Re: [R-pkg-devel] Warnings and notes while building package with nimble

On 6 April 2025 at 01:25, Lluís Revilla wrote: | To solve it, it might be as simple as writing nimDim <- NULL inside your | package or there might be a real issue there. Or call utils::globalVariables(c("nimDim")) where, if needed, you could add to that argument vector any other variables listed

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

On 19 March 2025 at 09:29, Michael Chirico wrote: | data.table is doing the same in a number of places, Ivan even went so far | as to pin down a specific SVN commit for those as well: | | #if R_VERSION < R_Version(4, 5, 0) || R_SVN_REVISION < 86702 | # define isDataFrame(x) isFrame(x) // #6180

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

On 24 March 2025 at 09:10, Josiah Parry wrote: | 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 r8799

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

On 19 March 2025 at 11:16, Ben Bolker wrote: |FWIW Rcpp handles this (for CLOENV) with an ifdef: | | #if (defined(R_VERSION) && R_VERSION >= R_Version(4,5,0)) | return R_ClosureEnv(fun); | #else | return CLOENV(fun); | #endif

Re: [R-pkg-devel] How to resolve missing packages without Notes

On 9 March 2025 at 15:03, Stephen Abrams wrote: | Hi again - I'm working through the final details of a submission. My | current problem is that I make use of a dependency of the caret package | (kernlab) in one of my vignettes. If I don't include kernlab in my | DESCRIPTION file, I get the follo

Re: [R-pkg-devel] Package with JS dependency

On 24 February 2025 at 22:08, Viechtbauer, Wolfgang (NP) wrote: | Like Duncan's rgl package, the mathjaxr package (https://cran.r-project.org/package=mathjaxr) also contains JS code (for MathJax). And one of the requirements to get the package onto CRAN was that the source package had to conta

Re: [R-pkg-devel] False positive antivirus reports on package vignettes

On 18 February 2025 at 15:14, Iñaki Ucar wrote: | What happened in Rcpp is that the antivirus were detecting an old | version of ghostscript that could produce potentially vulnerable | outputs. We solved it by rebuilding the vignettes with a newer version | of ghostscript. This is most likely the

Re: [R-pkg-devel] False positive antivirus reports on package vignettes

This really is Dadaism (or maybe Absurdism? Where are our art historians?) By now I heard from one of the affected scientists via a private slack message. A choice quote: basically the pdf is moved into quarantine, and our IT are now threatening us to format all our laptops This is beyon

Re: [R-pkg-devel] False positive antivirus reports on package vignettes

On 18 February 2025 at 16:26, Ivan Krylov wrote: | On Tue, 18 Feb 2025 07:05:06 -0600 | Dirk Eddelbuettel wrote: | | > one of the two pdf vignettes (which I happen to create as a shallow | > Rnw -> pdf wrapper around a pre-made pdf, here that inner pdf had not | > changed in five

[R-pkg-devel] False positive antivirus reports on package vignettes

Something that had happened to the Rcpp package in the past (but seemingly went away on its own ?) is now apparently hitting package RcppArmadillo. I received private email from the CRAN maintainers reporting, without offering a fix as there seems to be none, that one of the two pdf vignettes (w

Re: [R-pkg-devel] Retrieving versioned csv datasets for use in an R package

Hi Thierry, On 17 February 2025 at 09:16, Thierry Onkelinx wrote: | Zenodo does offer storage. The default quota are 50GB and 100 files per record | (version). See https://help.zenodo.org/docs/deposit/manage-files/#prepare So TIL! Thanks for the heads-up and correction. Dirk -- dirk.eddelbue

Re: [R-pkg-devel] Retrieving versioned csv datasets for use in an R package

On 15 February 2025 at 19:50, Simon Urbanek wrote: | Github is not reliable enough for reproducible research (your files can | disappear at any point - or can change without notice), I'm curious: Do you have a concrete example of a no-longer-reproducible study whose data or other support files

