[Rd] clarifying and adjusting the C API for R

This is an update on some current work on the C API for use in R extensions. The internal R implementation makes use of tens of thousands of C entry points. On Linux and Windows, which support visibility restrictions, most of these are visible only within the R executble or shared library. About

Re: [Rd] R for Windows FAQ

https://cran.r-project.org/bin/windows/base/old/ Tomas On 6/3/24 21:30, Rubiana Viana wrote: Hi! How can I get older versions of R software? Thank you! __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] R for Windows FAQ

Hi! How can I get older versions of R software? Thank you! -- *Rubiana Viana* Psicóloga e Mestra em Sociologia Política Gênero Raça e Direitos Humanos • Pesquisa • Projetos • Cultura e Diversidade LinkedIn | Portfolio

Re: [Rd] How to call directly "dotTcl" C-function of the tcltk-package from the C-code of an external package?

> Apparently this works: > getNativeSymbolInfo("dotTcl",PACKAGE=getLoadedDLLs()$tcltk) Thank you Peter! This solved the problem. > and the tcltk behavior was changed by > r84265 | hornik | 2023-04-15 08:44:36 +0200 (Sat, 15 Apr 2023) | 1 line > Try forcing symbols in ff calls. > I don't know

Re: [Rd] Segfault when parsing UTF-8 text with srcrefs

On 5/28/24 20:41, Tomas Kalibera wrote: On 5/28/24 19:35, Hadley Wickham wrote: Hi all, When I run the following code, R segfaults: text <- "×" srcfile <- srcfilecopy("test.r", text) parse(textConnection(text), srcfile = srcfile) It doesn't segfault if text is ASCII, or it's not wrapped

[Rd] R 4.4.1 scheduled for June 14

Full schedule is available on developer.r-project.org (pending update from SVN). -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com

Re: [Rd] How to call directly "dotTcl" C-function of the tcltk-package from the C-code of an external package?

I asked Tomas. Apparently this works: getNativeSymbolInfo("dotTcl",PACKAGE=getLoadedDLLs()$tcltk) and the tcltk behavior was changed by r84265 | hornik | 2023-04-15 08:44:36 +0200 (Sat, 15 Apr 2023) | 1 line Try forcing symbols in ff calls. Index: library/tcltk/src/init.c

Re: [Rd] [External] Re: Segfault when parsing UTF-8 text with srcrefs

On 5/30/24 09:29, Barry Rowlingson wrote: I get an R error and no segfault: > parse(textConnection(text), srcfile = srcfile) Error in parse(textConnection(text), srcfile = srcfile) :   test.r:1:1: unexpected $end 1: ×     ^ This is R 4.3.0, so maybe the bug has been introduced since then...

Re: [Rd] [External] Re: Segfault when parsing UTF-8 text with srcrefs

I get an R error and no segfault: > parse(textConnection(text), srcfile = srcfile) Error in parse(textConnection(text), srcfile = srcfile) : test.r:1:1: unexpected $end 1: × ^ This is R 4.3.0, so maybe the bug has been introduced since then... Version and system info: > version

[Rd] How to call directly "dotTcl" C-function of the tcltk-package from the C-code of an external package?

I have a use case with tcltk-package where I need to repeatedly call Tcl/Tk functions very quickly. For such purpose, the standard R-interface turned out to be too slow, and better option has been to call package's C-function dotTcl directly from my own C-code. Before R 4.4.0 it was possible

Re: [Rd] Segfault when parsing UTF-8 text with srcrefs

On 5/28/24 19:35, Hadley Wickham wrote: Hi all, When I run the following code, R segfaults: text <- "×" srcfile <- srcfilecopy("test.r", text) parse(textConnection(text), srcfile = srcfile) It doesn't segfault if text is ASCII, or it's not wrapped in textConnection, or srcfile isn't set.

