[Rd] R 4.5.1 is released

2025-06-13 Thread Peter Dalgaard via R-devel
The build system rolled up R-4.5.1.tar.gz and .xz (codename “Great Square Root") this morning. This is a patch release with a handful of minor changes and mixups. The list below details the changes in this release. You can get the source code from https://cran.r-project.org/src/base/

Re: [Rd] FR: improve "use" function

2025-06-04 Thread Roland Fuß via R-devel
- Ursprüngliche Mail - > Von: "Kurt Hornik" > An: "Laurent Gatto" > CC: "Kurt Hornik" , "Trevor Davis" > , r-devel@r-project.org, "roland > fuss" > Gesendet: Dienstag, 3. Juni 2025 19:23:01 > Betreff: Re: [Rd] FR: improve &quo

Re: [Rd] Bug in prettyNum

2025-06-02 Thread Marttila Mikko via R-devel
Hi, Thanks, Ivan, for the additional diagnosis and debugging tips. Thanks, Martin, for the prompt fix. Thanks, Toby, for sharing the R Dev Container link. I tried it out and was able to easily test some changes. I'll be using that in the future! Best, Mikko -Original Message-

[Rd] Specifying a long string literal across several lines

2025-05-27 Thread Pavel Krivitsky via R-devel
Dear All, Perhaps this should go in r-package-devel, but I suspect that this is going to turn into a feature request, and I want to run it by the list before filing it in the Bugzilla. I would like to specify a long string literal without making the line of code too long. In R, "ab

Re: [Rd] sqrt(.Machine$double.xmax)^2 == Inf, but only on Windows in R

2025-05-27 Thread Pavel Krivitsky via R-devel
Dear All, Thanks for looking into it, and apologies for bumping this. I think the strangest thing for me is that the C and the R implementations on Windows yield different results. I don't know if it warrants a deeper look. Ultimately, I rewrote the code that relied on this behaviour. (I n

Re: [Rd] FR: improve "use" function

2025-05-27 Thread Laurent Gatto via R-devel
> What definitely needs attention is the fact that currently the above is > silently ignored. So at least for now we should teach attachNamespace() > to throw a suitably classed error if called with include.only that > contradicts a previous specification. > > Contributions welcom

Re: [Rd] Bug in prettyNum

2025-05-23 Thread Ivan Krylov via R-devel
В Fri, 23 May 2025 11:47:33 + Marttila Mikko via R-devel пишет: > When called with a numeric vector, the `replace.zero` argument is > disregarded. > > > prettyNum(0, zero.print = "- ", replace.zero = TRUE) > [1] "-" > Warning message:

[Rd] Bug in prettyNum

2025-05-23 Thread Marttila Mikko via R-devel
ce.zero) : 'zero.print' is truncated to fit into formatted zeros; consider 'replace=TRUE' A character vector as input works as expected: > prettyNum("0", zero.print = "- ", replace.zero = TRUE) [1] "- " Please see below a patch which I believe wou

[Rd] FR: improve "use" function

2025-05-23 Thread Roland Fuß via R-devel
Braunschweig, Germany Tel./Webex: ++49 531 25701967 Email: roland.f...@thuenen.de Arbeitsgruppe "Emissionsberichterstattung"/ Working group "Emission Inventories" Email: emissionsinvent...@thuenen.de __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Is it possible to gracefully interrupt a child R process on MS Windows?

2025-05-11 Thread Ivan Krylov via R-devel
On Sun, 11 May 2025 10:58:18 -0700 Henrik Bengtsson wrote: > Is it possible to gracefully interrupt a child R process on MS > Windows, e.g. a PSOCK cluster node? Not in the general case (I think, based on the code paths leading to Rf_onintr() on Windows), but PSOCK cluster nodes are ins

Re: [Rd] array-bound error with GCC 13/14

2025-05-09 Thread Olivier Benz via R-devel
your package code. > > Best, > Kevin > > On Fri, May 9, 2025 at 6:18 AM Ivan Krylov via R-devel > wrote: >> >> В Fri, 9 May 2025 11:09:22 +1000 >> Stephen Wade пишет: >> >>>inlined from ‘std::vector literanger::adjust_pvalues(const &g

Re: [Rd] array-bound error with GCC 13/14

2025-05-09 Thread Ivan Krylov via R-devel
aths that cannot be taken, but they don't see an easy way to fix the warnings on the compiler side. -- Best regards, Ivan __________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] sqrt(.Machine$double.xmax)^2 == Inf, but only on Windows in R

