Re: [Rd] Printing digits.secs on data.frame?

On 18 July 2024 at 12:14, John Muschelli wrote: | Is there a way to have printing data.frames with POSIXct to display | milliseconds if digits.secs is set as a default? I suspect this would require a change to the corresonding print method. | You can use the digits argument in print, such as p

Re: [Rd] [External] Non-API updates

On 25 June 2024 at 12:25, Josiah Parry wrote: | Is there a link you can provide regarding the "Moving into C compliance?" It | cannot be found at https://cran.r-project.org/doc/manuals/R-exts.html. https://rstudio.github.io/r-manuals/r-exts/The-R-API.html#moving-into-c-api-compliance That's the

Re: [Rd] R-devel on Windows temporarily broken?

To bring closure to this thread, everything is back to normal at both the CRAN machine that balked as well as at windows r-devel. Thanks, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://

Re: [Rd] R-devel on Windows temporarily broken?

On 13 June 2024 at 15:26, Martin Maechler wrote: | >>>>> Dirk Eddelbuettel | >>>>> on Thu, 13 Jun 2024 07:20:00 -0500 writes: | | > I had a very routine CI job fail twice this morning on r-devel on Windows; | > the package (in fine standard f

[Rd] R-devel on Windows temporarily broken?

I had a very routine CI job fail twice this morning on r-devel on Windows; the package (in fine standard form) doesn't even install under win-builder r-devel. Whereas on Linux with r86731 everything is peachy. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___

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 cas

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 a

Re: [Rd] read.csv

As an aside, the odd format does not seem to bother data.table::fread() which also happens to be my personally preferred workhorse for these tasks: > fname <- "/tmp/r/filename.csv" > read.csv(fname) Gene SNP prot log10p 1 YWHAE 13:62129097_C_T 1433 7.35 2 YWHAE 4:72617557_T_TA 1

Re: [Rd] read.csv

On 16 April 2024 at 10:46, jing hua zhao wrote: | Dear R-developers, | | I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, | | Gene,SNP,prot,log10p | YWH

Re: [Rd] RSS Feed of NEWS needs a hand

On 2 April 2024 at 09:41, Duncan Murdoch wrote: | On 02/04/2024 8:50 a.m., Dirk Eddelbuettel wrote: | > On 2 April 2024 at 07:37, Dirk Eddelbuettel wrote: | > blosxom, simple as it is, takes (IIRC) filesystem ctime as the posting | > timestamp so would be best if you had a backup wit

Re: [Rd] RSS Feed of NEWS needs a hand

On 2 April 2024 at 07:37, Dirk Eddelbuettel wrote: | | On 2 April 2024 at 08:21, Duncan Murdoch wrote: | | I have just added R-4-4-branch to the feeds. I think I've also fixed | | the \I issue, so today's news includes a long list of old changes. | | These feeds can fussy: look

Re: [Rd] RSS Feed of NEWS needs a hand

On 2 April 2024 at 08:21, Duncan Murdoch wrote: | I have just added R-4-4-branch to the feeds. I think I've also fixed | the \I issue, so today's news includes a long list of old changes. These feeds can fussy: looks like you triggered many updates. Feedly currently greets me with 569 new post

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

On 29 March 2024 at 17:56, Andrea Gilardi via R-devel wrote: | Dear all, | | I have a question regarding the R-devel version of .make_numeric_version() function. As far as I can understand, the current code (https://github.com/wch/r-source/blob/66b91578dfc85140968f07dd4e72d8cb8a54f4c6/src/libr

Re: [Rd] paths capability FALSE on devel?

