Re: [R-pkg-devel] Help with clang-san warnings for package "tidyfit"

Hi Ivan, thanks for your helpful response and for the background info! Much appreciated! I'll reply-all as you suggested. Best regards, Johann On 16.01.25 21:30, Ivan Krylov wrote: В Wed, 15 Jan 2025 22:13:36 +0100 Johann Pfitzinger пишет: I have, so far, failed to reproduce this or to f

Re: [R-pkg-devel] Help with clang-san warnings for package "tidyfit"

В Wed, 15 Jan 2025 22:13:36 +0100 Johann Pfitzinger пишет: > I have, so far, failed to reproduce this or to find any useful > information on how to fix it. My best guess based on the output.txt > is that it originates in "purrr" (which I depend on). This is, indeed, a purrr bug: https://github.

[R-pkg-devel] Help with clang-san warnings for package "tidyfit"

Dear community, my R package "tidyfit" is failing CRAN submission checks with the following warning (see email below for complete results): Flavor: r-devel-linux-x86_64-debian-special-clang-san Check: Post-processing issues found for clang-san, Result: WARNING File: tidyfit-Ex.Rout cleanca

Re: [R-pkg-devel] Help with 2 NOTES

В Thu, 10 Oct 2024 13:10:39 + Jaime Salvador пишет: > * The \dontrun in examples. To run the examples, we need a > database, the package doesn't include a sample database, so the code > can't be run. I remove \dontrun in functions that can run without a > database (for example redatam_ver

Re: [R-pkg-devel] Help with 2 NOTES

mailto:jaime.salva...@ideasybits.com>> Cc "r-package-devel@r-project.org" mailto:r-package-devel@r-project.org>> Fecha 10/10/2024 3:30:18 Asunto Re: [R-pkg-devel] Help with 2 NOTES Dear Jaime Salvador, Welcome to R-package-devel! В Wed, 9 Oct 2024 20:42:24 + Jaime Salvador

Re: [R-pkg-devel] Help with 2 NOTES

Dear Jaime Salvador, Welcome to R-package-devel! В Wed, 9 Oct 2024 20:42:24 + Jaime Salvador пишет: > New submission This one is expected for new packages. > Possibly misspelled words in DESCRIPTION: > DICX (12:67) > RXDB (12:59) > Redatam (2:34, 12:40) Wrap the abbreviations and s

[R-pkg-devel] Help with 2 NOTES

How I can solve this NOTES: * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Jaime Salvador < jaime.salva...@ideasybits.com>’ New submission Possibly misspelled words in DESCRIPTION: DICX (12:67) RXDB (12:59) Redatam (2:34, 12:40)

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

May be a completely red herring, but I've recently had what might be a similar issue with reference classes, which kept me pulling my hair for a few hours (when method calls that used to work suddenly stopped doing so, unless called manually first). IIRC, the culprit was a method obj$basis() be

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

В Wed, 25 Sep 2024 16:57:55 -0400 Ben Bolker пишет: > Next question, is this (in your opinion) worth escalating to > r-devel ? I think so, yes. Hopefully there will be a way to temporarily re-enable the S4 dispatch for primitive operators in methods:::.requirePackage (that lives in R/RClassUtil

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

Please let me know if I can be of any help. I kind of "caused" this issue by submitting the new version of brms to CRAN. Of course, the issue is not really in brms but somehow deeper as your investigations shows. Would it help if brms extracted variables names from rstan objects somehow differently

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

Yikes. Next question, is this (in your opinion) worth escalating to r-devel ? I can definitely implement something where I require() rstan up front, (which should be harmless if it's really not available but will fix issues that brms is having?) ... that might resolve the symptoms cleanl

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

В Wed, 25 Sep 2024 12:28:25 -0400 Ben Bolker пишет: >What is your current estimate of the probability that this is > something that I've done wrong vs. exposing something wonky elsewhere > (i.e. at the level of testthat, brms, rstan, Rcpp, R-devel, ...) ? I didn't have a good answer (the m

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

On 9/25/24 12:21, Ivan Krylov wrote: Hmm, so it's *not* a machine-specific problem after all [1,2] and can now be reproduced on a regular R-devel build on Debian Sid. I'm sorry for jumping to conclusions. No need to apologize, you've gotten 1000x farther than I would have on my own.