Re: [Rd] Segfault when parsing UTF-8 text with srcrefs

On 2024-05-28 1:35 p.m., Hadley Wickham wrote: Hi all, When I run the following code, R segfaults: text <- "×" srcfile <- srcfilecopy("test.r", text) parse(textConnection(text), srcfile = srcfile) It doesn't segfault if text is ASCII, or it's not wrapped in textConnection, or srcfile isn't

[Rd] Segfault when parsing UTF-8 text with srcrefs

Hi all, When I run the following code, R segfaults: text <- "×" srcfile <- srcfilecopy("test.r", text) parse(textConnection(text), srcfile = srcfile) It doesn't segfault if text is ASCII, or it's not wrapped in textConnection, or srcfile isn't set. Hadley -- http://hadley.nz

Re: [Rd] FR: Customize background colour of row and column headers for the View output

I think we should do more than this trivial change. The two real dialogs used by the data editor would then also get the new background color (setting the cell width, the "variable" editor). Then, the code clearly distinguishes between cells for names (row, column) and cells for data, so

Re: [Rd] Keep class attribute when applying c() to hexmodes

On 2024-05-27 11:49 a.m., Schuhmacher, Dominic wrote: Dear list, The following behavior in base R is unexpected to me: a <- as.hexmode("99ac") b <- as.hexmode("9ce5") v <- c(a,b) v #> [1] 39340 40165 class(v) #> [1] "integer" Is there a good reason why v should not be of class "hexmode"? I

[Rd] Keep class attribute when applying c() to hexmodes

Dear list, The following behavior in base R is unexpected to me: a <- as.hexmode("99ac") b <- as.hexmode("9ce5") v <- c(a,b) v #> [1] 39340 40165 class(v) #> [1] "integer" Is there a good reason why v should not be of class "hexmode"? I can see that this is exactly as documented. The help for

Re: [Rd] Mismatches for methods registered for non-generic:

В Mon, 27 May 2024 10:52:26 + "Koenker, Roger W" пишет: > that have been fine until now and on my fresh R version 4.4.0 > (2024-04-24) are still ok with R CMD check —as-cran This extra check requires the environment variable _R_CHECK_S3_METHODS_SHOW_POSSIBLE_ISSUES_ to be set to TRUE to

[Rd] Mismatches for methods registered for non-generic:

I’m trying to repair my SparseM package to meet new CRAN rules. The fun part was rewriting the arithmetic-ifs in cholesky.f — to conform with new fortran rules. (This struck me as a bit like updating “the wine dark seas” in Homer.) Now, my remaining trouble is that I have several functions

Re: [Rd] Undesirable behaviour of base::factor

I think this is a "Doctor, it hurts when I do this" issue. The root of it is that as.character() behaves differently on integers and floating values. > factor(10) [1] 1e+05 Levels: 1e+05 > factor(10,levels=10) [1] 1e+05 Levels: 1e+05 > factor(10,levels=10:10) [1] >

[Rd] Undesirable behaviour of base::factor

This thread on stackoverflow illustrates the problem... https://stackoverflow.com/questions/78523612/r-factor-from-numeric-vector-drops-every-100-000th-element-from-its-levels The issue is that factor(), applied to numeric values, uses as.character(), which converts numbers to character strings

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

Hello, It is from the stats package and applied to the output of logistic regression as implemented by glm with setting family = "binomial". So, it is a base package and not an add-on CRAN package. I shall recommend linking to FlexiBLAS to our system administrator.

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"

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

В Tue, 21 May 2024 08:00:11 + Dario Strbenac via R-devel пишет: > Would a less resource-intensive value, such as 1, be a safer default > CPU value for confint? Which confint() method do you have in mind? There is at least four of them by default in R, and many additional classes could make

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

Hello, Would a less resource-intensive value, such as 1, be a safer default CPU value for confint? I noticed excessive CPU usage on a I.T. administrator-managed server which was being three-quarters used by another staff member when the confidence interval calculation in an R Markdown document

Re: [Rd] Output pipes to TTY hang

Thank you, that makes sense. Not worth messing with those changes on my account, but since you asked, my actual use case was for an R script (or rather my package used by one) to display text (e.g. for --help) using the system PAGER, without writing temporary files for file.show() because

Re: [Rd] config.site settings for M3 Mac typo in manual?

