Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

Kurt, Could you do me a favour and run on that clang18-using machine in question the following one-liner (provided your session has access to a .libPaths() including Rcpp) and, in the case of success, the resulting function? > Rcpp::cppFunction("int ompconfigtest() { return

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

On 23 May 2024 at 20:02, Ivan Krylov wrote: | On Wed, 22 May 2024 09:18:13 -0500 | Dirk Eddelbuettel wrote: | | > Testing via 'nm' as you show is possible but not exactly 'portable'. | > So any suggestions as to what to condition on here? | | (My apologies if you already got an answe

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

On 22 May 2024 at 14:03, Duncan Murdoch wrote: | On 2024-05-22 10:18 a.m., Dirk Eddelbuettel wrote: | > | > On 22 May 2024 at 13:54, Nixon, Michelle Pistner wrote: | > | Thank you both for your responses and help! Kurt-- your message makes a lot of | > | sense. I'll try t

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

the Right Thing (TM) by 'borrowing' from the fairly mature check in RcppArmadillo. Dirk | | Thanks, | Michelle | ━━━ | From: Kurt Hornik | Sent: Wednesday, May 22, 2024 3:57 AM | To: Dirk Eddelbuettel | Cc: Nixon, Michelle

Re: [R-pkg-devel] handling documentation build tools

As lyx is not listed in 'Writing R Extensions', the one (authorative) manual describing how to build packages for R, I would not assume it to be present on every CRAN machine building packages. Also note that several user recently had to ask here how to deal with less common fonts for style

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

Hi Michelle, On 21 May 2024 at 13:46, Nixon, Michelle Pistner wrote: | Hi all, | | I'm running into build issues for my package (fido: https://github.com/jsilve24/fido) on the r-devel-linux-x86_64-debian-clang system on CRAN (full check log here:

Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

On 16 May 2024 at 05:34, Duncan Murdoch wrote: | I forget now, but presumably the thinking at the time was that Suggested | packages would always be available for building and checking vignettes. Yes. I argued for years (cf https://dirk.eddelbuettel.com/blog/2017/03/22/ from seven (!!) years

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

Software Heritage (see [1] for their website and [2] for a brief intro I gave at useR! 2019 in Toulouse) covers GitHub and CRAN [3]. It is by now 'in collaboration with UNESCO', supported by a long and posh list of sponsors [4] and about as good as it gets to 'ensure longevity of artifacts'. It

Re: [R-pkg-devel] Fast Matrix Serialization in R?

On 9 May 2024 at 03:20, Sameh Abdulah wrote: | I need to serialize and save a 20K x 20K matrix as a binary file. Hm that is an incomplete specification: _what_ do you want to do with it? Read it back in R? Share it with other languages (like Python) ? I.e. what really is your use case? Also,

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

On 8 May 2024 at 11:02, Josiah Parry wrote: | CRAN has rejected this package with: | | * Size of tarball: 18099770 bytes* | | *Please reudce to less than 5 MB for a CRAN package.* Are you by chance confusing a NOTE (issued, but can be overruled) with a WARNING (more severe, likely a

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: [R-pkg-devel] Problem with loading package "devtools" from CRAN.

On 30 April 2024 at 01:21, Rolf Turner wrote: | On Mon, 29 Apr 2024 06:30:20 -0500 | Dirk Eddelbuettel wrote: | | | | > These days, I strongly recommend r2u [1]. As you already use R via | > CRAN through apt, r2u adds one more repository after which _all_ R | > packages are ha

Re: [R-pkg-devel] Problem with loading package "devtools" from CRAN.

Rolf, This question might have been more appropriate for r-sig-debian than here. But as Simon noted, the lack of detail makes is difficult to say anything to aid. It likely was an issue local to your setup and use. These days, I strongly recommend r2u [1]. As you already use R via CRAN

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] 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

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 |

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: looks like you

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

Re: [R-pkg-devel] Order of repo access from options("repos")

On 1 April 2024 at 17:44, Uwe Ligges wrote: | Untested: | | install.packages() calls available.packages() to find out which packages | are available - and passes a "filters" argument if supplied. | That can be a user defined filter. It should be possible to write a user | defined filter which

Re: [R-pkg-devel] Order of repo access from options("repos")