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

Hmm, so it's *not* a machine-specific problem after all [1,2] and can now be reproduced on a regular R-devel build on Debian Sid. I'm sorry for jumping to conclusions. Why would Rcpp::loadModule() (called from rstan's .onLoad) end up trying to apply a non-function, but only when being called from

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

Thanks both. Josiah Parry says: > Ben, the issue is that {rstan} is not available. Since it is a suggested package it is not expected to always be there. The thing is that the checks for rstan-based objects *are* conditional. This is actually failing on the tests for brms-based object

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

В Tue, 24 Sep 2024 10:27:34 -0400 Ben Bolker пишет: >Weirdly, I can't get this to fail on my local system even if I > remove rstan -- maybe rstan needs to be present for brms at install > time but not at runtime ... ??? I'm noticing that despite broom.mixed having Suggests: rstan and it bein

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

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

broom.mixed is failing tests on Fedora. With apologies for the mangled formatting, here is the test failure (full properly formatted details at https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/broom.mixed-00check.html). ══ Failed tests ═

Re: [R-pkg-devel] Help for understanding CRAN rejection

Dear Ivan, Thank you so much for your help. I followed your advices and I reduced the size of the example data, move one package from Import to Suggest. The type of the license is unfortunately not depending on me so I’ll try one last time with the CC license and the new improvements. Thank y

Re: [R-pkg-devel] Help for understanding CRAN rejection

(I am adding the mailing list back in Cc: because package licensing is a complicated topic.) В Tue, 9 Jul 2024 09:25:14 + Matei Teleman пишет: > I’ve added “ … SuperCell uses > [velocyto.R](https://github.com/velocyto-team/velocyto.R) for RNA > velocity. ” in the Description field. Is that e

Re: [R-pkg-devel] Help for understanding CRAN rejection

В Mon, 8 Jul 2024 15:12:24 + Matei Teleman пишет: > Non-FOSS package license (file LICENSE) > The license we’re using is the standard CC BY-NC-ND 4.0 and is listed > among the accepted licenses for CRAN Instead of putting the license text in a file inside the package (that would have to mat

[R-pkg-devel] Help for understanding CRAN rejection

Hello everyone, I hope this email finds you well. I’m sorry to bother you, it’s the very first time I’m submitting a package to CRAN. Recently my submission got rejected with the following feedback: Non-FOSS package license (file LICENSE) Suggests or Enhances not in mainstream repositories:

Re: [R-pkg-devel] Help needed with CRAN check error under MacOS and old-rel

Hello, Pedro et al.: Your package is on GitHub with GitHub Actions.[1] If whoever manages GitHub actions feels inclined to add macos-latest (oldrel-1), this would be one argument for doing that, though this kind of problem may be too rare to justify the expense. That's particularly true si

Re: [R-pkg-devel] Help needed with CRAN check error under MacOS and old-rel

On 2024-06-30 5:17 a.m., Aphalo, Pedro J wrote: Hello, A few days ago I submitted to CRAN an updated version of package 'ggpp', it passed checks during submission and version 0.5.8 is now on CRAN. However I see errors for old-rel only for MacOS at https://cran.r-project.org/web/checks/check_re

[R-pkg-devel] Help needed with CRAN check error under MacOS and old-rel

Hello, A few days ago I submitted to CRAN an updated version of package 'ggpp', it passed checks during submission and version 0.5.8 is now on CRAN. However I see errors for old-rel only for MacOS at https://cran.r-project.org/web/checks/check_results_ggpp.html and I am stuck as I do not have w

Re: [R-pkg-devel] Help with detritus on temporary directory note

On 2024-05-30 7:43 a.m., Ivan Krylov via R-package-devel wrote: В Thu, 30 May 2024 11:12:05 +0200 Héctor Meleiro Suárez пишет: So why is this a problem? Is it that there are too many files aftes examples and tests are run? or would this NOTE be an issue to CRAN even if only one file was detect