On 20/05/2024 09:06, Duncan Murdoch wrote: I've just upgraded to an M3 Mac laptop, and I'm working through getting the right configure settings to build R. The Installation and Administration manual says to have this in config.site: FFLAGS="-g -O2 -mmacos-version-min=11.0" FCFLAGS="-g -O2

Re: [Rd] Output pipes to TTY hang

On 5/20/24 07:36, Zafer Barutcuoglu wrote: Hi, I am seeing this on Linux as well as MacOS: Opening any output pipe from R 4.4.0 to TTY programs like "less"/"more" hangs, SIGINT-proof: $ R/4.4.0/bin/Rscript -e 'pipe("less", "w")' $ R/4.4.0/bin/Rscript -e 'cat("test", file="|less") $

[Rd] config.site settings for M3 Mac typo in manual?

I've just upgraded to an M3 Mac laptop, and I'm working through getting the right configure settings to build R. The Installation and Administration manual says to have this in config.site: FFLAGS="-g -O2 -mmacos-version-min=11.0" FCFLAGS="-g -O2 -mmacos-version-min=11.0" but those give an

[Rd] Output pipes to TTY hang

Hi, I am seeing this on Linux as well as MacOS: Opening any output pipe from R 4.4.0 to TTY programs like "less"/"more" hangs, SIGINT-proof: > $ R/4.4.0/bin/Rscript -e 'pipe("less", "w")' > $ R/4.4.0/bin/Rscript -e 'cat("test", file="|less") > $ R/4.4.0/bin/Rscript -e 'cat("test", file="|more")

Re: [Rd] [External] Re: R for the US Air Force

> that's not strictly true though is it? Anyone can form a company and > supply R, as long as everyone complies with the license. You are also free > to download R from public services and do it without any corporate > wrappings and trappings, which is what Posit (ex-RStudio) do, right? > >

Re: [Rd] [External] Re: R for the US Air Force

R is not a product that is provided by a company or any vendor that can be > procured through a vendor e.g. something on a GSA schedule. > > that's not strictly true though is it? Anyone can form a company and supply R, as long as everyone complies with the license. You are also free to download

Re: [Rd] R for the US Air Force

. From: ADAMS, DOUGLAS L CIV USAF AFMC OO-ALC/OBWA via R-devel on behalf of ADAMS, DOUGLAS L CIV USAF AFMC OO-ALC/OBWA via R-devel Sent: Thursday, May 16, 2024 8:11:30 PM To: R-devel@R-project.org Subject: [Rd] R for the US Air Force Hello, The US Air Force used to have R available on our

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

d idea. Thanks very much! Doug From: Josiah Parry Sent: Thursday, May 16, 2024 1:05 PM To: ADAMS, DOUGLAS L CIV USAF AFMC OO-ALC/OBWA Cc: R-devel@R-project.org Subject: [Non-DoD Source] Re: [Rd] R for the US Air Force You don't often get email from josiah.pa...@gma

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

my time here. That’s a really good idea. Thanks very much! Doug From: Josiah Parry Sent: Thursday, May 16, 2024 1:05 PM To: ADAMS, DOUGLAS L CIV USAF AFMC OO-ALC/OBWA Cc: R-devel@R-project.org Subject: [Non-DoD Source] Re: [Rd] R for the US Air Force You don't often

Re: [Rd] R for the US Air Force

Hey Doug, R is not a product that is provided by a company or any vendor that can be procured through a vendor e.g. something on a GSA schedule. Seems like you're caught in the bureaucracy hell hole. I used to help the USAF, and other DoD members use R when I was at RStudio (now Posit). I

[Rd] R for the US Air Force

Hello, The US Air Force used to have R available on our main network, but now those who need to accept it back are being very particular about what they're accepting in terms of official documentation. Would you be able to help me with this endeavor? I'm attaching a pdf that shows what

