[R-pkg-devel] extendr packages on CRAN

a PR, please let Mossa (on the TO line) and myself know and we will assist with a PR. Release notes with migration guide at: https://github.com/extendr/extendr/releases/tag/extendr-api-v0.8.0 Thanks, Josiah Parry [[alternative HTML version de

Re: [R-pkg-devel] R CMD build segfault (r88038)

Thank you! I suspect it is because I installed stringi from a binary created on r-universe and it may not have been compatible with my machine or version of R-devel. On Mon, Mar 24, 2025 at 9:48 AM Dirk Eddelbuettel wrote: > > On 24 March 2025 at 09:10, Josiah Parry wrote: > | In

Re: [R-pkg-devel] R CMD build segfault (r88038)

👍 Josiah Parry reacted via Gmail <https://www.google.com/gmail/about/?utm_source=gmail-in-product&utm_medium=et&utm_campaign=emojireactionemail#app> On Mon, Mar 24, 2025 at 9:48 AM Dirk Eddelbuettel wrote: > > On 24 March 2025 at 09:10, Josiah Parry wrote: > | I

[R-pkg-devel] R CMD build segfault (r88038)

In trying to address new WARNINGs on R-devel I'm trying to rebuild my package environment on R 4.6 (r88038) so I can try and remediate. However, I'm encountering a segfault when doing so which doesn't occur for R 4.5.0 alpha (2025-03-18 r87991). Is there a known change to building using R CMD buil

[R-pkg-devel] New API in R-devel & minimum version of R

I'm trying to work through some new WARNINGs that I am experiencing *only* in R-devel. Found non-API calls to R: ‘BODY’, ‘CLOENV’, ‘ENCLOS’, ‘FORMALS’ Take FORMALS, for example. IIUC, we should now be using R_ClosureFormals instead. However, my understanding is that this is available only in R 4

Re: [R-pkg-devel] How do you make it possible to run the example that requires a Conda environment?

Whereas, I just had a CRAN submission fail for using \dontrun{} just once! 🙈 On Fri, Mar 7, 2025 at 06:47 McCrowey, Clinton via R-package-devel < r-package-devel@r-project.org> wrote: > I wrapped my examples in \dontrun{} and the CRAN maintainers never > complained to me. > > > > Clinton Mccrowey

Re: [R-pkg-devel] Failed: Future File Timestamp Check

d. Do you produce it before > preparing the tarball, or is it produced as part of the installation > process? > > Duncan Murdoch > > On 2025-02-04 6:27 p.m., Josiah Parry wrote: > > The file was written using writeLines() but it is just a normal R script > > with normal

Re: [R-pkg-devel] Failed: Future File Timestamp Check

> files, then maybe you should use textConnection to run from internal RAM. > > On February 4, 2025 1:11:10 PM PST, Josiah Parry > wrote: > >I'm running R CMD check for my package {calcite} (source: > >https://github.com/r-arcGIS/calcite) which is failing due to what

[R-pkg-devel] Failed: Future File Timestamp Check

I'm running R CMD check for my package {calcite} (source: https://github.com/r-arcGIS/calcite) which is failing due to what *looks* like a bug. R CMD check fails at "checking for future file timestamps" I get this error: ...Error in if (abs(unclass(now_local) - unclass(now)[1]) > 300) missing va

Re: [R-pkg-devel] [External] Re: Confusing error

you can wrap your example like: if (rlang::is_installed(“survey”)) { Example code here } On Mon, Dec 2, 2024 at 13:17 Cohen, Aaron wrote: > Thank you [and Josiah Parry] for your help; I had already seen that > PracTools uses `survey` but only suggests it, and I was unsure what to do &

Re: [R-pkg-devel] Confusing error

My guess is that one of your packages uses survey as a Suggested package. And your calling a function from that package that uses survey via Suggests. Is your package on GitHub? Or could you share your Imports? On Mon, Dec 2, 2024 at 12:09 Duncan Murdoch wrote: > On 2024-12-02 11:38 a.m., Cohen

Re: [R-pkg-devel] Alternative to ifeq for Makevars

.com/Rdatatable/data.table/blob/08e94b7f4af3fc4403959282bf81c490ebdf9e72/src/Makevars.in#L7 On Fri, Nov 8, 2024 at 12:04 PM Ivan Krylov wrote: > В Fri, 8 Nov 2024 11:44:15 -0800 > Josiah Parry пишет: > > > Do you know of any good documentation on the use of Makevars.in with > > c

Re: [R-pkg-devel] Alternative to ifeq for Makevars

Thanks, Ivan! Do you know of any good documentation on the use of Makevars.in with configure? The @VARNAME@ syntax is quite confusing and isn't explained in WRE from what I can tell. On Fri, Nov 8, 2024 at 11:33 AM Ivan Krylov wrote: > В Fri, 8 Nov 2024 11:21:16 -0800 > Josiah P

[R-pkg-devel] Alternative to ifeq for Makevars

I am working on refactoring some Makevars files and I am quite stuck. I want to conditionally set the value of CRAN_FLAGS like so in my Makevars files ifeq ($(NOT_CRAN), false) CRAN_FLAGS = -j 2 --offline else CRAN_FLAGS = endif Using ifeq appears to be the only way to get the value of CRAN_F

Re: [R-pkg-devel] new version jumps in minor?