Re: [R-pkg-devel] Help with detritus on temporary directory note

В Thu, 30 May 2024 11:12:05 +0200 Héctor Meleiro Suárez пишет: > So why is this a problem? Is it that there are too many files aftes > examples and tests are run? or would this NOTE be an issue to CRAN > even if only one file was detected at the end? This problem has two sides. The side that R

Re: [R-pkg-devel] Help with detritus on temporary directory note

Dear Hector, The tmp dir depends on the R session. Use tools::R_user_dir("your_package", which = "cache") if you want a permanent cache of the files. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK /

[R-pkg-devel] Help with detritus on temporary directory note

Hello everybody. I'm having a problem submitting a package to CRAN. It involves a NOTE about detritus files on the temporary directory. The thing is my package basically downloads a zip file to the temporary directory, unzips, reads and processes some of the extracted files and imports the data t

Re: [R-pkg-devel] help diagnosing win-builder failures

On 18.03.2024 02:07, Ben Bolker wrote:   I think I may actually have figured this out.   The Matrix package is being updated to version 1.7.0 soon, with expected ABI breakage.  This version is **already installed on win-builder/r-devel**, so the Matrix/TMB/glmmTMB binary stack fails (digg

Re: [R-pkg-devel] help diagnosing win-builder failures

I think I may actually have figured this out. The Matrix package is being updated to version 1.7.0 soon, with expected ABI breakage. This version is **already installed on win-builder/r-devel**, so the Matrix/TMB/glmmTMB binary stack fails (digging into the logs a bit deeper showed that t

Re: [R-pkg-devel] help diagnosing win-builder failures

Hi, This may need the help of Uwe Ligges to diagnose. I suspect this may be related to the Windows machine having too much memory committed (as Uwe has been able to pinpoint recently [*] about a package that failed to compile some heavily templated C++), but there is not enough information to give

[R-pkg-devel] help diagnosing win-builder failures

Hi folks, We're in the final stages of preparing a revised version of the glmmTMB package for CRAN and are stuck troubleshooting checks on win-builder/r-devel. Testing is working everywhere *except* win-builder/r-devel. Win-builder is OK with r-oldrel and r-devel; the same package is O

Re: [R-pkg-devel] help with revdep_check

Thanks. Although I have had Xtools for quite a while, it had not been activated. Installing a new copy made all the difference Bill > On Sep 25, 2023, at 12:24 PM, Gábor Csárdi wrote: > > Seems like you are on macOS. You need to install XCode or the Command > Line Tools to be able to compil

Re: [R-pkg-devel] help with revdep_check

Seems like you are on macOS. You need to install XCode or the Command Line Tools to be able to compile packages with C/C++/Fortran code. Gabor On Mon, Sep 25, 2023 at 7:02 PM William Revelle wrote: > > Dear friends, > I am trying to release a new update to psych and psychTools and am having > p

[R-pkg-devel] help with revdep_check

Dear friends, I am trying to release a new update to psych and psychTools and am having problems with revdep_check The error message from revdep_check is less than helpful:’ fn is fn <- "/Users/WR/Library/CloudStorage/Dropbox/psychTools/" revdep_check(fn,num_workers=8) ── CHECK ───

Re: [R-pkg-devel] Help with a github/Rstudio mess

rom: R-package-devel on behalf of Duncan Murdoch Sent: Wednesday, July 5, 2023 10:03:11 AM To: chrish...@psyctc.org ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] Help with a github/Rstudio mess I think this isn't the right place to ask for this sort of help. Maybe stackoverflow ins

Re: [R-pkg-devel] Help with a github/Rstudio mess

First, apologies for being off topic.  I guess I can see that this was pretty pure git/github/Rstudio with hindsight.  I am very leary of stackoverflow, probably wrongly, but I find such a mix of misinformation and showboating there.  By contrast this list is a haven for me to learn. However, poi

Re: [R-pkg-devel] Help with a github/Rstudio mess

On Wed, 5 Jul 2023 09:44:26 +0100 Chris Evans wrote: > OK.  So I try to pull thinking that made sense and that the change to > pkgdown.yaml on github that I made yesterday is the offending change. You are right about this. > However, when I pull (in Rstudio again) I get this: > > >>> /usr/bi