2025-04-29 Thread Ivan Krylov via R-devel
On Tue, 29 Apr 2025 12:00:09 +0200 Martin Maechler wrote: > Would you (or anybody else) know if this is new behaviour or it > also happened e.g. in R 4.4.x versions on Windows? R-4.3.1 on Windows 7 in a virtual machine gives: dput(sqrt(.Machine$double.xmax), control = 'hex')

[Rd] sqrt(.Machine$double.xmax)^2 == Inf, but only on Windows in R

2025-04-27 Thread Pavel Krivitsky via R-devel
Hello, Under R 4.5.0 on Windows (x86-64), I get: > sqrt(.Machine$double.xmax)^2 [1] Inf > sqrt(.Machine$double.xmax)*sqrt(.Machine$double.xmax) [1] Inf On other hand on other platforms, including Debian Linux (x86-64), I get: d> sqrt(.Machine$double.xmax)^2 [1] 1.7976931348623155085

[Rd] Inappropriate modifications to R C source related to bool

2025-04-16 Thread Suharto Anggono Suharto Anggono via R-devel
tion 'check_session_exit'. But it works fine. src/library/grid/src/grid.c r87924 The comment before function 'findInChildren' and before function 'findViewport'  are R code. There, 'FALSE' should not be replaced with 'false' and 'TRUE'  shou

Re: [Rd] [EXTERNAL] Re: Request for comment: namespace resolution in terms(, specials=) [::, etc.]

2025-04-15 Thread Therneau, Terry M., Ph.D. via R-devel
rd mandating namespaces on all function calls and > falling over things like strata() in the survival package. Then package > author(s) chose to comply rather than explain... > > -pd [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R does not build with conda libcurl

2025-04-14 Thread Ivan Krylov via R-devel
rl-config > command line program, which R is using to get this flag: > -I/home/local/USHERBROOKE/hoct2726/miniconda3/include With libcurl installed from conda, what do the following commands print? curl-config --built-shared curl-config --static-libs curl-config --libs > To fix the build,

Re: [Rd] table() and as.character() performance for logical values

2025-04-12 Thread Suharto Anggono Suharto Anggono via R-devel
:54:03 pm GMT+7, Martin Maechler wrote: >>>>> Suharto Anggono Suharto Anggono via R-devel >>>>>    on Thu, 10 Apr 2025 07:53:04 + (UTC) writes:     > Chain of calls of C functions in coerce.c for as.character() in R:     > do_asatomic     >

Re: [Rd] table() and as.character() performance for logical values

2025-04-11 Thread Suharto Anggono Suharto Anggono via R-devel
f it is, I think of clearing the cache for each first filling. For example, by abusing 'warn' argument, the following is added to my changed 'StringFromLogical'. if (*warn) TrueCh = FalseCh = NULL; Correspondingly, in 'coerceToString', warn = i == 0; is inserted before

Re: [Rd] table() and as.character() performance for logical values

2025-04-11 Thread Suharto Anggono Suharto Anggono via R-devel
cache for each first filling. For example, by abusing 'warn' argument, the following is added to my changed 'StringFromLogical'. if (*warn) TrueCh = FalseCh = NULL; Correspondingly, in 'coerceToString', warn = i == 0; is inserted before SET_STRING_ELT(ans, i, StringFromLogical

Re: [Rd] table() and as.character() performance for logical values

2025-04-11 Thread Suharto Anggono Suharto Anggono via R-devel
nged 'StringFromLogical'. if (*warn) TrueCh = FalseCh = NULL; Correspondingly, in 'coerceToString', warn = i == 0; is inserted before SET_STRING_ELT(ans, i, StringFromLogical(LOGICAL_ELT(v, i), &warn)); for LGLSXP case. - On Thursday, 10 April

Re: [Rd] table() and as.character() performance for logical values

2025-04-10 Thread Suharto Anggono Suharto Anggono via R-devel
Chain of calls of C functions in coerce.c for as.character() in R: do_asatomic ascommon coerceVector coerceToString StringFromLogical (for each element) The definition of 'StringFromLogical' in coerce.c : attribute_hidden SEXP StringFromLogical(int x, int *warn) { int w; format

Re: [Rd] table() and as.character() performance for logical values

2025-04-08 Thread Suharto Anggono Suharto Anggono via R-devel
ls = sqrt(2)^2) gives NA, different from factor(2, levels = sqrt(2)^2) With the change to 'factor', factor(2L, exclude = sqrt(2)^2) has 1 level (nothing is excluded), different from factor(2, exclude = sqrt(2)^2) ---- Am 21.03.25 um 15:42 schrieb Aidan Lakshman via R-devel: >

Re: [Rd] Suggestion: Install packages on non-appendable file systems (e.g. databricks volumes)