On 31 March 2024 at 11:43, Martin Morgan wrote: | So all repositories are consulted and then the result filtered to contain just | the most recent version of each. Does it matter then what order the | repositories are visited? Right. I fall for that too often, as I did here. The order matters

Re: [R-pkg-devel] Order of repo access from options("repos")

Greg, There are AFAICT two issues here: how R unrolls the named vector that is the 'repos' element in the list 'options', and how your computer resolves DNS for localhost vs 172.17.0.1. I would try something like options(repos = c(CRAN = "http://localhost:3001/proxy;,

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

Re: [R-pkg-devel] using portable simd instructions

: https://github.com/google/highway docs: https://google.github.io/highway/en/master/ | | Op di 26 mrt 2024 om 15:41 schreef Dirk Eddelbuettel : | > | > | > On 26 March 2024 at 10:53, jesse koops wrote: | > | How can I make this portable and CRAN-acceptable? | > | > But wri

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

Re: [R-pkg-devel] Check results on r-devel-windows claiming error but tests seem to pass?

On 26 March 2024 at 09:37, Dirk Eddelbuettel wrote: | | Avi, | | That was a hickup and is now taken care of. When discussing this (off-line) | with Jeroen we (rightly) suggested that keeping an eye on Typo, as usual, "he (rightly) suggested". My bad. D. | |https://con

Re: [R-pkg-devel] using portable simd instructions

On 26 March 2024 at 10:53, jesse koops wrote: | How can I make this portable and CRAN-acceptable? But writing (or borrowing ?) some hardware detection via either configure / autoconf or cmake. This is no different than other tasks decided at install-time. Start with 'Writing R Extensions', as

Re: [R-pkg-devel] Check results on r-devel-windows claiming error but tests seem to pass?

Avi, That was a hickup and is now taken care of. When discussing this (off-line) with Jeroen we (rightly) suggested that keeping an eye on https://contributor.r-project.org/svn-dashboard/ is one possibility to keep track while we have no status alert system from CRAN. I too was quite

Re: [R-pkg-devel] How to store large data to be used in an R package?

On 25 March 2024 at 11:12, Jairo Hidalgo Migueles wrote: | I'm reaching out to seek some guidance regarding the storage of relatively | large data, ranging from 10-40 MB, intended for use within an R package. | Specifically, this data consists of regression and random forest models | crucial for

Re: [R-pkg-devel] Request for assistance: error in installing on Debian (undefined symbol: omp_get_num_procs) and note in checking the HTML versions (no command 'tidy' found, package 'V8' unavailable

Salut Annaig, On 21 March 2024 at 09:26, Annaig De-Walsche wrote: | Dear R-package-devel Community, | | I hope this email finds you well. I am reaching out to seek assistance regarding package development in R. | | Specifically, I am currently developing an R package for querying composite

Re: [R-pkg-devel] new maintainer for CRAN package XML

Dear Uwe, Did CRAN ever reach a decision here with a suitable volunteer (or group of volunteers) ? The state of XML came up again recently on mastodon, and it might be helpful to share an update if there is one. Thanks, as always, for all you and the rest of the team do for CRAN. Cheers,

[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

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 15:12, Duncan Murdoch wrote: | On 05/03/2024 2:26 p.m., Dirk Eddelbuettel wrote: | > The default behaviour is to build after every commit to the main branch. But | > there are options. On the repo I mentioned we use | > | > "branch": "*rele

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 13:28, Duncan Murdoch wrote: | What I'm seeing is that the tags are ignored, and it is distributing the | HEAD of the main branch. I don't think most users should be using that | version: in my packages it won't have had full reverse dependency | checks, I only do that

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 11:56, Duncan Murdoch wrote: | I have mixed feelings about r-universe. On the one hand, it is really | nicely put together, and it offers the service described above. On the | other, it's probably a bad idea to follow its advice and use | install.packages() with `repos`

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 06:25, Duncan Murdoch wrote: | You could make a compatible version of `survivalmodels` available on a | non-CRAN website, and refer to that website in the | Additional_repositories field of DESCRIPTION. Every r-universe sub-site fits that requirement. For this package

Re: [R-pkg-devel] Unable to access log operator in C

On 28 February 2024 at 19:05, Avraham Adler wrote: | I am hoping the solution to this question is simple, but I have not | been able to find one. I am building a routine in C to be called from | R. I am including Rmath.h. However, when I have a call to "log", I get | the error "called object