Re: [R-pkg-devel] [External] 'library' or 'require' call not declared

On 7 February 2025 at 11:15, Duncan Murdoch wrote: | On 2025-02-07 10:09 a.m., Dirk Eddelbuettel wrote: | > | > On 7 February 2025 at 05:05, Richard M. Heiberger wrote: | > | Michael and Brian. | > | | > | thank you | > | exactly correct. | > | > For completeness: this

Re: [R-pkg-devel] [External] 'library' or 'require' call not declared

On 7 February 2025 at 05:05, Richard M. Heiberger wrote: | Michael and Brian. | | thank you | exactly correct. For completeness: this check is a fairly recent addition to r-devel and hence a 'policy change'. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___

Re: [R-pkg-devel] [SPAM Warning!]Re: CRAN Debian error installation time

On 4 February 2025 at 16:16, Graeme Hickey wrote: | Having spent the best part of a month troubleshooting an almost | identical issue, I came across Dirk's blog post here: https:// | dirk.eddelbuettel.com/blog/2023/10/31/. He discusses how to throttle the number | of threads, and exports 2 handy

Re: [R-pkg-devel] Rcpp in vignette

Hi Wolfgang, On 31 January 2025 at 15:02, Wolfgang Rolke via R-package-devel wrote: | In the vignette of my package Rgof I create a function written in Rcpp, which is then passed and executed in some of the routines included in Rgof. The package passes all the checks on the various platform wit

Re: [R-pkg-devel] [SPAM Warning!]Re: CRAN Debian error installation time

Excellent (as usual) sleuthing by Ivan -- colour me impressed (again). As an aside, your package makes wide use of the excellent resources provided by other CRAN packages. But with this comes added complexity. Depending on over sixty (!!) other packages (when counting recursively, over seventy

Re: [R-pkg-devel] CRAN Debian error installation time

Thank you for actually posting a reference to your package and its source code. That allows us to take a closer look. On 28 January 2025 at 16:07, Guillermo Vinue wrote: | Thank you for your help, Ben and Ivan. Unfortunately, the note persists: | https://win-builder.r-project.org/incoming_prete

Re: [R-pkg-devel] Is it possible to install a pre-compiled R package from Github?

On 28 January 2025 at 14:27, Iñaki Ucar wrote: | El mar., 28 ene. 2025 14:25, John Clarke | escribió: | | > Hi all, | > | > I'm wondering if there is a way to point an R package installer to a | > pre-compiled release on Github rather than rely on CRAN. | | | Yes, see https://r-universe.dev/

Re: [R-pkg-devel] Rcpp: how best to include source from another Github repository

On 21 January 2025 at 12:04, Jonathan Berrisch wrote: | first of all: I'm not an expert on this and don't really know if there | is a recommended way. | | However, you may look at my 'rcpptimer' package and how it includes | 'cpptimer' as a submodule. | | You can find the repository here: htt

Re: [R-pkg-devel] Package builds on all systems except on Fedora with clang

On 19 January 2025 at 20:42, Pepijn de Vries wrote: | I think I could write a similar test as used by `cpp11tesseract`: | | https://github.com/pachadotdev/cpp11tesseract/blob/2ea8287ef2c27901446bafa402728014d99904d4/configure#L66-L85 Taking an example from a package not on CRAN 'for policy vio

Re: [R-pkg-devel] SystemRequirements & configure check for FFTW with single precision support

Lukas, It is, as you noticed, complicated. One way forward might be to rely on what you can rely on (i.e. a suitable system fftw on two of the three platforms) and to embed and locally build where not. Nowadays a number of packages embedding external libraries and resorting to eg cmake to build

Re: [R-pkg-devel] Removing packages files

On 2 January 2025 at 13:41, Henrik Bengtsson wrote: | Agree, it would be neat if a package could clean up after itself when | uninstalled. Indeed many things could be nicer if we had more package manager integrations and hooks besides `cleanup` and `configure`. Someone would have to start with