2025-04-02 Thread Ivan Krylov via R-devel
В Thu, 27 Mar 2025 13:26:47 +0100 Sergio Oller пишет: > Our current workaround kind of works, but when users expect to be able > to install packages > using renv or other tools that use install.packages to work; our > wrapper is not that convenient. Here's an idea that might

Re: [Rd] request for discussion on lonely doc patch suggestion

2025-03-25 Thread Serguei Sokol via R-devel
source.  I've been using it for a very long time (20 years or more, I think), and I suspect there are very good open source competitors out there now (and may have been for all the time I've been using BC). Suggestions? Duncan Murdoch __

Re: [Rd] table() and as.character() performance for logical values

2025-03-21 Thread Aidan Lakshman via R-devel
t including to potentially start discussion for optimization. For reference, the relevant section is in src/library/base/R/table.R:L75-85 -Aidan --- Aidan Lakshman (he/him) http://www.ahl27.com/ On 21 Mar 2025, at 8:26, Karolis Koncevičius wrote: > [You don't often g

Re: [Rd] [External] Suppressed "graphical parameter" warnings reviving themselves magically

2025-03-21 Thread luke-tierney--- via R-devel
Warnings are not "reviving themselves magically". Try resizing the window a few times and hitting return in the REPL. That should give you a hint on what is going on. Best, luke On Fri, 21 Mar 2025, Henrik Bengtsson wrote: What's going on here? $ R --vanilla --

[Rd] Problems with ::

2025-03-19 Thread Therneau, Terry M., Ph.D. via R-devel
added to the "user written packages" document, where it talks about specials. What other packages use specials? Terry T. [[alternative HTML version deleted]] ______ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R-devel, bool, and C23

2025-03-15 Thread Ivan Krylov via R-devel
On Sat, 15 Mar 2025 07:51:11 -0500 Dirk Eddelbuettel wrote: > /usr/local/lib/R-devel/lib/R/include/R_ext/Boolean.h:62:16: warning: ISO C > does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] > 62 | typedef enum :int { FALSE = 0, TRUE } Rboolean; //

Re: [Rd] R-devel, bool, and C23

2025-03-15 Thread Ivan Krylov via R-devel
On Fri, 14 Mar 2025 22:25:54 -0500 Dirk Eddelbuettel wrote: > An older package I looked at apparently currently fails to build under > r-devel (and with that my thanks to R-universe for giving us a > 'broad' range of builds for free -- off our development sources) over >

Re: [Rd] Depends: R (>= 4.1) for packages that use |> and \(...)

2025-03-05 Thread Ivan Krylov via R-devel
em for older versions of R. Please accept my apologies. Indeed, the script [1] called at configuration time does replace the examples section to avoid parse errors for example(...). And having example() do nothing (with all code and an explanation in the help page) is a small cost for having the

Re: [Rd] Depends: R (>= 4.1) for packages that use |> and \(...)

2025-03-05 Thread Serguei Sokol via R-devel
Le 05/03/2025 à 14:47, Hadley Wickham a écrit : Unfortunately your test generates a false positive for httr2 ( https://cran.r-project.org/web/checks/check_results_httr2.html) and other tidyverse packages where we use the base pipe in examples, but carefully disable them for older versions of R

Re: [Rd] R CMD check and CRAN's Rust policy

2025-03-02 Thread Mossa Merhi Reimert via R-devel
Dear Simon Urbanek, There has been very little engagement with the issue I referred to. If it was decided that this “check” ought to be part of the default checks for R, then that could have been written to us. Either on the bugs.r-project.org or the proposed patch. Before we talk about

[Rd] R CMD check and CRAN's Rust policy

2025-03-01 Thread Mossa Merhi Reimert via R-devel
Hello everyone! I'm Mossa, I'm one of the maintainers of extendr, an automated generation of bindings project for Rust code, for use in R-packages. I'm writing to you, as R 4.4.3 was just released, and there have not been follow-up on an issue important to us. Link to the issue

Re: [Rd] Vuori - Due Diligence

2025-02-26 Thread Geoff Wolkis via R-devel
Appreciate the response. We're trying to find someone there now. Geoff -Original Message- From: Ben Bolker Sent: Tuesday, February 25, 2025 4:30 PM To: r-devel@r-project.org Cc: Geoff Wolkis ; Stevie Ratto Subject: Re: [Rd] Vuori - Due Diligence External Sender - STOP, ASSES

Re: [Rd] Customizing width of input in Rterm

2025-02-26 Thread Ivan Krylov via R-devel
ing. The automatic resizing doesn't look nice due to gl_redraw() starting a new line newline before redrawing the prompt, but it works. This may have accessibility implications since it changes the behaviour of Rterm.exe, which is what A. Jonathan R. Godfrey recommends for blind Windows users