Re: [R-pkg-devel] Help with a github/Rstudio mess

I think this isn't the right place to ask for this sort of help. Maybe stackoverflow instead? What I'd do in this case is to rename the local dir holding the repository, then clone a new copy from Github. Assuming that works, compare all the files to make sure that you have all recent changes

[R-pkg-devel] Help with a github/Rstudio mess

I hope this is a legitimate question here.  I have a package of very simple functions: https://github.com/cpsyctc/CECPfuns.  For the forseeable future it's really only to stop me constantly having to rewrite functions I use and it is only also used by probably two or three colleagues who also us

Re: [R-pkg-devel] help fixing CRAN package sos-now fails on GitHub

On 5/22/23 2:38 PM, Duncan Murdoch wrote: On 22/05/2023 3:07 p.m., Ivan Krylov wrote: I fed your vignette to R CMD Sweave, and here's the relevant fragment from the resulting *.tex file: This returned a {\tt "findFn"} object identifying 405 help pages. When this was run while preparing this

Re: [R-pkg-devel] help fixing CRAN package sos-now fails on GitHub

On 23/05/2023 6:53 a.m., Martin Maechler wrote: Duncan Murdoch on Mon, 22 May 2023 15:38:10 -0400 writes: > On 22/05/2023 3:07 p.m., Ivan Krylov wrote: >> I fed your vignette to R CMD Sweave, and here's the >> relevant fragment from the resulting *.tex file: >> >>>

Re: [R-pkg-devel] help fixing CRAN package sos-now fails on GitHub

> Duncan Murdoch > on Mon, 22 May 2023 15:38:10 -0400 writes: > On 22/05/2023 3:07 p.m., Ivan Krylov wrote: >> I fed your vignette to R CMD Sweave, and here's the >> relevant fragment from the resulting *.tex file: >> >>> This returned a {\tt "findFn"} object iden

Re: [R-pkg-devel] help fixing CRAN package sos-now fails on GitHub

On 22/05/2023 3:07 p.m., Ivan Krylov wrote: I fed your vignette to R CMD Sweave, and here's the relevant fragment from the resulting *.tex file: This returned a {\tt "findFn"} object identifying 405 help pages. When this was run while preparing this manuscript, the sixth row was {\tt pspline_ch

Re: [R-pkg-devel] help fixing CRAN package sos-now fails on GitHub

I fed your vignette to R CMD Sweave, and here's the relevant fragment from the resulting *.tex file: > This returned a {\tt "findFn"} object identifying 405 help pages. > When this was run while preparing this manuscript, the sixth row was > {\tt pspline_checker} in the \pkg{JOPS} package, which h

Re: [R-pkg-devel] help fixing CRAN package sos-now fails on GitHub

A simple fix might be to redefine findFn in the global environment of the vignette, have it explicitly call sos::findFn, and return a result sanitized for LaTeX output. According to this: https://stackoverflow.com/questions/32865384/function-to-sanitize-strings-for-latex-compilation it looks like t

Re: [R-pkg-devel] help fixing CRAN package sos-now fails on GitHub

Hi, Uwe et al.: The sos vignette sos.Rnw now fails on GitHub, complaining of a LaTeX error in "{\tt pspline_ checker}". I don't find it in the code for sos.Rnw. It may be triggered by a response to an internet search that's different from before. https://github.com/sbgraves237/sos

Re: [R-pkg-devel] help fixing CRAN package sos

Hi, Uwe et al.: Uwe suggests I postprocess output with gsub("_", "_", output). It's not clear to me where I should apply this. The "WARN" flags the sos vignette sos.Rnw, but the offending code refers to pspline_checker, which is not in the version of the vignette available on CRAN.[1]

Re: [R-pkg-devel] help fixing CRAN package sos

On 16.05.2023 14:02, Spencer Graves wrote: On 5/16/23 6:06 AM, Uwe Ligges wrote: On 16.05.2023 01:46, Spencer Graves wrote: Hello, All:    The sos package is failing some CRAN checks, complaining:[1] LaTeX errors: ! Missing $ inserted. $ l.303 {\tt pspline_

Re: [R-pkg-devel] help fixing CRAN package sos

On 5/16/23 6:06 AM, Uwe Ligges wrote: On 16.05.2023 01:46, Spencer Graves wrote: Hello, All:    The sos package is failing some CRAN checks, complaining:[1] LaTeX errors: ! Missing $ inserted. $ l.303 {\tt pspline_     checker} in the I can only