Rolf, The versioning method they’re using is referred to as CalVer https://calver.org/ (not as catchy as SemVer) and it is actually quite useful! With one look at the version you can get a good sense of it’s general release date. Posit, for example, moved their professional products to use this v

Re: [R-pkg-devel] Installation took CPU time elapsed time for rust-based package

Thanks, Ivan! Yes, I would use the NOT_CRAN flag. But in the case of that package, the CRAN_FLAGS are not set dynamically. It would be a welcome PR to rextendr if anyone more comfortable with Make would like to. The current template Makevars is at https://github.com/extendr/rextendr/blob/main/inst/

Re: [R-pkg-devel] help with CRAN failures (broom.mixed, rstan-related)

Ben, the issue is that {rstan} is not available. Since it is a suggested package it is not expected to always be there. This is referred to is the "hard" check. Here is a GitHub CI workflow I use to perform this check: https://github.com/JosiahParry/sfdep/blob/008a59b6009d01e5e1625319f6525c1e0ba

Re: [R-pkg-devel] R CMD BATCH plot output

fault. However, there is not any use of `dev.new()` or `pdf()` called anywhere in the code. On Sun, Jul 28, 2024 at 3:44 PM Duncan Murdoch wrote: > On 2024-07-28 1:48 p.m., Josiah Parry wrote: > > Hey folks! I am working with R CMD BATCH and providing a providing a > > logfile o

[R-pkg-devel] R CMD BATCH plot output

Hey folks! I am working with R CMD BATCH and providing a providing a logfile output e.g. R CMD BATCH main.R 2024-07-28.log This creates the desired log file with the contents of stdout and stderr. However, if plots are generated in the process, the plots are stored in Rplots.pdf. Is there a way

[R-pkg-devel] MSRV on Fedora

Hi all! I have 2 errors related to minimum supported rust version (MSRV) on fedora https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/rsgeo-00install.html that I do not know how to resolve. The package {rsgeo} has a dependency on the rust crate geo which itself has a depend

Re: [R-pkg-devel] cpp11 and "non-API calls to R"

Hi Mark, As someone else affected by this issue, it is actually quite tough to resolve. This is because quite literally every other day, the list of what is and is not non-API is changing. It is particularly challenging since this is in R-devel and not any stable R release. If there were a stable

[R-pkg-devel] R-devel non-API & extendr v0.7.0

Hi folks, A new release of extendr v0.7.0 is now available. This release addresses the R-devel WARNings from non-API functions being used. This release also comes with breaking changes. We've written a brief migration guide which can be found at: htttps://extendr.github.io/blog/posts/2024-06-30-

Re: [R-pkg-devel] NOTEs in packages using Rust

from a similar affliction. > Thanks. > -Naras > > Balasubramanian Narasimhan > -- > *From:* R-package-devel on behalf > of Josiah Parry > *Sent:* Thursday, June 20, 2024 9:32:04 AM > *To:* Jeff Newmiller > *Cc:* r-package-devel@r-project.org

Re: [R-pkg-devel] NOTEs in packages using Rust

To be clear, you need to delete the untarred folders after the build process. You only need the dependencies at build time. After the build time it has been compiled into a .so/.dll and then you must delete the vendored sources. There's no reason that installing an R package should keep the *source

Re: [R-pkg-devel] NOTEs in packages using Rust

; > I’m not sure I know at which point to intervene in Makevars to fix things > myself… > > Thanks. > -Naras > > Balasubramanian Narasimhan > -- > *From:* Josiah Parry > *Sent:* Thursday, June 20, 2024 9:08:10 AM > *To:* Balasubra

Re: [R-pkg-devel] NOTEs in packages using Rust

Hi Naras, this should be handled by the Makevars itself. Are you using extendr to do this? Using `rextendr::use_cran_defaults()` should handle it for you. Then you can use `rextendr::vendor_pkgs()` to handle vendoring. On Thu, Jun 20, 2024 at 11:57 AM Balasubramanian Narasimhan < na...@stanford.