[Rd] Vuori - Due Diligence

2025-02-25 Thread Geoff Wolkis via R-devel
Hello - My name is Geoff Wolkis and I'm with Vuori's Third Party Risk Management Team. I've been assigned to conduct due diligence on the services and/or products your organization is providing to Vuori. In this case R Studio is providing statistical data and create repor

Re: [Rd] [External] More precise documentation of on.exit() [when leaving function vs. "context"]

2025-02-14 Thread luke-tierney--- via R-devel
ion() expr)(), but not until someone spends some time making sure it is exactly true for the interpreted case; not something I could justify giving high priority to. I'm not sure this word has a precise meaning in R but I think of on.exit() as running upon leaving the "context" in

[Rd] A few problems with Sys.setLanguage()

2025-02-11 Thread Ivan Krylov via R-devel
Hello R-devel, Currently, Sys.setLanguage() interprets an empty/absent environment variable LANGUAGE to mean unset="en", which disagrees with gettext(): it defaults to the LC_MESSAGES category of the current locale [1]. As a result, on systems with $LANGUAGE normally unset, Sys.s

Re: [Rd] Depends: R (>= 4.1) for packages that use |> and \(...)

2025-02-06 Thread Ivan Krylov via R-devel
Rd files without installing the packages. Attaching a patch that checks the syntax used in Rd examples at the same time as the main R code, not necessarily the best way to perform this check. Is it perhaps worth separating R/* checks from man/*.Rd checks? Should R CMD check try to reuse the Rd d

Re: [Rd] boolean and logical types -draft

2025-02-03 Thread Prof Brian Ripley via R-devel
Sent in error (and not moderated). On 03/02/2025 17:36, Prof Brian Ripley via R-devel wrote: Tomas, I am thinking of writing something for R-devel, and hope to have your input first. I get moderated on R-devel as I am now subscribed as brian.ripley@R- project.org which of course I cannot

[Rd] boolean and logical types -draft

2025-02-03 Thread Prof Brian Ripley via R-devel
Tomas, I am thinking of writing something for R-devel, and hope to have your input first. I get moderated on R-devel as I am now subscribed as brian.rip...@r-project.org which of course I cannot send from. So I am even more discouraged from posting there. (R-core is bad enough with Luke

Re: [Rd] Suggestion to emphasize Rboolean is unrelated to LGLSXP in R-exts

2025-02-03 Thread Prof Brian Ripley via R-devel
On 02/02/2025 15:50, Ivan Krylov via R-devel wrote: The good news is that without a C23-enabled compiler, the problem will only happen to source files that #include . The bad news is that such a source file will technically disagree with the rest of R about the type of Rboolean, including the

Re: [Rd] Suggestion to emphasize Rboolean is unrelated to LGLSXP in R-exts

2025-02-02 Thread Ivan Krylov via R-devel
The good news is that without a C23-enabled compiler, the problem will only happen to source files that #include . The bad news is that such a source file will technically disagree with the rest of R about the type of Rboolean, including the prototypes of the API functions that accept Rboolean

Re: [Rd] [SPAM Warning!] Suggestion to emphasize Rboolean is unrelated to LGLSXP in R-exts

2025-02-01 Thread Ivan Krylov via R-devel
Rboolean; Rboolean E; @@ * E == NA_LOGICAL [2] Coccinelle scripts: @@ typedef Rboolean; int* E; @@ * (Rboolean*)E This one will offer a diff to fix the bug: @@ int *E1; int *E2; typedef Rboolean; @@ ( memcpy | memmove ) (E1, E2, <+... -sizeof(Rboolean) +sizeof(int) ...+> ) __

[Rd] Bug Report: Incorrect precedence between / and %/% in R 4.4.1

2025-01-31 Thread Lionel Fotie via R-devel
Dear R Development Team, I have encountered an unexpected behavior in R 4.4.1 regarding the precedence of / and %/%. Steps to reproduce: print(2 * 10 / 2 %/% 50) Expected result: Since *, / and %/% have the same precedence, evaluation should be left-to-right: (2 * 10) / 2 %/% 50 # Expected: 0

Re: [Rd] 64bit integers

2025-01-26 Thread Prof Brian Ripley via R-devel
with 64-bit integers. But only 64-bit integers as in S pointers and integers had to be the same size. That is not something we could contemplate for R, as vast numbers of packages assume that R's integers map to C int (tested to be 32-bit) and Fortran 32-bit INTEGER. Cheers, Simon

Re: [Rd] Depends: R (>= 4.1) for packages that use |> and \(...)