Re: [R-pkg-devel] help fixing CRAN package sos

On 16.05.2023 01:46, Spencer Graves wrote: Hello, All:   The sos package is failing some CRAN checks, complaining:[1] LaTeX errors: ! Missing $ inserted.     $ l.303 {\tt pspline_    checker} in the I can only guess this is part of the response you go

Re: [R-pkg-devel] help fixing CRAN package sos

On Mon, 15 May 2023 18:46:00 -0500 Spencer Graves wrote: > I can NOT replicate these locally nor with GitHub action, and I > failed to find 'psp' in 'sos.Rnw'.[2] This raises two issue: > > > OBVIOUS: What can I do to fix this error, or at least to understand > it better? How does the outpu

[R-pkg-devel] help fixing CRAN package sos

Hello, All: The sos package is failing some CRAN checks, complaining:[1] LaTeX errors: ! Missing $ inserted. $ l.303 {\tt pspline_ checker} in the ! Emergency stop. $ l.303 {\tt pspline_ checker} in the ! ==> Fat

Re: [R-pkg-devel] Help with CRAN-only Windows-only package build error: System.Rd not found

This was a temporary hicc up on the Windows machine, all check should have been triggered again. Best, Uwe Ligges On 31.01.2023 16:02, Mike Blazanin wrote: Hi all, trying to troubleshoot my way through my first CRAN package submission. I've addressed all the other issues so far (much thanks t

[R-pkg-devel] Help with CRAN-only Windows-only package build error: System.Rd not found

Hi all, trying to troubleshoot my way through my first CRAN package submission. I've addressed all the other issues so far (much thanks to Uwe from CRAN for that). In the second-to-last version I submitted via devtools::release(), it raised 1 WARNING on both Windows and Debian: * checking sizes of

Re: [R-pkg-devel] Help with fixing problems for new R package

On 19.12.2022 22:45, Anna Carolina Resende wrote: Hello, I'm running test to check if my package is working properly, and for Fedora, Windows and Ubuntu I get the following note: * checking CRAN incoming feasibility ... [5s/25s] NOTE Maintainer: ‘Anna Carolina Resende ’ I read online that i

Re: [R-pkg-devel] Help with fixing problems for new R package

В Tue, 20 Dec 2022 10:45:38 +1300 Anna Carolina Resende пишет: > * checking CRAN incoming feasibility ... [5s/25s] NOTE > Maintainer: ‘Anna Carolina Resende ’ > > I read online that it's a note for CRAN so they can check that the > maintainer made changes, could you confirm that that is the case

[R-pkg-devel] Help with fixing problems for new R package

Hello, I'm running test to check if my package is working properly, and for Fedora, Windows and Ubuntu I get the following note: * checking CRAN incoming feasibility ... [5s/25s] NOTE Maintainer: ‘Anna Carolina Resende ’ I read online that it's a note for CRAN so they can check that the maintain

Re: [R-pkg-devel] Help - Shiny app on CRAN

Thank you. On Tue, Oct 18, 2022 at 4:28 PM Uwe Ligges wrote: > See my response to the list. > > Best, > Uwe Ligges > > > On 18.10.2022 14:11, Jahajeeah, Havisha wrote: > > Hello, > > > > Grateful if you could please help with the following comments: > > > > Please add small executable examples i

Re: [R-pkg-devel] Help - Shiny app on CRAN

See my response to the list. Best, Uwe Ligges On 18.10.2022 14:11, Jahajeeah, Havisha wrote: Hello, Grateful if you could please help with the following comments: Please add small executable examples in your Rd-files to illustrate the use of the exported function but also enable automatic te

Re: [R-pkg-devel] Help - Shiny app on CRAN

Hello, Grateful if you could please help with the following comments: Please add small executable examples in your Rd-files to illustrate the use of the exported function but also enable automatic testing. The greymodels package loads data from spreadsheets and each model accepts a set of data a