Re: [R-pkg-devel] Case of package name

On 30 December 2024 at 11:24, Kevin Coombes wrote: | Thanks; I suspected as much. I will try changing the name of the algorithm | (in the manuscript) to uppercase, and leave the package name alone. Some (software-centric) journals (JSS, R Journal, ...) use a distinct font for software components

Re: [R-pkg-devel] use of assert in C++

On 19 December 2024 at 06:06, Duncan Murdoch wrote: | I think it would be really misleading to have code that routinely | ignored the assert() calls. In a year would you remember that those | asserts were effectively just comments, not being acted on without some | trickery to enable them? Or

Re: [R-pkg-devel] use of assert in C++

On 18 December 2024 at 19:46, Bielow, Chris wrote: | hoping this is the right place for this: | I stumbled upon documentation regarding the use of `assert` in C++ code, in | particular, https://cran.r-project.org/web/packages/policies.html states | that | | ``` | Thus C/C++ calls to assert/abort

Re: [R-pkg-devel] Cannot create C code with acceptable performance with respect to internal R command.

Luc, As Tomas mentioned, matrix-multiplication can take advantage of multiple threads, and the 'text book' nexted loops do not do that. Now, one alternative that appeals a lot to me is to farm out to Armadillo which also calls LAPACK for you (as R does). And via RcppArmadillo, the setup becomes

Re: [R-pkg-devel] update.packages Error in if (any(diff)) { : missing value where TRUE/FALSE needed

On 17 November 2024 at 15:16, Patrick Giraudoux wrote: | Thus, this latter works fine. Does this help to identify the trouble ? I think this resonates with the fine work Ivan had already done. I suspect you have a bad local with the repo information (possible PACKAGE.rds) and it does not get ove

Re: [R-pkg-devel] update.packages Error in if (any(diff)) { : missing value where TRUE/FALSE needed

On 17 November 2024 at 14:23, Patrick Giraudoux wrote: | Le 17/11/2024 à 14:17, Ivan Krylov a écrit : | > В Sun, 17 Nov 2024 14:04:56 +0100 | > Patrick Giraudoux пишет: | > | >> trying URL | >> 'https://pbil.univ-lyon1.fr/CRAN/bin/windows/contrib/4.4/xfun_0.49.zip' | >> Content type 'application/

Re: [R-pkg-devel] Possible false negative for compiled C++ code in CRAN checks

On 15 November 2024 at 12:16, Mauricio Vargas Sepulveda wrote: | [...] and I now asked Dr. Ligges for the possibility to know more about the CRAN specific configuration to add it to R-Hub. It is (and has always been) documented in a text file on the server https://www.stats.ox.ac.uk/pub/bd

Re: [R-pkg-devel] Possible false negative for compiled C++ code in CRAN checks

On 14 November 2024 at 16:24, Mauricio Vargas Sepulveda wrote: | After enabling the SAN flags, I cannot reproduce the gcc-san error [2]. | | Should I report this as a false positive? No. Replicating ASAN/UBSAN issues is known to be potentially tricky. It drove me so batty a decade ago that I

Re: [R-pkg-devel] CRAN build error on Windows

On 12 November 2024 at 10:47, Dirk Eddelbuettel wrote: | | On 12 November 2024 at 12:40, Pepijn de Vries wrote: | | "Cannot create temporary file in D:\temp\2024_11_12_ 1_50_00_12637\: No such file or directory" | | Based on your quote and the log [1] it looks like you have a sp

Re: [R-pkg-devel] CRAN build error on Windows

On 12 November 2024 at 12:40, Pepijn de Vries wrote: | "Cannot create temporary file in D:\temp\2024_11_12_ 1_50_00_12637\: No such file or directory" Based on your quote and the log [1] it looks like you have a space in the directory name. Windows can accommodate these but you must then quote

Re: [R-pkg-devel] CRAN build error on Windows

On 12 November 2024 at 12:40, Pepijn de Vries wrote: | "Cannot create temporary file in D:\temp\2024_11_12_ 1_50_00_12637\: No such file or directory" Based on your quote and the log [1] it looks like you have a space in the directory name. Windows can accommodate these but you must then quote

Re: [R-pkg-devel] Cascade effect of non-available packages?