Re: [Rd] FR: Customize background colour of row and column headers for the View output

The change suggested by Iago Giné Vázquez is indeed very simple. It sets the background colour of the row and column headers to the background of the rest of the dataentry window. With this patch, R passes 'make check'. As Duncan Murdoch mentions, the X11 editor already behaves this way. If it's

Re: [Rd] FR: Customize background colour of row and column headers for the View output

A criticism of your suggestion is that it is not backwards compatible. Does that matter? I don't know, but probably not. The X11 version of the viewer does what you suggest. Duncan Murdoch On 2024-05-15 2:20 a.m., Iago Giné Vázquez wrote: About the decisions: Actually, the same way

Re: [Rd] FR: Customize background colour of row and column headers for the View output

About the decisions: Actually, the same way dataedittext modifies the text colour not only of data, but also of row and column names, and dataedituser modifies the colour of all the borders, I think dataeditbg should modify the background of all the window, at least that "inside" those borders.

[Rd] Support for as(x, "raw")

Hi, as(x, "") is supported and does as.(x) for all vector types except for raw. For example all the following coercions work and do what you'd expect: as(1L, "logical"), as(1L, "double"), as(1L, "complex"), as(1L, "character"), as(1L, "list"). But as(1L, "raw") does not:     > as(1L, "raw")

Re: [Rd] Altrep and translations (was "[R] Description of error is untranslated when ....")

Hello On the other hand, i find that R_compact_intrange checks whether (r = n2 - n1 + 1) >= R_XLEN_T_MAX, while seq_colon checks for (r = fabs(n2 - n1)) >= R_XLEN_T_MAX. And only then n is defined as r + 1 + epsilon. r is not used again That is why seq_colon does not reject that size at first and

Re: [Rd] FR: Customize background colour of row and column headers for the View output

This seems like something that should be fairly easily doable. Why don't you work out a patch? Some decisions to make: - What colours are we talking about? Would you want the labels to have their colour set independent of the dialog colours? If so, would you also want to configure the

[Rd] FR: Customize background colour of row and column headers for the View output

Thanks again Duncan and Ivan, I forward then the email to R-devel. Summarizing, the dataedit options (in RGui preferences or RConsole) to colouring the View output do not have effect on the background of the row and column names (see https://ibb.co/Dkn2pVs). Could this be implemented? Thank

[Rd] Altrep and translations (was "[R] Description of error is untranslated when ....")

> Ivan Krylov via R-help > on Tue, 14 May 2024 08:08:58 +0300 writes: > Dear Ricardo Villalba, Thank you for spotting this corner > case! > В Mon, 13 May 2024 11:37:57 -0300 Ricardo Villalba > пишет: >> I track the messages to be coded here: >>

Re: [Rd] [External] R hang/bug with circular references and promises

On Mon, 13 May 2024, Ivan Krylov wrote: [You don't often get email from ikry...@disroot.org. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] On Mon, 13 May 2024 09:54:27 -0500 (CDT) luke-tierney--- via R-devel wrote: Looks like I added that warning 22 years

Re: [Rd] [External] R hang/bug with circular references and promises

On Mon, 13 May 2024 09:54:27 -0500 (CDT) luke-tierney--- via R-devel wrote: > Looks like I added that warning 22 years ago, so that should be enough > notice :-). I'll look into removing it now. Dear Luke, I've got a somewhat niche use case: as a way of protecting myself against rogue *.rds

Re: [Rd] [External] R hang/bug with circular references and promises

On Sat, 11 May 2024, Peter Langfelder wrote: On Sat, May 11, 2024 at 9:34 AM luke-tierney--- via R-devel wrote: On Sat, 11 May 2024, Travers Ching wrote: The following code snippet causes R to hang. This example might be a bit contrived as I was experimenting and trying to understand

[Rd] Change between 86152 and 86534 - probably 86265 - that looks for zspmv in BLAS and not LAPACK causes R with OpenBLAS to fail