Re: [R-pkg-devel] Help - Shiny app on CRAN

Hello, Thank you for the clarification. Havisha On Thu, 29 Sep 2022 at 01:24, Henrik Bengtsson wrote: > Hi, > > it's not just you; the win-builder server is down for all of us (e.g. > https://downforeveryoneorjustme.com/win-builder.r-project.org?proto=https > ). > Uwe Ligges, who maintains thi

Re: [R-pkg-devel] Help - Shiny app on CRAN

Hi, it's not just you; the win-builder server is down for all of us (e.g. https://downforeveryoneorjustme.com/win-builder.r-project.org?proto=https). Uwe Ligges, who maintains this, mentioned (in another thread somewhere) that there were networking issues at his university that are being worked on

Re: [R-pkg-devel] Help - Shiny app on CRAN

Dear team, I am having trouble submitting my package to CRAN because the link https://win-builder.r-project.org/ is not accessible. Please advise. Thank you Havisha Jahajeeah On Mon, Sep 26, 2022 at 11:17 PM Ivan Krylov wrote: > It might be easier to help you if you show us your package by >

Re: [R-pkg-devel] Help - Shiny app on CRAN

It might be easier to help you if you show us your package by publishing the source code somewhere. On Mon, 26 Sep 2022 22:22:48 +0400 "Jahajeeah, Havisha" wrote: > CIvalue2: no visible global function definition for 'qt' > andgm11: no visible binding for global variable 'ParticleSwarm' > andgm1

Re: [R-pkg-devel] Help - Shiny app on CRAN

Hello, are you aware of https://win-builder.r-project.org/? It'll allow you to validate that your package passes all the requirements before submitting it to CRAN. My $.02 /Henrik On Mon, Sep 26, 2022 at 11:23 AM Jahajeeah, Havisha wrote: > > Dear team, > > My second attempt at submitting the

Re: [R-pkg-devel] Help - Shiny app on CRAN

Dear team, My second attempt at submitting the package GreymodelsPackage_1.0.tar.gz to CRAN. Grateful if you could please assist me with the following issues: CIvalue2: no visible global function definition for 'qt' andgm11: no visible binding for global variable 'ParticleSwarm' andgm11: no visi

Re: [R-pkg-devel] Help - Shiny app on CRAN

On 26.09.2022 17:14, Jahajeeah, Havisha wrote: Dear team, I have submitted the package GreymodelsPackage_1.0.tar.gz to CRAN and it's a shiny app. However, I received the following * using log directory 'd:/RCompile/CRANincoming/R-devel/GreymodelsPackage.Rcheck' * using R Under development

Re: [R-pkg-devel] Help - Shiny app on CRAN

В Mon, 26 Sep 2022 19:14:04 +0400 "Jahajeeah, Havisha" пишет: > * checking extension type ... ERROR > Extensions with Type 'Shiny application' cannot be checked. Since you're writing a package, you can either specify Type: Package in the DESCRIPTION file, or omit the field entirely: https://cran

[R-pkg-devel] Help - Shiny app on CRAN

Dear team, I have submitted the package GreymodelsPackage_1.0.tar.gz to CRAN and it's a shiny app. However, I received the following * using log directory 'd:/RCompile/CRANincoming/R-devel/GreymodelsPackage.Rcheck' * using R Under development (unstable) (2022-09-25 r82916 ucrt) * using platform

Re: [R-pkg-devel] help/advice on debugging

Comments in-line: > Date: Sat, 9 Jul 2022 16:29:57 -0400 > From: Ben Bolker > To: R Package Development > Subject: [R-pkg-devel] help/advice on debugging > Message-ID: > Content-Type: text/plain; charset="utf-8"; Format="flowed" > >For some stu

Re: [R-pkg-devel] help interpreting a response from CRAN

On 23.11.2020 04:13, Roy Mendelssohn - NOAA Federal wrote: I have found win-builder timings come close, but only close. My experience is that the CRAN timings were uniformly slower than those on win-builder. But I also find that I can get quite significant differences between win-builder

Re: [R-pkg-devel] help interpreting a response from CRAN

I have found win-builder timings come close, but only close. My experience is that the CRAN timings were uniformly slower than those on win-builder. But I also find that I can get quite significant differences between win-builder-release and win-builder-devel. So I also take the slowest that

Re: [R-pkg-devel] help interpreting a response from CRAN

And one more (last for a while): presumably there is no way to check CRAN windows timing without submitting to CRAN ... ? (I will obviously do my best by doing arithmetic on the tests that I set to be skipped, but it would be nice to be able to double-check without wasting everyone's time ..