Tiago, Looking at https://www.stats.ox.ac.uk/pub/bdr/noSuggests/pliman.out we see it errors after trying '* checking examples ...': * checking examples ... ERROR Running examples in ‘pliman-Ex.R’ failed The error most likely occurred in: > ### Name: as_image > ### Title: Crea

Re: [R-pkg-devel] Cascade effect of non-available packages?

On 3 November 2024 at 11:02, Tiago Olivoto wrote: | Today, I noticed that several stable packages, such as Rcpp and sf, were | unavailable during the check process for this submission. This wasn’t an | issue in the previously published version of pliman. Could this be a | temporary problem with t

Re: [R-pkg-devel] R-extension requirement about third-party random number generators (RNG)

On 27 September 2024 at 16:58, John Clarke wrote: | [...] -- the RNG state management strategy appears almost 'magical' to me | especially inside RCPP. It is possible, I just don't understand how to use it. See Section 6.3 of WRE: The pair of GetRNGstate() and PutRNGstate() is all there is in te

Re: [R-pkg-devel] R-extension requirement about third-party random number generators (RNG)

Hi John, I think you are reading the text too literally. The intent of WRE is to ensure that standard use of a RNG in an extension package uses the RNGs that come with R (which includes an updated mersenne twister algorithm) so that users are not "surprised". It explicitly mentions the problem

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 21 August 2024 at 15:47, Kurt Hornik wrote: | > Kurt Hornik writes: | | Committed now. That is just *lovely*: > aut <- tools::CRAN_authors_db() > dim(aut) [1] 47433 7 > head(aut) given family email orcid role comment

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 21 August 2024 at 07:43, Dirk Eddelbuettel wrote: | | On 20 August 2024 at 15:47, Kurt Hornik wrote: | | >>>>> Kurt Hornik writes: | | | | The variant attaches drops the URL and does unique. | | Nice. Alas, some of us default to r-release as the daily driver and then | |

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 20 August 2024 at 15:47, Kurt Hornik wrote: | > Kurt Hornik writes: | | The variant attaches drops the URL and does unique. Nice. Alas, some of us default to r-release as the daily driver and then Error in unname(tools:::.ORCID_iD_canonicalize(o)) : object '.ORCID_iD_canonicalize

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 20 August 2024 at 07:57, Dirk Eddelbuettel wrote: | | Hi Kurt, | | On 20 August 2024 at 14:29, Kurt Hornik wrote: | | I think for now you could use something like what I attach below. | | | | Not ideal: I had not too long ago starting adding orcidtools.R to tools, | | which e.g. has

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

many things at once... Dirk | I think that has become both recursive and demonstrating excellent | test-retest stability!  Oh boy do I know that issue! | | Chris | | On 20/08/2024 14:57, Dirk Eddelbuettel wrote: | > Hi Kurt, | > | > On 20 August 2024 at 14:29, Kurt Hornik wrote: | >

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

Hi Kurt, On 20 August 2024 at 14:29, Kurt Hornik wrote: | I think for now you could use something like what I attach below. | | Not ideal: I had not too long ago starting adding orcidtools.R to tools, | which e.g. has .persons_from_metadata(), but that works on the unpacked | sources and not th

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

Salut Thierry, On 20 August 2024 at 13:43, Thierry Onkelinx wrote: | Happy to help. I'm working on a new version of the checklist package. I could | export the function if that makes it easier for you. Would be happy to help / iterate. Can you take a stab at making the per-column split more rob

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 19 August 2024 at 15:15, Thierry Onkelinx wrote: | Maybe checklist:::author2df() might be useful. It is an unexported function | from my checklist package. It converts a person() object to a dataframe. | https://github.com/inbo/checklist/blob/5649985b58693acb88337873ae14a7d5bc018d96 | /R/stor