Executive summary: I believe revision 86265 makes it more difficult to build R with OpenBLAS on Windows as now the entire LAPACK needs to be built to obtain zspmv. Is there anything that can be done to allow the former behavior to be used, something in Mkrules.local perhaps? Detailed

Re: [Rd] [External] R hang/bug with circular references and promises

On Sat, May 11, 2024 at 9:34 AM luke-tierney--- via R-devel wrote: > > On Sat, 11 May 2024, Travers Ching wrote: > > > The following code snippet causes R to hang. This example might be a > > bit contrived as I was experimenting and trying to understand > > promises, but uses only base R. > >

Re: [Rd] [External] R hang/bug with circular references and promises

On Sat, 11 May 2024, Travers Ching wrote: The following code snippet causes R to hang. This example might be a bit contrived as I was experimenting and trying to understand promises, but uses only base R. It looks like it is looking for "not_a_variable" recursively but since it doesn't exist

[Rd] R hang/bug with circular references and promises

The following code snippet causes R to hang. This example might be a bit contrived as I was experimenting and trying to understand promises, but uses only base R. It looks like it is looking for "not_a_variable" recursively but since it doesn't exist it goes on indefinitely. x0 <- new.env() x1

[Rd] lmer error: number of observations <= number of random effects

I am running a multilevel growth curve model to examine predictors of social anhedonia (SA) trajectory through ages 12, 15 and 18. SA is a continuous numeric variable. The age variable (Index1) has been coded as 0 for age 12, 1 for age 15 and 2 for age 18. I am currently using a time varying

Re: [Rd] [R-sig-ME] lmer error: number of observations <= number of random effects

Dear Srinidhi, You are trying to fit 1 random intercept and 2 random slopes per individual, while you have at most 3 observations per individual. You simply don't have enough data to fit the random slopes. Reduce the random part to (1|ID). Best regards, Thierry ir. Thierry Onkelinx Statisticus

Re: [Rd] [External] Re: Patches for CVE-2024-27322

That should do it Sent from my iPad On Apr 30, 2024, at 9:57 AM, Iñaki Ucar wrote:  Many thanks both. I'll wait for Luke's confirmation to trigger the update with the backported fix. Iñaki On Tue, 30 Apr 2024 at 12:42, Dirk Eddelbuettel mailto:e...@debian.org>> wrote: On 30 April 2024 at

Re: [Rd] Patches for CVE-2024-27322

Many thanks both. I'll wait for Luke's confirmation to trigger the update with the backported fix. Iñaki On Tue, 30 Apr 2024 at 12:42, Dirk Eddelbuettel wrote: > > On 30 April 2024 at 11:59, peter dalgaard wrote: > | svn diff -c 86235 ~/r-devel/R > > Which is also available as > >

Re: [Rd] Patches for CVE-2024-27322

On 30 April 2024 at 11:59, peter dalgaard wrote: | svn diff -c 86235 ~/r-devel/R Which is also available as https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7 Dirk | (or 86238 for the port to the release branch) should be easily backported. | | (CC Luke in

Re: [Rd] Patches for CVE-2024-27322

svn diff -c 86235 ~/r-devel/R (or 86238 for the port to the release branch) should be easily backported. (CC Luke in case there is more to it) - pd > On 30 Apr 2024, at 11:28 , Iñaki Ucar wrote: > > Dear R-core, > > I just received notification of CVE-2024-27322 [1] in RedHat's Bugzilla. We

[Rd] Patches for CVE-2024-27322

Dear R-core, I just received notification of CVE-2024-27322 [1] in RedHat's Bugzilla. We updated R to v4.4.0 in Fedora rawhide, F40, EPEL9 and EPEL8, so no problem there. However, F38 and F39 will stay at v4.3.3, and I was wondering if there's a specific patch available, or if you could point me

Re: [Rd] max on numeric_version with long components

> Kurt Hornik writes: Should be fixed now. Best -k > Ivan Krylov via R-devel writes: > Indeed, apparently using which.min/which.max on the string encoding is > not good enough. ? which.min says that x can also be > an R object for which the internal coercion to ‘double’ works >