Re: [R-pkg-devel] help interpreting a response from CRAN

Thanks all for the help. The reward (as usual) is another dumb question. If I add up the elapsed times listed in https://win-builder.r-project.org/incoming_pretest/lme4_1.1-26_20201122_184744/Windows/examples_and_tests/examples_x64/lme4-Ex.timings I get 21.43 seconds. But the output in

Re: [R-pkg-devel] help interpreting a response from CRAN

Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 min, so the overall check time exceeds 10 min. So one can follow Dirk's advise. As a general remark for others who will read this in the future: tests should test the software, but it is generally not important to hav

Re: [R-pkg-devel] help interpreting a response from CRAN

On 22 November 2020 at 13:44, Ben Bolker wrote: |My current guess is that the problem is with the too-long check time on Windows (NOTE: "Overall checktime 18 min > 10 min") Yes. | I guess I have to get busy setting more tests and examples to skip-on-CRAN (kind of a pain as there's no l

[R-pkg-devel] help interpreting a response from CRAN

My submission from auto-check, and I'm not sure why because Windows and Debian checks both list "OK" and there are no unresolved problems on the CRAN status ... My current guess is that the problem is with the too-long check time on Windows (NOTE: "Overall checktime 18 min > 10 min") I gu

Re: [R-pkg-devel] Help in getting past CRAN submission rejections

Just to close the loop on this: the drat suggestion for both packages and also moving things to enhances worked. I could do this also for Gurobi because it is LGPL'd. Thanks Toby and Dirk (for drat). -Naras On 9/9/20 5:16 PM, Balasubramanian Narasimhan wrote: Thanks Toby, so there is hope.  T

Re: [R-pkg-devel] Help in getting past CRAN submission rejections

Thanks Toby, so there is hope.  The drat suggestion for rcbc is worth a try, gurobi is noted as you recommend. -Naras On 9/9/20 4:38 PM, Toby Hocking wrote: > Hi Naras > I had a similar issue recently with > https://cloud.r-project.org/web/packages/nc/ --- it Suggests: re2r > which is a packag

Re: [R-pkg-devel] Help in getting past CRAN submission rejections

Hi Naras I had a similar issue recently with https://cloud.r-project.org/web/packages/nc/ --- it Suggests: re2r which is a package that is no longer on CRAN, but available on github. To solve the issue I just copied the re2r into a drat repo, which is a CRAN-like repository hosted on github. More i

[R-pkg-devel] Help in getting past CRAN submission rejections

We've been struggling to get past CRAN's rejections for a new upload of CVXR.  The new version makes essentially one change to the existing version on CRAN: the addition of a DOI to an article to appear in JSS.  We realize that CRAN may tighten policies in the meantime forcing some changes to b

Re: [R-pkg-devel] Help with a note

Thank you for the helpful replies! I got it now, I overlooked the return on the ifelse() before. Thanks a lot again! - Anirban On Thu, Sep 3, 2020, 11:18 AM Anirban wrote: > Hi, I've one note in my package which I can't seem to resolve while > submitting to CRAN: > > New submission > > Flavo

Re: [R-pkg-devel] Help with a note

behalf of Anirban Sent: Thursday, September 3, 2020 12:48 AM To: r-package-devel@r-project.org Subject: [R-pkg-devel] Help with a note Caution: This message was sent from outside the University of Manitoba. *

Re: [R-pkg-devel] Help with a note

`return()` is a function in R, so `return` does nothing. You probably want `return()`. Here: https://github.com/Anirban166/testComplexity/blob/c991c31e5250bcaf804c3ad781fbc126c6a17e57/R/asymptoticMemoryUsage.R#L22 https://github.com/Anirban166/testComplexity/blob/master/R/asymptoticTimings.R#L22

[R-pkg-devel] Help with a note

Hi, I've one note in my package which I can't seem to resolve while submitting to CRAN: New submission Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 Check: R code for possible problems, Result: NOTE Possibly missing '()' after 'return' in the following functions: 'a