On 27 March 2024 at 11:03, Prof Brian Ripley via R-devel wrote: | On 27/03/2024 10:28, Alexandre Courtiol wrote: | > Hi all, | > | > I don't know if it is a local issue on my hands or not, but after | > installing R-devel the output of grDevices::dev.capabilities()$paths is | > FALSE, while it i

[Rd] RSS Feed of NEWS needs a hand

Years ago Duncan set up a nightly job to feed RSS based off changes to NEWS, borrowing some setup parts from CRANberries as for example the RSS 'compiler'. That job is currently showing the new \I{...} curly protection in an unfavourable light. Copying from the RSS reader I had pointed at this s

Re: [Rd] Compiling libR as a standalone C library for java+jni (-fPIC)

Salut Pierre, On 20 February 2024 at 10:33, Pierre Lindenbaum wrote: | (cross-posted on SO: https://stackoverflow.com/questions/78022766) | | Hi all, | | I'm trying to compile R as a static library with the -fPIC flag so I can use it within java+JNI (is it only possible ?), but I cannot find

Re: [Rd] Tcl socket server (tcltk) does not work any more on R 4.3.2

On 20 February 2024 at 12:27, webmail.gandi.net wrote: | Dear list, | | It seems that something changed between R 4.2.3 and R 4.3 (tested with 4.3.2) that broke the Tcl socket server. Here is a reproducible example: | | - R process #1 (Tcl socket server): | | library(tcltk) | cmd <- r"( | pr

Re: [Rd] Advice debugging M1Mac check errors

On 4 February 2024 at 20:41, Holger Hoefling wrote: | I wanted to ask if people have good advice on how to debug M1Mac package | check errors when you don´t have a Mac? Is a cloud machine the best option | or is there something else? a) Use the 'mac builder' CRAN offers: https://mac.r-project

Re: [Rd] eval(parse()) within mutate() returning same value for all rows

On 29 December 2023 at 22:31, Mateo Obregón wrote: | Thanks Gabor, I like your solution that splits the args into separate columns, | in turn making the sprintf() call more interpretable . Well you may also like `tstrsplit()`, a gem inside data.table: > suppressMessages(library(data.table)) >

Re: [Rd] eval(parse()) within mutate() returning same value for all rows

On 29 December 2023 at 14:13, Mateo Obregón wrote: | Hi all- | | Looking through stackoverflow for R string combining examples, I found the | following from 3 years ago: | | | | The top a

Re: [Rd] Segmentation fault early in compilation of revision 85514

Avi, Might be toolchain-dependent, might be options-dependent--it built fine here. Easier for you to vary option two so maybe try that? Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://st

Re: [Rd] [R] Why Rprofile.site is not built with manual installation of R devel in linux?

On 10 November 2023 at 14:19, Martin Maechler wrote: | >> 2. In the installed R in /where/you/want/R/to/go, there is no even etc folder, there are only the folders bin, lib and share. That would appear to be an error in the locally installed R. What the package does has been discussed bef

Re: [Rd] Wayland Display Support in R Plot

On 30 October 2023 at 13:17, Willem Ligtenberg via R-devel wrote: | I just tried it on Ubuntu 23.10. It seems to just work. | See screenshot here: https://nextcloud.wligtenberg.nl/s/jnbDT4ZiHw2JQ8H | I should be using wayland, and as far as I know I haven't done anything | special to make this w

Re: [Rd] Wayland Display Support in R Plot

On 30 October 2023 at 09:20, Simon Urbanek wrote: | > On 30/10/2023, at 8:38 AM, Dirk Eddelbuettel wrote: | > On 30 October 2023 at 07:54, Paul Murrell wrote: | > | I am unaware of any Wayland display support. | > | | > | One useful way forward would be an R package that provide

Re: [Rd] Wayland Display Support in R Plot

On 30 October 2023 at 07:54, Paul Murrell wrote: | I am unaware of any Wayland display support. | | One useful way forward would be an R package that provides such a device | (along the lines of 'Cairo', 'tikzDevice', et al) As I understand it, it is a protocol, and not a device. Several Linu

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

Hi Hadley, On 8 August 2023 at 08:34, Hadley Wickham wrote: | Do you think it's worth also/instead considering a fix to S4 to avoid | this caching issue in future R versions? That is somewhat orthogonal to my point of "'some uses' of the 20 year old S4 system (which as we know is fairly widely

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

On 8 August 2023 at 13:17, Simon Urbanek wrote: | To be honest I think the motivation of this thread is dubious at best: it is a bad idea to use detectCore() blindly to specify parallelization and we explicitly say it's a bad idea - any sensible person will set it according to the demands, the