Re: [R-pkg-devel] Package required but not available: ‘arrow’

On 26 February 2024 at 09:19, Simon Urbanek wrote: | [requiring increased is] best way [..] and certainly the only good practice. No, not really. Another viewpoint, which is implemented in another project I contribute to, is where a version + build_revision tuple exists if, and only if, the

Re: [R-pkg-devel] Package required but not available: ‘arrow’

On 23 February 2024 at 15:53, Leo Mada wrote: | Dear Dirk & R-Members, | | It seems that the version number is not incremented: | # Archived | arrow_14.0.2.1.tar.gz   2024-02-08 11:57  3.9M | # Pending | arrow_14.0.2.1.tar.gz   2024-02-08 18:24  3.9M | | Maybe this is the reason why it got

Re: [R-pkg-devel] Package required but not available:‘arrow’

On 22 February 2024 at 04:01, Duncan Murdoch wrote: | For you to deal with this, you should make arrow into a suggested | package, For what it is worth, that is exactly what package tiledb does. Yet the Suggests: still lead to a NOTE requiring a human to override which did not happen until I

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"( |

Re: [R-pkg-devel] CRAN uses an old version of clang

On 9 February 2024 at 08:59, Marcin Jurek wrote: | I recently submitted an update to my package. It previous version relied on | Boost for Bessel and gamma functions but a colleague pointed out to me that | they are included in the standard library beginning with the C++17 | standard. There is

Re: [R-pkg-devel] failing CRAN checks due to problems with dependencies

On 8 February 2024 at 13:28, Marcin Jurek wrote: | Ok, this makes sense! I saw that Rcpp was failing the checks too but I | wasn't sure if I should resubmit or wait. Thanks! For completeness, it was not caused by Rcpp but rather by a mix on new clang and gcc versions which somehow got into each

Re: [R-pkg-devel] r-oldrel-linux- not in CRAN checks?

On 7 February 2024 at 09:15, Vincent van Hees wrote: | Thanks Ivan, In that case I will conclude that it is time to upgrade my | Ubuntu 18 machine. I just wasn't sure whether there is still a need for | keeping my own package Ubuntu 18 compatible, but if dependencies like Rfast | do not do it

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:

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

Ivan, On 30 January 2024 at 18:56, Ivan Krylov via R-package-devel wrote: | Hello R-package-devel, | | What would you recommend in order to run reverse dependency checks for | a package with 182 direct strong dependencies from CRAN and 66 from | Bioconductor (plus 3 more from annotations and

Re: [R-pkg-devel] lost braces note on CRAN pretest related to \itemize

On 23 January 2024 at 19:39, Patrick Giraudoux wrote: | Has anyone an idea about what is going wrong ? \item has no braces following it. From a package I submitted today and for which I still have NEWS.Rd in the editor (indented here): \section{Changes in version 0.0.22 (2024-01-23)}{

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

Johann, On 20 January 2024 at 14:38, Johann Gaebler wrote: | Hi everyone, | | I received the following message regarding `rar` , a package that I put up on CRAN two days ago: | | > Dear maintainer, | > | > Please see the problems shown on | >

Re: [R-pkg-devel] current docker image for ASAN

On 16 January 2024 at 15:54, Steven Scott wrote: | Greetings everyone, though I expect this message is mainly for Dirk. | | CRAN checks of my bsts/Boom package generate an ASAN error that the CRAN | maintainers have asked me to look into. I recall doing this before (this | error has been there

Re: [R-pkg-devel] checking CRAN incoming feasibility

On 17 January 2024 at 09:42, Simon Urbanek wrote: | that check always hangs for me (I don't think it likes NZ ;)), so I just use | | _R_CHECK_CRAN_INCOMING_REMOTE_=0 R CMD check --as-cran ... You can also set it in Renviron files consulted just for checks: $ grep INCOMING_=

Re: [R-pkg-devel] test failure: oldrel

done 4.3.2 2024-01-16 America/Chicago 4.2.2 2024-01-15 18:00:00 America/Chicago edd@rob:~$ Thanks to Seb for the cluebat wave. Dirk | | | On Tue, Jan 16, 2024 at 9:59 AM Dirk Eddelbuettel wrote: | | | Doesn't seem to be the case as it moderately easy to check (especially when | y