Re: [Rd] Petition to set warnPartialMatch* options to TRUE

> Therneau, Terry M , Ph D writes: > Let me give partial assent to Michael's suggestion:  a) have an easy way to > turn this on and b) add a strong suggestion to do so to the WRE manual.    > Kurt's example in the email shows how to do (a);  but I just looked in the > WRE manual and don't see

Re: [Rd] max on numeric_version with long components

> Ivan Krylov via R-devel writes: Indeed, apparently using which.min/which.max on the string encoding is not good enough. ? which.min says that x can also be an R object for which the internal coercion to ‘double’ works and I guess we found a case where it does not work. I'll look into

Re: [Rd] max on numeric_version with long components

В Sat, 27 Apr 2024 13:56:58 -0500 Jonathan Keane пишет: > In devel: > > max(numeric_version(c("1.0.1.1", "1.0.3.1", > "1.0.2.1"))) > [1] ‘1.0.1.1’ > > max(numeric_version(c("1.0.1.1000", "1.0.3.1000", > "1.0.2.1000"))) > [1] ‘1.0.3.1000’ Thank

[Rd] max on numeric_version with long components

I've noticed something in R devel which seems a little off and not the behavior I see in 4.4.0 or earlier versions. With numeric_versions that have long (>8 digit) final components max and min return the first element and not the max or min: In devel: > max(numeric_version(c("1.0.1.1",

Re: [Rd] read.csv

I was horrified when I saw John Weinstein's article about Excel turning gene names into dates. Mainly because I had been complaining about that phenomenon for years, and it never remotely occurred to me that you could get a publication out of it. I eventually rectified the situation by publishing

Re: [Rd] Should c(..., recursive = TRUE) and unlist(x, recursive = TRUE) recurse into expression vectors?

On 2024-04-27 10:53 am, Mikael Jagan wrote: Reading the body of function 'AnswerType' in bind.c, called from 'do_c' and 'do_unlist', I notice that EXPRSXP and VECSXP are handled identically in the recurse = TRUE case. A corollary is that c(recursive = TRUE) and unlist(recursive = TRUE)

[Rd] Should c(..., recursive = TRUE) and unlist(x, recursive = TRUE) recurse into expression vectors?

Reading the body of function 'AnswerType' in bind.c, called from 'do_c' and 'do_unlist', I notice that EXPRSXP and VECSXP are handled identically in the recurse = TRUE case. A corollary is that c(recursive = TRUE) and unlist(recursive = TRUE) treat expression vectors like expression(a, b)

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

Everyone, take a deep breath - there have been many disruptions in last few days - some obvious, others associated with the R release and the BioC disruptions on CRAN, so there is no need to panic and start devising "solutions" for issues that are temporary. Things are being sorted out and some

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

On Fri, 26 Apr 2024 13:15:47 +0200 Gábor Csárdi wrote: > That's not how this worked in the past AFAIR. Simply, the packages in > the x.y.z/Recommended directories were included in > src/contrib/PACKAGES*, metadata, with the correct R version > dependencies, in the correct order, so that

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

On Fri, Apr 26, 2024 at 1:06 PM Ivan Krylov wrote: > > On Fri, 26 Apr 2024 12:32:59 +0200 > Martin Maechler wrote: > > > Finally, I'd think it definitely would be nice for > > install.packages("Matrix") to automatically get the correct > > Matrix version from CRAN ... so we (R-core) would be

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

On Fri, 26 Apr 2024 12:32:59 +0200 Martin Maechler wrote: > Finally, I'd think it definitely would be nice for > install.packages("Matrix") to automatically get the correct > Matrix version from CRAN ... so we (R-core) would be grateful > for a patch to install.packages() to achieve this Since

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

On Fri, 26 Apr 2024, at 11:32 AM, Martin Maechler wrote: >> Gábor Csárdi >> on Fri, 26 Apr 2024 11:55:36 +0200 writes: > > > I don't know if this is a bug, but it is certainly weird. AFAICT R > > 4.4.0 has Matrix 1.7-0. > > Yes, it *is* available from CRAN: You can see it