2025-01-23 Thread Ivan Krylov via R-devel
o also depend on R >= 4.2.0? That's a good find! For the R >= 4.2 syntax, we only need to check for getParseData(...)$token %in% 'PLACEHOLDER'. The R >= 4.3 syntax feature is harder to test for: >> As an experimental feature the placeholder _ can now also be

Re: [Rd] Creating a long list triggers billions of messages

2025-01-21 Thread Ivan Krylov via R-devel
В Tue, 21 Jan 2025 16:51:34 +1100 Hugh Parsonage пишет: > x <- vector("list", 2^31) > > which triggers (presumably) billions of error messages like > Error: long vectors are not supported yet ../include/Rinlinedfuns.h I couldn't reproduce this with some releas

[Rd] How setClass() may introduce a binary dependency between packages

2025-01-18 Thread Ivan Krylov via R-devel
Hello R-devel, Since Pavel has mentioned ABI-level dependencies between packages [1], it may be relevant to revisit the related problem mentioned ~1.5 years ago by Dirk [2]. While the current version of SeuratObject doesn't exhibit this problem, a combination of package versions describ

Re: [Rd] as.data.frame() methods for model objects

2025-01-17 Thread SOEIRO Thomas via R-devel
/manuals/r-devel/R-exts.html#Generic-functions-and-methods) - shouldn't we use match.fun(transFUN)? diff --git a/src/library/stats/R/lm.R b/src/library/stats/R/lm.R index 13a458797b..2ce6b16f6e 100644 --- a/src/library/stats/R/lm.R +++ b/src/library/stats/R/lm.R @@ -982,3 +982,18 @@ labe

Re: [Rd] as.data.frame() methods for model objects

2025-01-17 Thread SOEIRO Thomas via R-devel
9 0.14520270 0.9304302 1.676239 4tensionH 1.395612 0.1501714 2.2196863 0.03100435 1.0397735 1.873229 Thank you. Best regards, Thomas -Message d'origine- De : SOEIRO Thomas Envoyé : jeudi 16 janvier 2025 14:36 À : r-devel@r-project.org Objet : as.data.frame() methods for model object

Re: [Rd] UTF-8 encoding issue with R CMD check with install-args="--latex"

2025-01-17 Thread Peter Ruckdeschel via R-devel
Thanks Ivan and Kurt, for nailing this down, best regards, Peter Am 17.01.2025 um 09:01 schrieb Kurt Hornik: Ivan Krylov via R-devel writes: Thanks. Will try to fix ... Best -k В Thu, 16 Jan 2025 18:09:25 +0100 Peter Ruckdeschel via R-devel пишет: this is to report some minor UTF-8

Re: [Rd] UTF-8 encoding issue with R CMD check with install-args="--latex"

2025-01-16 Thread Ivan Krylov via R-devel
В Thu, 16 Jan 2025 18:09:25 +0100 Peter Ruckdeschel via R-devel пишет: > this is to report some minor UTF-8 encoding issue with R CMD check > with option --install-args="--latex" (and possibly more install-args). Thank you for a very detailed report! This doesn't happe

[Rd] UTF-8 encoding issue with R CMD check with install-args="--latex"

2025-01-16 Thread Peter Ruckdeschel via R-devel
Hi, this is to report some minor UTF-8 encoding issue with R CMD check with option --install-args="--latex" (and possibly more install-args). More specifically, in my Windows system (see the cloud link below for details on my system), but also on the Linux machine of my collaborato

[Rd] as.data.frame() methods for model objects

2025-01-16 Thread SOEIRO Thomas via R-devel
70 -0.07210825 0.5165527 4tensionH 0. 0.03100435 0.03900286 0.6276638 Thank you. Best regards, Thomas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Depends: R (>= 4.1) for packages that use |> and \(...)

2025-01-16 Thread Ivan Krylov via R-devel
Hello R-devel, Approximately [*] the following CRAN packages make use of the pipe syntax in their source code or examples without depending on R >= 4.1: [1] "biplotEZ" "CaseBasedReasoning" "collinear" [4] "cubble"

Re: [Rd] Build error with gcc 15

2025-01-15 Thread Prof Brian Ripley via R-devel
On 15/01/2025 16:06, Iñaki Ucar wrote: Dear R Core, GCC 15 is already in Fedora rawhide, because it will be part of the next release, Fedora 42. R 4.4.2 fails to build with the following error [1]: sys-std.c:1189:1: warning: ‘noreturn’ attribute ignored [-Wattributes] 1189 | void

Re: [Rd] Package compression benchmarks for zstd vs gzip

2025-01-12 Thread Ivan Krylov via R-devel
zeros can be compressed to 697202 bytes of repetitive compressed stream that can be bzipped further to 248 bytes. Binary packages are probably the most obvious target for new compression methods because there is no need to install them on older versions of R. -- Best regards, Ivan _