[R-pkg-devel] test failure: oldrel

Doesn't seem to be the case as it moderately easy to check (especially when you happen to have local images of r-base around anyway): edd@rob:~$ for v in 4.3.2 4.2.2 4.1.3 4.0.5 3.6.3 3.5.3 3.4.4 3.3.3; do echo -n "R ${v}: "; docker run --rm -ti r-base:${v} Rscript -e 'as.POSIXct(Sys.Date(),

Re: [R-pkg-devel] Suggests with non-CRAN packages

On 10 January 2024 at 16:25, Uwe Ligges wrote: | | | On 10.01.2024 15:35, Josiah Parry wrote: | > Thanks, all. As it goes, the package submission failed. The package that | > is suggested is available at https://r.esri.com/bin/ | > and as such provided

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

Re: [R-pkg-devel] portability question

The point of my email was that if [ `uname -s` = 'Darwin' ]; then ... allows for a clean branch between the (new here) macOS behaviour and (old, prior) behavior removing all concerns about 'portability' (per the Subject:). You missed 100% of that. Dirk -- dirk.eddelbuettel.com |

Re: [R-pkg-devel] portability question

On 20 December 2023 at 11:10, Steven Scott wrote: | The Boom package builds a library against which other packages link. The | library is built using the Makevars mechanism using the line | | ${AR} rc $@ $^ | | A user has asked me to change 'rc' to 'rcs' so that 'ranlib' will be run on | the

Re: [R-pkg-devel] CRAN submission struggle

Emailing 10mb blobs to every list subscriber is not ideal. Dirk PS Fortunes has that covered too > fortunes::fortune("mind read") There are actual error messages, and until you show them, we can not help as the mind reading machine is currently off for repairs. -- D

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

On 13 December 2023 at 16:02, Tomas Kalibera wrote: | | On 12/13/23 15:59, Dirk Eddelbuettel wrote: | > On 13 December 2023 at 15:32, Tomas Kalibera wrote: | > | Please don't forget about what has been correctly mentioned on this | > | thread already: there is essentially a 260 charac

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

On 13 December 2023 at 15:32, Tomas Kalibera wrote: | Please don't forget about what has been correctly mentioned on this | thread already: there is essentially a 260 character limit on Windows | (see | https://blog.r-project.org/2023/03/07/path-length-limit-on-windows/index.html | for

Re: [R-pkg-devel] Status of -mmacosx-version-min

PS One aspect I didn't mention clearly (my bad) that this does not affect all or even most packages: in most cases the src/Makevars should indeed be as simple as possible. But in _some_ cases we need to cooperate with external libraries and in some of these cases the switch has been seen to be

Re: [R-pkg-devel] Status of -mmacosx-version-min

On 10 December 2023 at 17:07, Simon Urbanek wrote: | As discussed here before packages should *never* set -mmacosx-version-min | or similar flags by hand. a) That is in conflict with what was said in the past; we have used an explicit min version of 10.14 for the C++17 we were using then (and

[R-pkg-devel] Status of -mmacosx-version-min

Last month, I had asked about the setting '-mmacosx-version-min' here. The setting can be used to specify what macOS version one builds for. It is, oddly enough, not mentioned in Writing R Extension but for both r-release and r-devel the R Administration manual states • Current CRAN macOS

Re: [R-pkg-devel] problems with Maintainers in DESCRIPTION file

On 7 December 2023 at 20:58, María Olga Viedma Sillero wrote: | I receive the same note after fixing it, removing it, and checking Authors@R. I think the rejection is a false positive. | | Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64 | Check: CRAN incoming feasibility,

Re: [R-pkg-devel] macos x86 oldrel backups?

Hi Simon, On 5 December 2023 at 23:17, Simon Urbanek wrote: | The high-sierra build packages are currently not built due to hardware issues. The macOS version is so long out of support by Apple (over 6 years) that it is hard to maintain it. Only big-sur builds are supported at this point.

Re: [R-pkg-devel] URL woes at CRAN: Anaconda edition

Thank you all -- expecially Aron and Ivan for the deep dive on the underlying aspect of the hosting of that web property. And of course to Uwe for approving the package manually. For my taste, life is too short for all this. So users be damned, and I have now removed the badge. At the end of

[R-pkg-devel] URL woes at CRAN: Anaconda edition

I added a badge to point to Conda builds for the work repo: [](https://anaconda.org/conda-forge/r-tiledb) And as it goes with all good intentions I immediately got punished on the next upload: Found the following

Re: [R-pkg-devel] Can -mmacosx-version-min be raised to 10.15 ?

