would be my best guess. On 8/23/21 3:19 PM, Reed A. Cartwright wrote: If my submission is no longer visible using foghorn::cran_incoming(), that means it has expired and I should resubmit, right? -- Reed A. Cartwright, PhD Associate Professor of Genomics, Evolution, and Bioinformatics

[R-pkg-devel] advice on reminders/nags to CRAN maintainers

but I'm loath to do that unnecessarily ... thoughts? Ben Bolker --- (Some previous history omitted here for brevity; there had been a bit of back-and-forth about this package previously.) 07/30: Submitted version 1.1.2.2 of the glmmTMB package. Got a "pretest-waiting-recheck"

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 Bolker

Re: [R-pkg-devel] Using parallel:::sendMaster despite warnings

participates in the discussion on r-devel and is convinced of the utility and harmlessness of your modifications the last step might be unnecessary). cheers Ben Bolker On 7/23/21 1:17 PM, David Norris wrote: My understanding about this issue with progressr is that it is nontrivial

Re: [R-pkg-devel] best LICENSE practices: AGPL-3 + LaTeX Project Public License

there (as the required files seem to be present on every _other_ Linux platform I've tried). (For future readers/references, the huxtable package is driving these requirements.) cheers Ben Bolker On Thu, Jul 15, 2021 at 9:49 PM Hadley Wickham wrote: > > On Wed, Jul 14, 2021 at 9:11 AM Ben Bolker

Re: [R-pkg-devel] best LICENSE practices: AGPL-3 + LaTeX Project Public License

quot;AGPL-3 + file LICENCE" ? * Do I just include the files without comment, since I have complied (as far as I can tell) with the terms of the LPPL? * Is there a way to signal to R CMD check that I *have* complied with the terms?    cheers     Ben Bolker ___

[R-pkg-devel] best LICENSE practices: AGPL-3 + LaTeX Project Public License

(as far as I can tell) with the terms of the LPPL? * Is there a way to signal to R CMD check that I *have* complied with the terms? cheers Ben Bolker __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] clarification about missing suggested packages.

standing on CRAN but is not available on a particular CRAN testing platform, as long as package A only uses package B conditionally. Thoughts/opinions/evidence? cheers Ben Bolker --- From the current CRAN policy: Packages on which a CRAN package depends should be available from a mains

Re: [R-pkg-devel] weird C stack traces from win-builder, due to brms/rstan load?

On 7/5/21 2:01 PM, Duncan Murdoch wrote: On 05/07/2021 10:32 a.m., Ben Bolker wrote:    I'm running into trouble checking a new release of the 'broom.mixed' package <https://cran.r-project.org/web/packages/broom.mixed/index.html> on win-builder.  I think it is some kind of rstan p

[R-pkg-devel] weird C stack traces from win-builder, due to brms/rstan load?

with one of the brms references avoided instead runs into trouble when loading rstan ...), I don't see what I can do ... <https://win-builder.r-project.org/YArr24tuYZ8G/00check.log> cheers Ben Bolker __ R-package-devel@r-project.org mai

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