Re: [Rd] binomial()$linkinv no longer accepts integer values

2025-01-08 Thread Ivan Krylov via R-devel
On Wed, 8 Jan 2025 10:57:47 -0500 Ben Bolker wrote: > I haven't done the archaeology to figure out when this broke/exactly > what change in the R code base broke it: it happened within the last > month or so binomial() itself exhibits this property even in R-4.2.2 from more than

[Rd] Small typo in nlme documentation

2025-01-07 Thread Roland Fuß via R-devel
ederal Research Institute for Rural Areas, Forestry and Fisheries – Thünen Institute in brief – consists of 15 specialized institutes that carry out research and provide policy advice in the fields of economy, ecology and technology. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R_CheckUserInterrupt() can be a performance bottleneck within GUIs

2024-12-18 Thread Sokol Serguei via R-devel
m) { int i, j; double result; for (i=0;iprint(microbenchmark::microbenchmark(nonsense0(1e8, 10), nonsense_div(1e8,10,1000), nonsense_add(1e8,10,1000), times=10)) --- In R terminal, it gives: Unit: milliseconds expr min lq mean median uq

[Rd] stats glm Response Format Ambiguity

2024-12-17 Thread Dario Strbenac via R-devel
-- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Changes in the survival package (long)

2024-12-15 Thread Dario Strbenac via R-devel
__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Changes in the survival package (long)

2024-12-15 Thread Therneau, Terry M., Ph.D. via R-devel
d patience as we have worked through the reverse dependency checks. Current on github and (hopefully soon) on CRAN. An unaswered question is how to best document this behaviour so that users will find it. Terry Therneau [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Alternative to some recently changed parts of dates.R and datetime.R

2024-11-25 Thread Suharto Anggono Suharto Anggono via R-devel
0]; secs <- secs[is.finite(secs)] could be put inside if(np >= 1L) __________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Error compiling 87283 on Windows 10 using Rtools4.4 6335-6327

2024-10-31 Thread Prof Brian Ripley via R-devel
On 31/10/2024 16:30, Avraham Adler wrote: When compiling R, the build fails after byte compiling grDevices with the following error: byte-compiling package 'grDevices' make[4]: *** [../../../share/make/lazycomp.mk:9: ../../../library/grDevices/R/grDevices.rdb] Error

Re: [Rd] Good practice for packages with Fortran and C code

2024-10-25 Thread Ivan Krylov via R-devel
med the same as the package name. The routines > are called using .Fortran(binary module name, args) or .Call(C binary > module name, ...). > > Can anyone see any problem with streamlining in this way? "Writing R Extensions" 1.5.4 says: >> this approach is no

Re: [Rd] [External] Re: Could .Primitive("[") stop forcing R_Visible = TRUE?

2024-10-25 Thread Ivan Krylov via R-devel
Dear Luke, Thank you very much for taking the time to write an exhaustive answer! They are always a pleasure to read on the R mailing lists. On Fri, 25 Oct 2024 11:50:34 -0500 (CDT) luke-tier...@uiowa.edu wrote: > So there is a discrepancy between interpreted and compiled code which > is

Re: [Rd] [External] Re: Could .Primitive("[") stop forcing R_Visible = TRUE?

2024-10-25 Thread luke-tierney--- via R-devel
On Fri, 25 Oct 2024, Ivan Krylov via R-devel wrote: В Fri, 25 Oct 2024 08:39:39 -0400 Duncan Murdoch пишет: Surely you or they should be the ones to run the test across all of CRAN? That's fair. The question is, is there a fundamental reason I overlooked to deny such a change? Excep

Re: [Rd] Could .Primitive("[") stop forcing R_Visible = TRUE?

2024-10-25 Thread Ivan Krylov via R-devel
has been in names.c since SVN revision 2. The one regression test touched by the change has been there since 2010. -- Best regards, Ivan ______ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Could .Primitive("[") stop forcing R_Visible = TRUE?

2024-10-25 Thread Ivan Krylov via R-devel
On Thu, 24 Oct 2024 13:23:56 -0400 Toby Hocking wrote: > The patch you are proposing to base R is > https://github.com/Rdatatable/data.table/issues/6566#issuecomment-2428912338 > right? Yes, it's this one, thank you for providing the link. Surprisingly, a very cursory check o

[Rd] Could .Primitive("[") stop forcing R_Visible = TRUE?