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

On 8 August 2023 at 11:21, Simon Urbanek wrote: | First, detecting HT vs cores is not necessarily possible in general, Linux may assign core id to each HT depending on circumstances: | | $ grep 'cpu cores' /proc/cpuinfo | uniq | cpu cores : 32 | $ grep 'model name' /proc/cpuinfo | uniq | mo

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

Hi Ivan, I usually 'mentally applaud' when reading your replies on list but not here. On 7 August 2023 at 16:15, Ivan Krylov wrote: | SeuratObject 4.1.3. The breakage definitely exists, but not on the | source package level. You seem to overlook that a large part of the R Universe only works o

Re: [Rd] Detecting physical CPUs in detectCores() on Linux platforms

On 7 August 2023 at 08:48, Nils Kehrein wrote: | I recently noticed that `detectCores()` ignores the `logical=FALSE` | argument on Linux platforms. This means that the function will always | return the number of logical CPUs, i.e. it will count the number of threads | that theoretically can run i

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

CRAN, by relying on the powerful package management system that is part of R, provides an unparalleled framework for extending R with nearly 20k packages. We recently encountered an issue that highlights a missing element in the otherwise outstanding package management system. So we would like t

Re: [Rd] Correct use of tools::R_user_dir() in packages?

On 27 June 2023 at 15:36, Carl Boettiger wrote: | tools::R_user_dir() provides configurable directories for R packages | to write persistent information consistent with standard best | practices relative to each supported operating systems for | applications to store data, config, and cache infor

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

Ben, POSIX level / glibc level variables are set at process start and AGAIK cannot really be altered after start. They clearly work when set _before_ calling sqrt(-1): $ LANGUAGE=es Rscript -e 'sqrt(-1)' [1] NaN Warning message: In sqrt(-1) : Se han producido NaNs $ LANGUA

Re: [Rd] Heap access across multiple calls from R to C++

On 24 May 2023 at 09:09, Ivan Krylov wrote: | On Wed, 24 May 2023 02:08:25 +0200 | wrote: | > Is there a better way to do this? | | The .Call() interface (where functions take an arbitrary number of | native R objects and return a native R object) combined with external | pointers is likely to

Re: [Rd] Let R compile for libcurl8 ?

On 3 April 2023 at 15:07, Detlef Steuer wrote: | The same Inar reported for rawhide | (https://stat.ethz.ch/pipermail/r-devel/2023-March/082482.html) | is true for SuSE's distros. | | Right now R does not compile with libcurl8, but SuSE Tumbleweed/Factory | switched to 8 a week ago. | | Would

Re: [Rd] Request: better default R_LIBS_USER

On 16 March 2023 at 17:15, Henrik Bengtsson wrote: | We're all starting out with a fresh R_LIBS_USER once a year when a new | minor version of R is released, Maybe not "we all". I don't, and I know other Linux users who don't force a rebuild unless needed (as with R 3.6.* -> R 4.0.0). R signals

Re: [Rd] Request: better default R_LIBS_USER

On 16 March 2023 at 13:39, Felipe Contreras wrote: | I see R by default installs packages in ~/R. I know I can change the | default directory with R_LIBS_USER, but software shouldn't be | polluting the home directory. | | For example both python and node install packages to ~/.local/lib, | ruby

Re: [Rd] Object are not destroy while using error (Rf_error)

Antoine, I think there are few things going on here. One is that actual _R_ objects may only get destroyed when gc() gets called. Which we applications writer do not control. Another thing that may have an effect is the use of .C() which we all more or less moved away from. Anyway, if we mak

Re: [Rd] Problem installing gdb into Rtools42

On 18 January 2023 at 22:44, Dominick Samperi wrote: | On second thought, there is a lot of metapramming code in Rcpp that runs | before main, so | I was wrong to say nothing can happen before main() is called. | Strategically placed print | statements may be the best strategy. Yes, and if you w

Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack

On 12 January 2023 at 08:54, RICHET Yann wrote: | Thank you, Dirk. | But I also tried with ccache, without fails... can you give some details about you reverse-depend configuration ? docker image ? Mine was a standard ubuntu 20.04 packages... Nothing special -- I just the standard functions in

Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack

On 11 January 2023 at 17:35, RICHET Yann wrote: | Thank you all, for these advices. | | So I try to fix OMP_THREADS, cleanup tests, and display explicitly what test is running by moving in tests/ instead of tests/testthat/... | Next step should be to investigate blocking test using a reporter (

Re: [Rd] F77_CALL(dgetrs) C++ call in R-devel

On 20 December 2022 at 12:33, Lars Relund wrote: | In my package, I have the method: | | /** Solve equations transpose(P)w = r. */ | int LASolveT(MatSimple &P, MatSimple &w, const | MatSimple &r) { | int rows = P.rows; | int nrhs = 1; | int lda = rows; | i

Re: [Rd] Repeated segfault at installing sysdata.rda with clang/san build

y it suddenly appeared - perhaps some changes in toolchain or glibc? Yep. And as I had on schedule for some time with no issues it likely is external. No obvious how to minimize it to a smaller reproducible example though. Best, Dirk | Cheers, | Simon | | | > On 19/12/2022, a

[Rd] Repeated segfault at installing sysdata.rda with clang/san build

I have maintained two SAN/UBSAN builds (one gcc, one clang) for many years (even though I also happily use Winston's newer/bigger container and generally recommend its use) and still have GitHub actions build them on a weekly schedule (as they follow r-devel). The clang one started to fail a lit

Re: [Rd] Rscript -e EXPR fails to launch if stdin is closed

On 10 October 2022 at 09:34, Henrik Bengtsson wrote: | Thank you Peter for the quick fix. Will this make it into R-patched | to become R 4.2.2 soon? I checked when you posted this and didn't reply -- but this is also not an issue for littler so if you need alternative there is one $ Rscript

Re: [Rd] Proposal to limit Internet access during package load

Regarding 'system' libraries: Packages like stringi and nloptr download the source of, respectively, libicu or libnlopt and build a library _if_ the library is not found locally. If we outlaw this, more users may hit a brick wall because they cannot install system libraries (for lack of permissi

Re: [Rd] Better 'undefined columns' error for data.frame

Andre, On 25 September 2022 at 18:09, GILLIBERT, Andre wrote: | Please, find the patch attached, based on the latest R SVN trunk code. Well the mailing list software tends to drop attachments. There is a reason all these emails suggest to use bugs.r-project.org. Dirk -- dirk.eddelbuettel.co

Re: [Rd] How to access to internal header files

On 24 May 2022 at 15:23, Martin Maechler wrote: | Well, if you want to explore how R is written ... and that's the | only good reason for looking into such private header files ... | then get the sources of R and explore... | | The official sources (and even daily snapshots from both | "R-patche

Re: [Rd] CRAN webserver down

On 23 May 2022 at 10:29, peter dalgaard wrote: | Apparently resurrected now. As another maintainer told me, the submission page appears to be down. Going to https://cran.r-project.org/submit.html (and then refreshing over the stale iframe) gets me The webpage at https://xmpalantir.wu.a

Re: [Rd] R-devel tarball at ETH is zero

On 4 May 2022 at 11:32, Martin Maechler wrote: | I'm really sorry for this experience. Stuff happens -- thanks for fixing it. The weekly build for the rocker/drd container of r-devel (and r-patched) worked fine now that you restored the mirror, so big thanks! Dirk -- dirk.eddelbuettel.com |

[Rd] R-devel tarball at ETH is zero

Dear Martin as our trusted ETH point person, I have some automated builders fall over as the tarball of R-devel is currently empty: edd@rob:/tmp$ wget https://stat.ethz.ch/R/daily/R-devel.tar.bz2 --2022-05-03 06:52:20-- https://stat.ethz.ch/R/daily/R-devel.tar.bz2 Resolving stat.ethz.ch (stat

[Rd] Status of '=>'