Simon, One more thing: An alert reader pointed out to me that macOS-oldrel has r-oldrel-macos-x86_64 r-oldrelmacOS x86_64 macOS 10.13.6 (17G11023) in the table at https://cran.r-project.org/web/checks/check_flavors.html. So this seems to mesh with what the R-on-macOS FAQ says,

Re: [R-pkg-devel] Can -mmacosx-version-min be raised to 10.15 ?

Simon, On 17 November 2023 at 10:43, Simon Urbanek wrote: | > On 17/11/2023, at 10:28 AM, Dirk Eddelbuettel wrote: | > On 17 November 2023 at 09:35, Simon Urbanek wrote: | > | can you clarify where the flags come from? The current CRAN builds (big-sur-x86_64 and big-sur-a

Re: [R-pkg-devel] Can -mmacosx-version-min be raised to 10.15 ?

someone may want to refresh this. It is what I consulted as relevant info. Thanks, Dirk | | Cheers, | Simon | | | | > On 17/11/2023, at 2:57 AM, Dirk Eddelbuettel wrote: | > | > | > Hi Simon, | > | > We use C++20 'inside' our library and C++17 in the API. Part of our C++

[R-pkg-devel] Can -mmacosx-version-min be raised to 10.15 ?

Hi Simon, We use C++20 'inside' our library and C++17 in the API. Part of our C++17 use is now expanding to std::filesystem whose availability is dependent on the implementation. The compiler tells us (in a compilation using -mmacosx-version-min=10.14) that the features we want are only

Re: [R-pkg-devel] Package submission fail

On 13 November 2023 at 16:46, Ivan Krylov wrote: | Hello Christiaan and welcome to R-package-devel! Seconded but PLEASE do not send large attachments to the list and all its subscriber. Point us to your code repository, you will like get a kind response from a volunteer or two peeking at it.

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

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

[R-pkg-devel] Fortune candidate Re: Issue with R Package on CRAN - OpenMP and clang17

On 31 October 2023 at 19:58, Ivan Krylov wrote: | [...] The computers that helped launch the first | people into space had 2 kWords of memory, but nowadays you need more | than 256 MBytes of RAM to launch a bird into a pig and 10 GBytes of | storage in order to compile a compiler. This is what

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

I have some better news. While we established that 'in theory' setting the environment variable OMP_NUM_THREADS would help (and I maintain that it is a great PITA that CRAN does not do so as a general fix for this issue) it does *not help* once R is started. OpenMP only considers the variable

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

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

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

Hi Jouni, On 27 October 2023 at 13:02, Helske, Jouni wrote: | Actually, the OMP_NUM_THREADS worked for vignettes and testthat tests, but | didn't help with the examples. However, I just wrapped the problematic example Now I am confused. What is your understanding of why it helps in one place

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

Jouni, My CRANberriesFeed reports a new bssm package at CRAN, congratulations for sorting this out. [1,2] The OMP_NUM_THREADS setting is indeed all it takes, and it _does_ seem to be read even from a running session: i.e. you can set this inside an R session and the OpenMP code considers it in

Re: [R-pkg-devel] API client package failing due to API authentication

On 26 October 2023 at 11:14, Cole Johanson wrote: | My package https://github.com/cole-johanson/smartsheetr requires an | environment variable, the API access token, to run most of the functions. | The steps for setting this are documented in the README, but my package is | being auto-rejected

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

On 24 October 2023 at 08:15, Dirk Eddelbuettel wrote: | | On 24 October 2023 at 15:55, Ivan Krylov wrote: | | В Tue, 24 Oct 2023 10:37:48 + | | "Helske, Jouni" пишет: | | | | > Examples with CPU time > 2.5 times elapsed time | | > user system elapsed ratio |

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

On 24 October 2023 at 15:55, Ivan Krylov wrote: | В Tue, 24 Oct 2023 10:37:48 + | "Helske, Jouni" пишет: | | > Examples with CPU time > 2.5 times elapsed time | > user system elapsed ratio | > exchange 1.196 0.04 0.159 7.774 | | I've downloaded the archived copy of the