2024-10-24 Thread Ivan Krylov via R-devel
Hello, The "[" primitive operator currently has the 'eval' flag set to 0 in src/main/names.c. This means that the result of subsetting, whether R-native or implemented by a method, will never be invisible(). This is a very reasonable default: if the user goes as far as to

Re: [Rd] invalid permissions

2024-10-22 Thread Ivan Krylov via R-devel
tory, I was able to reproduce this crash by running R -d gdb # make sure that the package version under check will be loaded .libPaths(c("quantreg.Rcheck", .libPaths())) library(quantreg) example(plot.rqss) The crash happens in the Fortran code: Thread 1 "R" received signal SIG

Re: [Rd] Consider getNamespaceVersion() returning a numeric_version

2024-10-17 Thread Prof Brian Ripley via R-devel
This is what compareVersion() is for On 17/10/2024 13:22, Dirk Eddelbuettel wrote: On 17 October 2024 at 12:38, Tim Taylor wrote: | Would R-Core be receptive to having getNamespaceVersion() return a | numeric_version object instead of a named character? Is this good enough? What's

[Rd] WRE about R_strtod

2024-10-08 Thread Ivan Krylov via R-devel
Hello, This is what "Writing R extensions" currently says about R_atof and R_strtod: >> Function: void R_atof (const char* str) >> Function: void R_strtod (const char* str, char ** end) >> >> Implementations of the C99/POSIX functions atof and strtod whi

[Rd] Disabling S4 primitive dispatch during method resolution affects namespace load actions

2024-09-27 Thread Ivan Krylov via R-devel
eeds to load Rcpp modules, which uses load actions and reference classes. Since methods:::.findInheritedMethods temporarily disables primitive S4 dispatch [2], reference classes break and the namespace fails to load. I have prepared a small reproduction package [3], which will need to be install

Re: [Rd] Possible update to survival

2024-09-24 Thread Ivan Krylov via R-devel
В Sun, 15 Sep 2024 00:43:31 + "Therneau, Terry M., Ph.D. via R-devel" пишет: > 2. Before calling model.frame(), insert my copy of strata into the > calling chain coxenv <- new.env(parent= environment(formula)) > assign("strata", survival::strata,

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

2024-09-23 Thread Ivan Krylov via R-devel
wanted the data to be accessible, they could have set keep.data = TRUE. I can't tell whether evaluating object$call$data in environment(object$formula) is a better or worse idea than parent.frame(). -- Best regards, Ivan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

2024-09-21 Thread Ivan Krylov via R-devel
27;; NextMethod() } foo(x) # doesn't work # $foo # [1] "default" # # $baz # [1] "baz" # # $... # list() foo(x, 1) # does work # $foo # [1] "override" # # $baz # [1] "baz" # # $... # list() Evaluating object$call$data in the environment of the sugges

[Rd] Wrong/incomplete documentation regarding the 100-bytes path length limit.

2024-09-17 Thread Iago Bonnici via R-devel
Hello @r-devel,     From what I read in the following thread: https://stat.ethz.ch/pipermail/r-package-devel/2023q4/010197.html     The major reason to limit paths lengths in R packages is to help support MS Windows 260-chars paths lengths limit (pre-W10).     However, the official

[Rd] Possible update to survival

2024-09-14 Thread Therneau, Terry M., Ph.D. via R-devel
t test version also prints a warning when removing the extraneous �survival::� modifier, which I will retain for at least a little while although I personally detest receiving such messages. Terry T. [[alternative HTML version deleted]] ______ R-

Re: [Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Simon Andrews via R-devel
curl/issues/14315 suggests a libcurl option > and a curl command line option. > > Does download.file(method = 'curl', extra = '--ssl-no-revoke') work for you? Yes! Adding that option does indeed work and generates no warnings. > Since R-4.2.2, R understands the

Re: [Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Ivan Krylov via R-devel
OCATION_CHECK (0x80092012) - The revocation > function was unable to check revocation for the certificate. This extra error code is useful, thank you for trying the "curl" method. https://github.com/curl/curl/issues/14315 suggests a libcurl option and a curl c

Re: [Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Simon Andrews via R-devel
he system here may not fake the revocation infrastructure too, but I don't see that this is going to change, and it's only the winet method which actually allows anything to connect. Simon. -Original Message- From: Ivan Krylov Sent: 12 September 2024 15:28 To: Simon Andre

Re: [Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Ivan Krylov via R-devel
В Thu, 12 Sep 2024 12:01:54 + Simon Andrews via R-devel пишет: > readRDS('https://seurat.nygenome.org/azimuth/references/homologs.rds') > Error in gzfile(file, "rb") : cannot open the connection I don't think that gzfile works with URLs. gzcon(), on the

[Rd] Can gzfile be given the same method option as file

2024-09-12 Thread Simon Andrews via R-devel
Recently my employer has introduced a security system which generates SSL certificates on the fly to be able to see the content of https connections. To make this work they add a new root certificate to the windows certificate store. In R this causes problems because the default library used