R 4.1.0 brought the native pipe and the related ability to use '=>' if one opted into it by setting _R_USE_PIPEBIND_. I often forget about '=>' and sadly can never find anything in the docs either (particularly no 'see als' from '|>' docs) which is not all that heplful. Can we anticipate a chang

Re: [Rd] string concatenation operator (revisited)

On 8 December 2021 at 00:06, Simon Urbanek wrote: | Hence it's much easier to ban a package than to hack it out of R ;). Paging Achim for suggested `fortunes` inclusion. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-d

Re: [Rd] * checking CRAN incoming feasibility ... NOTE

Hi Witold, On 26 November 2021 at 17:09, Witold E Wolski wrote: | We have been using the package at work since 2018. We made some | feature requests in 2019 to the maintainer and Author Amir B.K. | Foroushani and was so kind to | implement them for us and release a new version in 2019. But then

Re: [Rd] * checking CRAN incoming feasibility ... NOTE

On 26 November 2021 at 14:40, Witold E Wolski wrote: | I am submitting a package to CRAN and I am asked to fix 2 NOTE's | I am not sure how I should ask the following NOTE? | | | * this is package 'sigora' version '3.0.9' | * checking CRAN incoming feasibility ... NOTE | Maintainer: 'Witold Wol

Re: [Rd] How can a package be aware of whether it's on CRAN

On 23 November 2021 at 12:19, Hervé Pagès wrote: | But why would you need to check for anything in the first place? | | If you only use 2 cores in your examples, vignettes, and unit tests, 'R | CMD check' will run fine everywhere and not eat all the CPU power of the | machine where it's runnin

Re: [Rd] How can a package be aware of whether it's on CRAN

This may be more of a question for r-package-devel than for r-devel. On 23 November 2021 at 14:11, Dipterix Wang wrote: | I recently received an email from Prof. Ripley. He pointed out that my package seriously violates the CRAN policy: "using 8 threads is a serious violation of the CRAN polic

Re: [Rd] Environment setting _R_CHECK_DEPENDS_ONLY_='true'

On 20 October 2021 at 09:31, Sebastian Meyer wrote: | If you set the environment variable inside a running R process, it will | only affect that process and child processes, but not an independent R | process launched from a shell like you seem to be doing here: Yes. That is somewhat common, i

Re: [Rd] [External] Re: Update on rtools4 and ucrt support

As I type this, we are eight messages into this thread -- but I am not sure it has been made clear what the actual contentious issues are. There appear to be two toolchains, and they appear to be interoperate (though Duncan stated he had issues with an (arguably demanding) package). Now, I have

Re: [Rd] [External] svd For Large Matrix

Dario, On 14 August 2021 at 00:00, Dario Strbenac via R-devel wrote: | Good day, | | Ah, I was confident it wouldn't be environment-specific but it is. My environment is | | R version 4.1.0 (2021-05-18) | Platform: x86_64-pc-linux-gnu (64-bit) | Running under: Debian GNU/Linux 10 (buster) |

Re: [Rd] Rprofile.site function or variable definitions break with R 4.1

On 12 August 2021 at 15:19, Andrew Piskorski wrote: | Ok, but what's the recommended way to actually USE Rprofile.site now? | Should I move all my local configuration into a special package, and | do nothing in Rprofile.site except require() that package? Exactly as before. I set my mirror as I

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

On 24 July 2021 at 15:53, Steve Haroz wrote: | I'd like to propose moving the default library install location on Windows from: | %USERPROFILE%/Documents/R | to some other location such as: | %USERPROFILE%/R Can you not set .Library.site in R_HOME/etc/Rprofile.site (or maybe setting R_LIBS_SITE

Re: [Rd] R-Forge http link redirection setup busted

Hi Gennadiy, On 20 July 2021 at 10:25, Gennadiy Starostin wrote: | Thank you for your feedback. There was a misconfigured redirection | indeed. It should work well now. Fabulous, thanks as always. | The top page does say "If you experience any problems or need help you | can submit a suppor