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

On 19 October 2023 at 05:57, Helske, Jouni wrote: | I am having difficulties in getting the latest version of the bssm (https://github.com/helske/bssm) package to CRAN, as the pretest issues a NOTE that the package uses too many cores in some of the examples ("Examples with CPU time > 2.5

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

else, specifically using R.rsp. | > | > Best, | > John | > | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: | >> Caution: External email. | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: | >> | Produce a PDF file yourself, then use the "as.is" feat

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

is not accessible. Loading a precomputed set is similar. I may be doing that in the much older never quite finished gcbd package and its vignette. Hope this helps, maybe more once I am back home. Cheers, Dirk | Best, | John | | On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: | > Caution: Exter

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

On 16 October 2023 at 10:42, Kevin R Coombes wrote: | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | package. For completeness, that approach also works directly with Sweave. Described in a blog post by Mark van der Loo in 2019, and used in a number of packages

[R-pkg-devel] Cadence of macOS builds at CRAN

Simon, A new package of mine [1] appeared on CRAN on Sep 5. Respecting the one week gap, I made a small update on Sep 12. Today is Sep 14. There are still no builds for macOS r-release (arm64) macOS r-oldrel (arm64) macOS r-release (x86_64) but we do have two oldrel releases. Weirder

Re: [R-pkg-devel] What to do when a package is archived from CRAN

On 31 August 2023 at 07:32, SHIMA Tatsuya wrote: | I submitted prqlr 0.5.1 yesterday, which is almost identical to prqlr | 0.5.0, and prqlr is now available again on CRAN. | Thanks to the CRAN reviewers for their quick reaction. And it is gone again (per CRANberries). Never a dull moment with

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

On 25 August 2023 at 18:48, Jeff Newmiller wrote: | You have a really bizarre way of twisting what others are saying, Dirk. I have seen no-one here saying 'limit R to 2 threads' except for you, as a way to paint opposing views to be absurd. That's too cute. Nobody needs to repeat it, and

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

On 26 August 2023 at 12:05, Simon Urbanek wrote: | In reality it's more people running R on their laptops vs the rest of the world. My point was that we also have 'single user on really Yuge workstation'. Plus we all know that those users are often not sysadmins, and do not have our levels

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

On 25 August 2023 at 18:45, Duncan Murdoch wrote: | The real problem is that there are two stubborn groups opposing each | other: the data.table developers and the CRAN maintainers. The former | think users should by default dedicate their whole machine to | data.table. The latter think

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

On 25 August 2023 at 15:37, Uwe Ligges wrote: | | | On 23.08.2023 16:00, Scott Ritchie wrote: | > Hi Uwe, | > | > I agree and have also been burnt myself by programs occupying the | > maximum number of cores available. | > | > My understanding is that in the absence of explicit

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

On 24 August 2023 at 07:42, Fred Viole wrote: | Hi, I am receiving a NOTE upon submission regarding the re-building of | vignettes for CPU time for the Debian check. | | I am unable to find any documented instances or solutions to this issue. | The vignettes currently build in 1m 54.3s locally

Re: [R-pkg-devel] Setting valgrind options when running R CMD check --use-valgrind

On 23 August 2023 at 16:49, Duncan Murdoch wrote: | On 23/08/2023 2:54 p.m., Dirk Eddelbuettel wrote: | > | > When I invoke valgrind via | > R -d valgrind -e '...' | > the options in the file ~/.valgrindrc are being picked up. Good. | > | > When I invok valgrind via |

[R-pkg-devel] Setting valgrind options when running R CMD check --use-valgrind

When I invoke valgrind via R -d valgrind -e '...' the options in the file ~/.valgrindrc are being picked up. Good. When I invok valgrind via R CMD check --use-valgrind ... the options in the file ~/.valgrindrc are NOT being picked up. Bad. And valgrind complains. How can I add the

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

' @param ncores A numeric or character variable with the desired ##' count of threads to use ##' @param verbose A logical value with a default of \sQuote{FALSE} to ##' operate more verbosely ##' @return The return value of the \pkg{data.table} function ##' \code{setDTthreads} which is called as a side

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

On 21 August 2023 at 15:16, Ivan Krylov wrote: | On Mon, 21 Aug 2023 12:02:55 +0100 | Scott Ritchie wrote: | | > remotes::install_github("sritchie73/ukbnmr") | > library(ukbnmr) | > system.time({ remove_technical_variation(test_data) }) | | data.tables, you say? Can you show us the NOTE

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