Re: [Rd] Inconsistency between row and nrow

2024-09-08 Thread Marc Schwartz via R-devel
MARGIN equal to 1 and 2, respectively when x is a matrix." further differentiating the behavior of row() and col() as more specific implementations in the 2-dimensional case. To my read then, the difference in behavior appears to be intentional and expected. Regards, Marc Schwartz -O

[Rd] R compilation (revision 87083) failed after upgrade to Ubuntu 24.04 (libtirpc missing)

2024-09-01 Thread Mark Clements via R-devel
ing libtirpc-dev: > sudo apt install libtirpc-dev compilation proceeded smoothly. I understand that this may be local to my system. Sincerely, Mark. N�r du skickar e-post till Karolinska Institutet (KI) inneb�r detta att KI kommer att behandla dina personuppgifter. H�r finns information om

Re: [Rd] specials and ::

2024-08-27 Thread Gregory R. Warnes
volve more > discussion with users ("if your software knows what I should be doing why > can't it just do it for me?") > > cheers > Ben Bolker > >> On 2024-08-27 9:43 a.m., Therneau, Terry M., Ph.D. via R-devel wrote: >> You are right of course, Peter, but

Re: [Rd] specials and ::

2024-08-27 Thread Therneau, Terry M., Ph.D. via R-devel
4570.10780.8521 > > > Or, to be facetious: > >> lm(y~base::"+"(x,z)) > Call: > lm(formula = y ~ base::"+"(x, z)) > > Coefficients: > (Intercept) base::"+"(x, z) > 0.4516 0.4383 >

Re: [Rd] specials and ::

2024-08-26 Thread Therneau, Terry M., Ph.D. via R-devel
likes to do…) Terry T From: Josiah Parry Date: Monday, August 26, 2024 at 5:09 PM To: Therneau, Terry M., Ph.D. Cc: r-devel@r-project.org Subject: [EXTERNAL] Re: [Rd] specials and :: I wouldn't go so far as to call people who don't want to wholesale attach namespaces as "nuts.&

Re: [Rd] specials and ::

2024-08-26 Thread Therneau, Terry M., Ph.D. via R-devel
stion".) Ditto for most of the rest of the package functions. The very worst kind of bug. 2. Using specials =c("strata", "survival::strata") could work. I always process the result with a small "untangle.specials" function, a leftover from when R and Splus

Re: [Rd] specials and ::

2024-08-26 Thread Ivan Krylov via R-devel
В Mon, 26 Aug 2024 09:42:10 -0500 "Therneau, Terry M., Ph.D. via R-devel" пишет: > For instance >   fit <- survival::survdiff( survival::Surv(time, status) ~ > ph.karno + survival::strata(inst),  data= survival::lung) > > This fails to give the correct answer be

Re: [Rd] specials and ::

2024-08-26 Thread Kevin R. Coombes
I know I'm a curmudgeon, but it seems to me that if their "company policy" is causing a problem while trying to use free software, then the company should pay to fix it.   Kevin On 8/26/2024 10:42 AM, Therneau, Terry M., Ph.D. via R-devel wrote: The survival package makes sig

[Rd] specials and ::

2024-08-26 Thread Therneau, Terry M., Ph.D. via R-devel
yo.edu "TERR-ree THUR-noh" [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Make factanal accept functions for rotation parameter

2024-08-22 Thread Haan, Stefan via R-devel
Dear Martin, The thing I was trying to do, when I tried to pass a function for the rotation parameter was to call factanal repeatedly with different rotations to see which factor model would give the best interpretability. ```R rotate <- function(phi) { G <- matrix(c(cos(phi), s

[Rd] Make factanal accept functions for rotation parameter

2024-08-22 Thread Haan, Stefan via R-devel
Dear R developers, Would it be possible to make `factanal` to also accept functions and not just function names for its `rotation` parameter? If I understand correctly, `do.call` also supports this. Best greetings, Stefan Index: src/library/stats/R/factanal.R

Re: [Rd] Certificates are not trusted

2024-08-15 Thread Ivan Krylov via R-devel
anwhile, the public key at https://download.copr.fedorainfracloud.org/results/iucar/cran/pubkey.gpg has not expired (the current file will expire in 2028). The suggested workaround is to download the public key anew and import it manually: https://github.com/fedora-copr/copr/issues/2894 Either way, this is a problem

Re: [Rd] R-patched on CRAN is R-4.3.3

2024-08-09 Thread Ivan Krylov via R-devel
В Fri, 9 Aug 2024 10:28:19 +0200 Gábor Csárdi пишет: > Possibly related to this, it seems that > https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz > is not available any more. I think it's now R-patched.tar.?z: https://github.com/r-devel/r-

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