[R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

Has anybody written a quick helper function that extracts the Authors@R field from tools::CRAN_package_db() and 'stems' it into 'Name, Firstname, ORCID' which one could use to look up ORCID IDs at CRAN? The lookup at orcid.org sometimes gives us 'private entries' that make it harder / impossible

Re: [R-pkg-devel] Build process generated non-portable files

On 17 August 2024 at 17:22, Ivan Krylov via R-package-devel wrote: | В Fri, 16 Aug 2024 18:53:55 + | anj5x...@nilly.addy.io пишет: | | > In the past other packages have failed to build and not only on the | > intel container see | > "https://github.com/SpeakEasy-2/speakeasyR/actions/runs/10

Re: [R-pkg-devel] rhub (version 2) baulking at building a vignette.

On 2 August 2024 at 16:12, Ivan Krylov via R-package-devel wrote: | В Fri, 2 Aug 2024 11:10:59 + | Rolf Turner пишет: | | > The advice was to the effect that if the vignette was actually just a | > *.tex file, one could (after putting in some preparatory code, in the | > form of comments,

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

On 29 July 2024 at 13:02, Ivan Krylov wrote: | On Sun, 28 Jul 2024 15:27:33 -0500 | Dirk Eddelbuettel wrote: | | > If we cannot (or do not want to) modify the given main.R, I would | > suggest something along the lines of | > | > Rscript -e 'pdf(myfilenamevar); source(&

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

On 28 July 2024 at 15:44, Duncan Murdoch wrote: | On 2024-07-28 1:48 p.m., Josiah Parry wrote: | > However, if plots are generated in the process, the plots are stored in | > Rplots.pdf. | > | > Is there a way via command line arguments to change the name of the pdf | > output. | > | > There mi

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

Hi Khue, On 19 July 2024 at 06:29, Khue Tran wrote: | I am currently trying to get precise inputs by taking strings instead of | numbers then writing a function to decompose the string into a rational | with the denominator in the form of 10^(-n) where n is the number of | decimal places. I am n

Re: [R-pkg-devel] No email with confirmation link on resubmission of package

On 6 June 2024 at 04:47, Paul Kabaila wrote: | When I resubmitted, I didn't realise that I needed to change the version number. As this comes up every now and then: This is still a _soft_ requirement. CRAN does not 'cache' what versions you used in uploads. I have often reiterated with the same

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

On 26 May 2024 at 13:31, Kurt Hornik wrote: | >>>>> Dirk Eddelbuettel writes: | | > 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() | > includin

Re: [R-pkg-devel] gcc14 checks on fedora

On 24 May 2024 at 20:01, Brad Eck wrote: | I received a note that my package -- epanet2toolkit -- was showing a | warning in the fedora-gcc results on CRAN. | https://www.stats.ox.ac.uk/pub/bdr/gcc12/epanet2toolkit.out | | I'd like to reproduce the warning and fix it. Usually I'd do that with |

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 omp_get_num_thread

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

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 to de

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

o condition on here? Michelle did AFAICT the Right Thing (TM) by 'borrowing' from the fairly mature check in RcppArmadillo. Dirk | | Thanks, | Michelle | ━━━ | From: Kurt Hornik | Sent: Wednesday, May 22, 2024

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 files

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: https://win-builder.r-project.org/incoming_pre

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 ag

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, y

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 must-be-

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 handle

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 through

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 f

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

ogle/crc32c [1] repo: 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? |

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 confu

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 h

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, Dirk

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 bef

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` as

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 Google

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 'log

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 unde

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 stuc

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 g

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 a

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 and

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 ex

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)}{ \i

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_= ~/.R/check.Renvir

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

), "\n")'; 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 c

[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(), t

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 `https://r.esr

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 | @eddelbu

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 a

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

epository. 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.

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 c

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