[Rd] R-Forge http link redirection setup busted

(Sorry for posting here but the top-level r-forge page does not make it all that clear where to contact its admins.) When an old-style 'http' URL at r-forge is resolved / redirected to 'https', it is corrupted and the redirect breaks. That required a package re-upload for me a few days ago (as

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

Randall, On 20 May 2021 at 07:12, Ben Bolker wrote: | splines is 'recommended' ( not sure about capitalization), not "base' If you install 'r-base' rather than just the narrower 'r-base-core' you also get 'r-recommended'. So please do that, or just do sudo apt install r-recommended The gra

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

On 5 May 2021 at 05:42, Duncan Murdoch wrote: | I think it would be useful to issue some kind of warning if tests are | skipped. As mentioned earlier, this is impossible in user-contributed | packages, which can only return OK or ERROR from their tests. Seconded! Dirk -- https://dirk.eddel

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

On 4 May 2021 at 14:10, Gabriel Becker wrote: | A couple of things. Firstly, so far asI have ever heard, it's valid that a | package have hard dependencies in its tests for packages listed only in | Suggests. In fact, that is one of the stated purposes of Suggests. An | argument could be made, I

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

On 4 May 2021 at 11:25, Henrik Bengtsson wrote: | FWIW, | | $ ./configure --help | ... | --with-recommended-packages | use/install recommended R packages [yes] Of course. But look at the verb in your Subject: no optionality _in testing_ there. You obviously need to

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

On 4 May 2021 at 11:07, Henrik Bengtsson wrote: | Thanks, but I don't understand. That's what I usually do when I build | R with 'recommended' packages. But here, I explicitly do *not* want | to build and install 'recommended' packages with the R installation. | So, I'm going down the --without-

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

On 4 May 2021 at 09:31, Henrik Bengtsson wrote: | I'm on Linux (Ubuntu 18.04). How do I check an R build when using | --without-recommended-packages? 'make check' assumes 'recommended' | packages are installed, so that fails without them available. [...] | BTW, isn't this a bug? Shouldn't this

Re: [Rd] [External] memory consumption of nested (un)serialize of sys.frames()

On 7 April 2021 at 16:06, Andreas Kersting wrote: | Hi Luke, | | Please see https://github.com/akersting/dumpTest for the package. | | Here a session showing my issue: | | > library(dumpTest) | > sessionInfo() | R version 4.0.5 (2021-03-31) | Platform: x86_64-pc-linux-gnu (64-bit) | Running un

Re: [Rd] R extension memory leak detection question

On 5 April 2021 at 18:27, xiaoyan yu wrote: | Thank you all for your help. | We embedded R in our program and found the memory in the process | accumulated while our expectation is that the memory will go down after | each R evaluation. | I started to write a test program with only a few lines of

Re: [Rd] custom allocators, Valgrind and uninitialized memory

Andreas, Thanks for the clarification. On 26 March 2021 at 20:48, Andreas Kersting wrote: | Sure, let me try to explain: | | CRAN ran the tests of my package using R which was configured --with-valgrind-instrumentation > 0. Valgrind reported many errors related to the use of supposedly unini

Re: [Rd] custom allocators, Valgrind and uninitialized memory

Andreas, Can you briefly describe what it is you are trying to do? In general, no R package would use valgrind directly; it is an optional debugger. Also note _Writing R Extensions_ has a few things to say about how memory destined for R object can and cannot be allocated -- I presume your cust

Re: [Rd] [Solved] Possible x11 window manager window aggregation under one icon?

On 24 March 2021 at 10:30, Martin Maechler wrote: | For this reason I've committed to R (the trunk, i.e., R-devel, | for R 4.1.0 in a month or so) in svn rev 80110. I just saw that via the (still extremely helpful) RSS feed of SVN changes and then pulled. You may have missed that Ivan conclude

Re: [Rd] [Solved] Possible x11 window manager window aggregation under one icon?