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

> Gábor Csárdi > on Fri, 26 Apr 2024 11:55:36 +0200 writes: > I don't know if this is a bug, but it is certainly weird. AFAICT R > 4.4.0 has Matrix 1.7-0. Yes, it *is* available from CRAN: You can see it when looking into the 4.4.0/ , specifically the

[Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

I don't know if this is a bug, but it is certainly weird. AFAICT R 4.4.0 has Matrix 1.7-0. However, currently CRAN has Package: Matrix Version: 1.6-5 Priority: recommended Depends: R (>= 3.5.0), methods ... (plus another version for R >= 4.5.0 only). Which has some weird consequences, e.g. if

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Thu, Apr 25, 2024 at 4:24 AM Ivan Krylov via R-devel wrote: > > On Wed, 24 Apr 2024 15:31:39 -0500 (CDT) > luke-tierney--- via R-devel wrote: > > > We would be better off (in my view, not necessarily shared by others > > in R-core) if we could get to a point where: > > > > all entry

Re: [Rd] Question regarding .make_numeric_version with non-character input

On 4/25/24 07:04, Kurt Hornik wrote: ... > Sure, I'll look into adding something. (Too late for 4.4.0, of course.) > > Best > -k Great. Thanks! H. -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]]

Re: [Rd] Big speedup in install.packages() by re-using connections

On Thu, 25 Apr 2024 14:45:04 +0200 Jeroen Ooms wrote: > Thoughts? How verboten would it be to create an empty external pointer object, add it to the preserved list, and set an on-exit finalizer to clean up the curl multi-handle? As far as I can tell, the internet module is not supposed to be

Re: [Rd] Question regarding .make_numeric_version with non-character input

> Hervé Pagès writes: > On 4/24/24 23:07, Kurt Hornik wrote: >>> Hervé Pagès writes: >>> Hi Kurt, >>> Is it intended that numeric_version() returns an error by default on >>> non-character input in R 4.4.0? >> Dear Herve, yes, that's the intention. >> >>> It seems that I can turn this

Re: [Rd] Question regarding .make_numeric_version with non-character input

> Dirk Eddelbuettel writes: > Hi Kurt, > On 25 April 2024 at 08:07, Kurt Hornik wrote: > | > Hervé Pagès writes: > | > | > Hi Kurt, > | > Is it intended that numeric_version() returns an error by default on > | > non-character input in R 4.4.0? > | > | Dear Herve, yes, that's the

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 clean/make,

Re: [Rd] Big speedup in install.packages() by re-using connections

I'd like to raise this again now that 4.4 is out. Below is a more complete patch which includes a function to properly cleanup libcurl when R quits. Implementing this is a little tricky because libcurl is a separate "module" in R, perhaps there is a better way, but this works: view:

Re: [Rd] Question regarding .make_numeric_version with non-character input

Hi Kurt, On 25 April 2024 at 08:07, Kurt Hornik wrote: | > Hervé Pagès writes: | | > Hi Kurt, | > Is it intended that numeric_version() returns an error by default on | > non-character input in R 4.4.0? | | Dear Herve, yes, that's the intention. | | > It seems that I can turn this into

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

I saw it also on some of my Ubuntu builds, but the issue went away after a make 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

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Wed, 24 Apr 2024 15:31:39 -0500 (CDT) luke-tierney--- via R-devel wrote: > We would be better off (in my view, not necessarily shared by others > in R-core) if we could get to a point where: > > all entry points listed in installed header files can be used in > packages, at least

Re: [Rd] Question regarding .make_numeric_version with non-character input

On 4/24/24 23:07, Kurt Hornik wrote: >> Hervé Pagès writes: >> Hi Kurt, >> Is it intended that numeric_version() returns an error by default on >> non-character input in R 4.4.0? > Dear Herve, yes, that's the intention. > >> It seems that I can turn this into a warning by setting >>