Re: [R-pkg-devel] help in identifying a segfault (rhub)

Is this reproducible on R-hub? Do you see it with the other R-devel containers as well? Some things to try: Try running address sanitizer on your package to see if it can find any memory errors. You can do this on R-hub as well, if you cannot do it on your machine. Try downloading the https://hu

[R-pkg-devel] help in identifying a segfault (rhub)

Hi all, I am reaching out to seeking help in debugging my package. The package has been already on CRAN for some time, updated twice. Also, I have been checking the package regularly on rhub, since my last submission to CRAN, with no errors. However, recently last checks on rhub end with a segm

Re: [R-pkg-devel] Help Debugging Debian Error

Thanks for the tips. It appears the error is indeed related to the matchingMarkets package, but specifically an issue with rJava configuration. Now I get the following (see https://artifacts.r-hub.io/PAutilities_1.0.0.tar.gz-54a555386e924de6a53385479a1e199f/PAutilities.Rcheck/00check.log ): VALIDA

Re: [R-pkg-devel] Help Debugging Debian Error

You don't need to move the files around, though, just use a more verbose testthat reporter, e.g. in testthat.R use test_check("PAutilities", reporter = "summary") and then at least you'll know where it crashes. But to fix this, you'll probably need to debug it locally. You can do that in Docker i

Re: [R-pkg-devel] Help Debugging Debian Error

On Fri, 15 May 2020 03:50:12 -0400 Paul Hibbing wrote: > Complete output: > > library(testthat) > > library(PAutilities) > > > > test_check("PAutilities") It seems to me that the R process crashes while running your tests, but since testthat::test_check captures everything to summarise

Re: [R-pkg-devel] Help Debugging Debian Error

Removing the startup message did not resolve the issue. Now I have just: * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(PAutilities) > > test_check("PAutilities") See https://artifacts.r-hu

Re: [R-pkg-devel] Help Debugging Debian Error

On 15 May 2020 at 02:30, Gábor Csárdi wrote: | It is unlikely that this is an R-hub issue because the first link is | CRAN's machine, and the same error happens there. My bad, sorry -- I read the original email(s) wrong. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: [R-pkg-devel] Help Debugging Debian Error

Ah, I hadn't considered that the startup message could be the problem - I thought the point of startup messages was to be distinct from errors and warnings, so I wouldn't have expected that to trip up R CMD Check. I assumed the failure was occurring somewhere inside the actual code for my unit test

Re: [R-pkg-devel] Help Debugging Debian Error

Apparently, this is not a warning, but the package itself is printing it as a startup message: https://github.com/cran/PAutilities/blob/ada73d8d44177c12867cc385cdca0054885ddae3/R/zzz.R#L5 Gabor On Fri, May 15, 2020 at 2:30 AM Gábor Csárdi wrote: > > It is unlikely that this is an R-hub issue bec

Re: [R-pkg-devel] Help Debugging Debian Error

It is unlikely that this is an R-hub issue because the first link is CRAN's machine, and the same error happens there. I can reproduce it on macOS: git clone https://github.com/paulhibbing/PAutilities R CMD INSTALL PAutilities R -q -e 'packageDescription("PAutilities")$Built' #> > packageDescrip

Re: [R-pkg-devel] Help Debugging Debian Error

On 14 May 2020 at 11:41, Paul Hibbing wrote: | * Here is the CRAN check (devel version 2020-05-13): | | https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/PAutilities-00check.html | | * Here is the successful R-hub check (devel version 2020-05-10): | | https://artifacts.

Re: [R-pkg-devel] Help Debugging Debian Error

* Here is the CRAN check (devel version 2020-05-13): https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/PAutilities-00check.html * Here is the successful R-hub check (devel version 2020-05-10): https://artifacts.r-hub.io/PAutilities_1.0.0.tar.gz-43f919fd5595416799d74bfb312fd

[R-pkg-devel] Help Debugging Debian Error

Hi all, At some point (I believe within the last week or so), my package `PAutilities` has developed the following error for r-devel-linux-x86_64-debian-gcc: * checking tests ... [3s/3s] ERROR Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > libr

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