-base (4.0.4-1.2010.3) groovy; urgency=medium * debian/r-base-core.dirs: Also create the directory usr/share/icons/hicolor/scalable/apps for the svg logo -- Dirk Eddelbuettel Tue, 23 Mar 2021 11:05:17 -0500 r-base (4.0.4-1.2010.2) groovy; urgency=medium * icon-class-patch/R.desktop: Add

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 09:38, Dirk Eddelbuettel wrote: | | On 23 March 2021 at 17:13, Ivan Krylov wrote: | | В Tue, 23 Mar 2021 08:58:49 -0500 | | Dirk Eddelbuettel пишет: | | | | > I still ship /usr/share/icons/hicolor/48x48/apps/rlogo_icon.png which | | > is from the 2012 patch, and I v

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 17:13, Ivan Krylov wrote: | В Tue, 23 Mar 2021 08:58:49 -0500 | Dirk Eddelbuettel пишет: | | > I still ship /usr/share/icons/hicolor/48x48/apps/rlogo_icon.png which | > is from the 2012 patch, and I vaguely recall the .desktop file being | > unhappy without it. Re

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 08:15, Dirk Eddelbuettel wrote: | Only one small downside: the regrouped icon switches to the old R icon (which | is probably the one we bitmapped). Would you know how we could force the new | one? Could well be my fault. =:-) I still ship /usr/share/icons/hicolor/48x48

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 07:44, Dirk Eddelbuettel wrote: | On 23 March 2021 at 13:18, Ivan Krylov wrote: | | Apparently Xfce uses libwnck [*] which groups windows by WM_CLASS in | | addition to WM_HINTS (as far as understand the code). | | | | Here is what GNOME Shell does [**] besides looking at

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 13:18, Ivan Krylov wrote: | On Mon, 22 Mar 2021 16:57:48 -0500 | Dirk Eddelbuettel wrote: | | > Do you want to send a proper patch to bugzilla? | | Would be glad to, especially if we manage to solve that problem you | uncovered while I was asleep. | | On Mon, 22 Mar 2

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 22 March 2021 at 16:57, Dirk Eddelbuettel wrote: | | On 23 March 2021 at 00:01, Ivan Krylov wrote: | | The surrounding code and | | <https://tronche.com/gui/x/xlib/ICC/client-to-window-manager/wm-hints.html> | | proved to be enough of an example. The following patch makes it | | possi

Re: [Rd] Possible x11 window manager window aggregation under one icon?

On 23 March 2021 at 00:01, Ivan Krylov wrote: | The surrounding code and | | proved to be enough of an example. The following patch makes it | possible to group x11() windows on my PC with Xfce running: [...] | Some ver

Re: [Rd] Possible x11 window manager window aggregation under one icon?

(Group reply to three emails at once) On 22 March 2021 at 10:27, Balasubramanian Narasimhan wrote: | Confession: haven't done this in decades. Equally green here. | Isn't the usual way to use 'xwininfo' to figure out the information | about any X window and set a specific resource in the .X1

[Rd] Possible x11 window manager window aggregation under one icon?

[ I hope the Subject: is arcane enough to reduce readership to a handful :) ] Running the default window manager in the Linux distribution I am running, multiple 'windows' of the same program are usually aggregated under one icon. I typically have numerous (gnome) terminals, several top-level em

Re: [Rd] boneheaded BLAS questions

On 18 March 2021 at 09:15, Tomas Kalibera wrote: | This is documented in R Admin manual, section A.3, and there is also | "configure --help". | | On my Ubuntu 20.04, using "--with-blas --with-lapack" when a BLAS/LAPACK | implementation is installed via "apt" works for me: | | with libblas3, l

Re: [Rd] boneheaded BLAS questions

On 17 March 2021 at 22:53, Ben Bolker wrote: |Thanks. I know it's supposed to Just Work (and I definitely | appreciate all the work that's gone into making it Just Work 99% of the | time!). And for what it is worth, the aforementioned 'switching from within' solution is using FlexiBLAS (n

Re: [Rd] boneheaded BLAS questions

Ben, This stuff has worked unchanged since the 1990s when we had a _really_ far sighted fellow in Debian come up with the 'switch the links' scheme which was (and is) subsequently deployed by many numerical applications within Debian, R and e.g. Octave included. And I used this ability to switc

Re: [Rd] Potential improvements of ave?