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

> > ...but that's a luxury someone would have to pay for. > I'd happily give up my Netflix subscription for this. I suspect the R-foundation/consortium could assist as well? Referring to the "Using Rust in CRAN packages" document we must be able to ...download a specific version from a secure an

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

like polars be able to exist on CRAN. On Wed, May 8, 2024 at 4:06 PM Uwe Ligges wrote: > > > On 08.05.2024 17:56, Josiah Parry wrote: > > Thank you, Dirk. This was a direct email from a CRAN member and not part > of > > the automatic checks. The whole email is below. I think

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

o go through all the work of creating a way to build, store, and retrieve the dependencies only for CRAN to decide they don't support it. On Wed, May 8, 2024 at 3:32 PM Ivan Krylov wrote: > В Wed, 8 May 2024 14:08:36 -0400 > Josiah Parry пишет: > > > With ChatGPT's abi

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

available or has changed (and not give > a check warning nor error)." > > Neal > > [1]: https://cran.r-project.org/web/packages/policies.html > > > On Wed, May 8, 2024 at 11:03 AM Josiah Parry > wrote: > > > > I am sorry for blowing up this thread lately. &g

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

kage. Best, Yes, prqlr is a great Rust-based package! My other Rust based packages that are on CRAN are based, in part on prqlr. On Wed, May 8, 2024 at 11:51 AM Dirk Eddelbuettel wrote: > > On 8 May 2024 at 11:02, Josiah Parry wrote: > | CRAN has rejected this package with: >

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

I am sorry for blowing up this thread lately. I've submitted a package to CRAN that uses Rust which thus requires dependencies to be vendored. https://github.com/R-ArcGIS/arcgisutils/ The vendored dependencies are 18mb when zipped and 16.4mb when zipped with XZ -9e. The *installed package size is

Re: [R-pkg-devel] Cannot repro failing CRAN autochecks

Thanks to @yutannihilation for pointing out that the issue repros on r-universe https://github.com/r-universe/r-arcgis/actions/runs/8990426306/job/24695887245 . Do folks know if there are any templates for the linux CRAN check? It appears that the r-lib/actions linux checks don't cover all of the

Re: [R-pkg-devel] Cannot repro failing CRAN autochecks

:40 Ivan Krylov wrote: > В Tue, 7 May 2024 14:03:42 -0400 > Josiah Parry пишет: > > > This NOTE does not appear in Ubuntu, Mac, or Windows checks > > > https://github.com/R-ArcGIS/arcgisutils > /actions/runs/8989812276/job/24693685840 > <https://github.com/

[R-pkg-devel] Cannot repro failing CRAN autochecks

I've submitted an R package to CRAN and am failing checks *only on Debian* https://win-builder.r-project.org/incoming_pretest/arcgisutils_0.3.0_20240507_194020/Debian/00check.log This NOTE does not appear in Ubuntu, Mac, or Windows checks https://github.com/R-ArcGIS/arcgisutils/actions/runs/8989

[R-pkg-devel] Linker / System Requirement

In my Makevars file (linked below) I link to ssl by adding `-lssl` to `PKG_LIBS`. Since I do this, does libssl need to be added to the System Requirements field? Makevars: https://github.com/R-ArcGIS/arcgisgeocode/blob/8194a478a616f7ddc3a25bcb024c0534007bcd51/src/Makevars#L4 If so, is there a pla

Re: [R-pkg-devel] Urgent Review of R Packages in Light of Recent RDS Exploit

I agree with Ivan here. And more generally, R is a fully featured programming language. You don't need just this one "exploit" (though, it really does feel like a feature to some degree lol!) to be a bad guy with R. You can link to a pre-compiled binary (like my team makes for an R package that co

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

Well, after trying to install the package, I believe the issue is because margins has been archived. https://cran.r-project.org/web/packages/margins/index.html You can check recursive dependencies using `tools::package_dependencies("pkg", recursive = TRUE)` which would help you in this case. I co

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

My understanding is that the order of CRAN repos available in `options("repos")` are tried sequentially. So if cran.r-rproject.org is first, that will be tried. If the package is not available there, the next repository will be tried. I do appreciate the ease of release to R-universe quite a bit p

Re: [R-pkg-devel] Changing package maintainers

name > and email address of the new maintainer. > > Best, > Josh > > > On Thu, Feb 8, 2024 at 10:38 AM Josiah Parry > wrote: > > > > I intend to change the maintainer of my package {sfdep} > > https://cran.r-project.org/package=sfdep. > > Is the process

Re: [R-pkg-devel] Changing package maintainers

[1] https://cran.r-project.org/web/packages/policies.html#Submission > > On February 8, 2024 8:37:50 AM PST, Josiah Parry > wrote: > >I intend to change the maintainer of my package {sfdep} > >https://cran.r-project.org/package=sfdep. > >Is the process as simple as submittin