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

On Wed, 24 Apr 2024 19:35:42 -0400 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. Not for me, sorry. If you have a sufficiently new processor, you can use `rr` [*] to

Re: [Rd] Question regarding .make_numeric_version with non-character input

> Hervé Pagès writes: > Hi Kurt, > Is it intended that numeric_version() returns an error by default on > non-character input in R 4.4.0? Dear Herve, yes, that's the intention. > It seems that I can turn this into a warning by setting >

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Wed, 24 Apr 2024, Hadley Wickham wrote: A few more thoughts based on a simple question: how do you determine the length of a vector? Rf_length() is used in example code in R-exts, but I don't think it's formally documented anywhere (although it's possible I missed it). Is using in an

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: [Rd] [External] Re: Is ALTREP "non-API"?

to make an explicit list of functions that > > you consider to be part of the exported API, and then grandfather in > > packages that used those functions prior to learning that we weren't > > supposed to. > > Making a list and hoping that it will remain up to date is not >

Re: [Rd] Question regarding .make_numeric_version with non-character input

Hi Kurt, Is it intended that numeric_version() returns an error by default on non-character input in R 4.4.0? It seems that I can turn this into a warning by setting _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_=false but I don't seem to be able to find any of this mentioned in the NEWS

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Wed, 24 Apr 2024, Hadley Wickham wrote: That is not true at all - the presence of header does not constitute declaration of something as the R API. There are cases where internal functions are in the headers for historical or other reasons since the headers are used both for the

Re: [Rd] Is ALTREP "non-API"?

> On Apr 25, 2024, at 12:55 AM, Hadley Wickham wrote: > > > > >>> That is not true at all - the presence of header does not constitute > >> declaration of something as the R API. There are cases where internal > >> functions are in the headers for historical or other reasons since the > >>

Re: [Rd] Is ALTREP "non-API"?

A few more thoughts based on a simple question: how do you determine the length of a vector? Rf_length() is used in example code in R-exts, but I don't think it's formally documented anywhere (although it's possible I missed it). Is using in an example sufficient to consider a function to be part

Re: [Rd] Is ALTREP "non-API"?

> And in general, I'd urge R Core to make an explicit list of functions that you consider to be part of the exported API While I believe R Core is in the process of such clarification, I'd also vote for this. Now that WRE has "experimental" category, and if we take the current definition of

Re: [Rd] Is ALTREP "non-API"?

> > > > >>> That is not true at all - the presence of header does not constitute > >> declaration of something as the R API. There are cases where internal > >> functions are in the headers for historical or other reasons since the > >> headers are used both for the internal implementation and

Re: [Rd] Is ALTREP "non-API"?

> On Apr 24, 2024, at 12:52 AM, Hadley Wickham wrote: > >> >> >> ALTREP is part of the official R api, as illustrated by the presence of src/include/R_ext/Altrep.h. Everything declared in the header files in >> that directory is official API AFAIK (and I believe that is more

Re: [Rd] Petition to set warnPartialMatch* options to TRUE

Let me give partial assent to Michael's suggestion:  a) have an easy way to turn this on and b) add a strong suggestion to do so to the WRE manual. Kurt's example in the email shows how to do (a);  but I just looked in the WRE manual and don't see any reference to it, nor any mention from R

Re: [Rd] Is ALTREP "non-API"?

> > > > > > ALTREP is part of the official R api, as illustrated by the presence of > > > src/include/R_ext/Altrep.h. Everything declared in the header files in > that > > > directory is official API AFAIK (and I believe that is more definitive > than > > > the manuals). > > > > > > > That is not

Re: [Rd] Petition to set warnPartialMatch* options to TRUE during R CMD check by default

> Michael Chirico writes: Michael, You may have seen that some time ago I added check.R:cprof <- Sys.getenv("_R_CHECK_EXAMPLES_PROFILE_", "") etc so one can use the _R_CHECK_EXAMPLES_PROFILE_ env var to specify a profile to use when running the examples, e.g.

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