On 16 March 2021 at 10:50, Martin Maechler wrote: | I vaguely remember (from Luke's docs/presentation on ALTREP) | that there are some "missing parts" here. | One of them the not-existing R level functionality, another may be | the C code below R's is.unsorted() ... maybe is.unsorted() | could

[Rd] r-devel windows gcc10-UCRT machine questions

I saw two (unchanged, long-existing) tests of main fail narrowly on this new platform (relative to the tolerance argument set). Attempting to change the tolerance if .Platform$OS.type == "windows" failed (any idea why that test would evaluate to FALSE?). Could it be that capabilities("long.doub

Re: [Rd] Inconsistency of c.Date: non-commutativity and non-integer Value

On 22 January 2021 at 21:35, Jens Heumann wrote: | Dear r-devel, | | Today I came across what I would call inconsistencies in the `c.Date` | method compared to what happens when concatenating other classes: 1. | Non-commutativity: The type in the arrangements of the elements does | matter (fi

Re: [Rd] [External] brief update on the pipe operator in R-devel

On 12 January 2021 at 20:38, Iñaki Ucar wrote: | On Tue, 12 Jan 2021 at 20:23, wrote: | > | > After some discussions we've settled on a syntax of the form | > | > mtcars |> subset(cyl == 4) |> d => lm(mpg ~ disp, data = d) | > | > to handle cases where the pipe lhs needs to be passed to an

Re: [Rd] URL checks

The idea of 'white lists' to prevent known (and 'tolerated') issues, note, warnings, ... from needlessly reappearing is very powerful and general, and can go much further than just URL checks. I suggested several times in the past that we can look at the format Debian uses in its 'lintian' packa

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

On 12 December 2020 at 21:26, luke-tier...@uiowa.edu wrote: | If R is receiving a kill signal there is nothing it can do about it. | | I am guessing you are running into a memory over-commit issue in your OS. | https://en.wikipedia.org/wiki/Memory_overcommitment | https://engineering.pivotal.io

Re: [Rd] Ignore Sites Option For libPaths

On 9 December 2020 at 09:49, Martin Maechler wrote: | Also, R allows the user to remove their own home directory, it | should also allow to get a .libPaths() which contains nothing compulsory | but R's own .Library {as only that can contain 'base' !} That would be a very nice-to-have feature! Bu

Re: [Rd] Ignore Sites Option For libPaths

On 9 December 2020 at 02:00, Dario Strbenac wrote: | That seems like a straightforward and reasonable thing to do, but: | | ~$ R_LIBS="/tmp" R_LIBS_SITE="/var" Rscript -e 'print(.libPaths())' | [1] "/dora/nobackup/biostat/Rpackages/v4" "/dora/users/course/splus/library/R" | [3] "/usr/lib/R/sit

Re: [Rd] Ignore Sites Option For libPaths

On 8 December 2020 at 23:00, Dario Strbenac wrote: | Could .libPaths gain an option to ignore all values other than the user-specified new parameter? Currently, it takes the union of new and .Library and .Library.site and there is no way to turn it off. Are you use? It is constructed from loo

Re: [Rd] Two ALTREP questions

On 21 November 2020 at 20:56, Jiefei Wang wrote: | Hello, | | I have two related ALTREP questions. It seems like there is no way to | assign attributes to an ALTREP vector without using C++ code. To be more | specifically, I want to make an ALTREP matrix, I have tried the following R | code but

Re: [Rd] formatting issue with gcc 9.3.0 on Ubuntu on WSL2

On 17 November 2020 at 12:34, Bill Dunlap wrote: | I just got a new Windows laptop (i7, 10th generation CPU), installed | 'Windows Subsystem for Linux 2' and then installed Ubuntu 20.04 and | used 'apt-get install' to install packages that the R build seems | to require. In particular, I am usin

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

The closest to a canonical reference for a static vignette is the basic blog post by Mark at https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ which I follow in a number of packages. Back to the original point by Alexandre: No, I do _not_ think we can do

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