[R-pkg-devel] Changing package maintainers

I intend to change the maintainer of my package {sfdep} https://cran.r-project.org/package=sfdep. Is the process as simple as submitting a new release where the DESCRIPTION file changes who has the role of `aut`? [[alternative HTML version deleted]] ___

Re: [R-pkg-devel] Native pipe in package examples

a.m., Henrik Bengtsson wrote: > > On Thu, Jan 25, 2024 at 7:48 AM Duncan Murdoch > wrote: > >> > >> On 25/01/2024 10:27 a.m., Josiah Parry wrote: > >>> Hey all, > >>> > >>> I've encountered use of the native pipe operator in the

[R-pkg-devel] Native pipe in package examples

Hey all, I've encountered use of the native pipe operator in the examples for 'httr2' e.g. request("http://example.com";) |> req_dry_run() Since r-oldrel (according to rversions::r_oldrel()) is now 4.2.3, can the native pipe be used in example code? I do notice that the package httr2 requires

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

Thanks for the update! Ill be submitting a change in the coming days and will report back :) On Tue, Jan 16, 2024 at 12:12 Dirk Eddelbuettel wrote: > > On 16 January 2024 at 10:28, Josiah Parry wrote: > | Oddly making the change has made CI happy. > | > https://github.com/R-Arc

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

Oddly making the change has made CI happy. https://github.com/R-ArcGIS/arcgisutils/actions/runs/7543315551/job/20534063601 It may be that the issue was OS related but I'm unsure since only oldrel for windows and macos check results are published https://cran.r-project.org/web/checks/check_results_

[R-pkg-devel] test failure: oldrel

Hey folks! I've received note that a package of mine is failing tests on oldrel. Check results: https://www.r-project.org/nosvn/R.check/r-oldrel-windows-x86_64/arcgisutils-00check.html I think I've narrowed it down to the way that I've written the test which uses `as.POSIXct(Sys.Date(), tz = "UTC

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

n 10, 2024 at 10:26 AM 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/ > > <https://r.esri.com/bin/> and as

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

; Best, > Uwe Ligges > > > > > On 03.01.2024 18:19, Josiah Parry wrote: > > Thanks, both. I'm not familiar with Additional_repositories. Must the > > package source be specified there? Or can it be specified via > > documentation a la Rd file? > > >

Re: [R-pkg-devel] Assigning an object to the global environment (shiny package)

Alternatively, you can create a new environment in your package and assign into it and fetch out of it. This is definitely safer and probably "more idiomatic." Hope that helps! # create a new environment

Re: [R-pkg-devel] [Rd] static html vignette

I understand that this doesn't actually *solve *your problem, but would like to offer an alternative perspective. I often find that vignettes may be most useful as an extended form of documentation. If you have a pkgdown site, you can use `usethis::use_article()` to create an article which will no

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

Thanks, both. I'm not familiar with Additional_repositories. Must the package source be specified there? Or can it be specified via documentation a la Rd file? On Wed, Jan 3, 2024 at 12:14 PM Uwe Ligges wrote: > > > On 03.01.2024 17:58, Duncan Murdoch wrote: > > On 03/01/202

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

Lovely, thank you! On Wed, Jan 3, 2024 at 11:43 AM Uwe Ligges wrote: > > > On 03.01.2024 17:33, Josiah Parry wrote: > > I have a scenario where I have an exported function that requires the > > installation a package that *is not* available on CRAN. The body of the >

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

I have a scenario where I have an exported function that requires the installation a package that *is not* available on CRAN. The body of the function is generally: fx <- function() { rlang::check_installed("noncranpkg") noncranpkg::gx() } As required, this package is in the Suggests field. B

Re: [R-pkg-devel] Update timing of machines on CRAN?

Unfortunately, it is often important for us to pay attention to what machines our code is being tested on. I think the point is more or less that we often find ourselves trying to make super small adjustments for machines and builds that are used by a number of users in the single digits. The vast

Re: [R-pkg-devel] Example files for functions reading binary files

Rafael, I believe the issue is that packages cannot include binary *executables.* If you have a binary file (such as a parquet file) in inst/extdata, I do not think that would be a problem. It would be a good idea to ensure that that file is small, though. I think downloading a file is a big no no

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

In these cases, I unfortunately find the best approach to be to wrap the examples in `if (interactive()) ` to ensure that they will not be ran on CRAN tests machines. It hampers the checks of CRAN but it makes it possible to get usable code to users. On Sun, Dec 3, 2023 at 9:54 AM Artur Araujo wr