Re: [R-pkg-devel] State of the art for UBSAN testing

2024-05-16 Thread Ralf Stubner
Thanks Gábor! If one checks the output, one can indeed find the UBSAN error. Problem solved! Ralf On Thu, May 16, 2024 at 8:40 PM Gábor Csárdi wrote: > > R-hub v2 has UBSAN testing, the clang-asan image also has UBSAN. [1] > > With the glitch that UBSAN errors do not fail the build because of a

Re: [R-pkg-devel] State of the art for UBSAN testing

2024-05-16 Thread Gábor Csárdi
R-hub v2 has UBSAN testing, the clang-asan image also has UBSAN. [1] With the glitch that UBSAN errors do not fail the build because of a bug [2], so you'll need to look at the results even if the build has passed. Gabor [1] https://r-hub.github.io/containers/ [2] https://github.com/r-hub/action

[R-pkg-devel] State of the art for UBSAN testing

2024-05-16 Thread Ralf Stubner
Dear all, I have been asked to fix a UBSAN error in my dqrng package. The error itself and the necessary fix are quite straight forward. However, I want to make 100% sure that I am really fixing the error. In the past I had used rhub for tasks like that. But it seems like the new rhub v2 offers on

Re: [R-pkg-devel] Altrep header, MSVC, and STRUCT_SUBTYPES macro

2024-05-16 Thread David Cortes
Thanks for the hints. Unfortunately, after some further testing, it seems this was just a matter of getting lucky - using the alternative non-STRUCT_SUBTYPES def. of Altrep still leads to memory corruptions and crashes, just at different points than when using the STRUCT_SUBTYPES definition. Sorr

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Ivan Krylov via R-package-devel
В Thu, 16 May 2024 16:01:45 + Zeinab Mashreghi пишет: > checking HTML version of manual ... NOTE > Found the following HTML validation problems: > All.data.html:4:1 (All.data.Rd:10): Warning: inserting "type" > attribute > All.data.html:12:1 (All.data.Rd:10): Warning:

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Michael Dewey
Dear Zeinab Perhaps the insights in https://github.com/tidymodels/infer/issues/455 will help you especially if you are using roxygen2 Michael On 16/05/2024 17:01, Zeinab Mashreghi wrote: Hi, Thank you very much for your helpful suggestion! Following your advice, I revisited the package and

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Goldfeld, Keith via R-package-devel
Zeinab I have found that setting this system value to FALSE eliminates the issue: Sys.setenv("_R_CHECK_RD_VALIDATE_RD2HTML_" = FALSE) - Keith On 5/16/24, 12:02 PM, "R-package-devel on behalf of Zeinab Mashreghi" mailto:r-package-devel-boun...@r-project.org> on behalf of z.mashre...@uwinnipeg

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Zeinab Mashreghi
Hi, Thank you very much for your helpful suggestion! Following your advice, I revisited the package and made necessary adjustments to the description file. However, it appears that there are now some issues with HTML validation in the .Rd files. Here's the relevant excerpt, and I've attached th

Re: [R-pkg-devel] Altrep header, MSVC, and STRUCT_SUBTYPES macro

2024-05-16 Thread Ivan Krylov via R-package-devel
В Wed, 15 May 2024 18:54:37 +0200 David Cortes пишет: > The code compiles without errors under MSVC, but executing code that > involves returning Altrep objects leads to segfaults and memory > corruptions, even though it works fine under other compilers. > > I see the R Altrep header has this se

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

2024-05-16 Thread Dirk Eddelbuettel
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] CRAN packages dependency on bioconductor packages

2024-05-16 Thread Sebastian Meyer
Am 16.05.24 um 11:34 schrieb Duncan Murdoch: On 2024-05-16 4:15 a.m., Sebastian Meyer wrote: Am 15.05.24 um 00:09 schrieb Lluís Revilla: Hi Junhui, There is a separate log for checking if your package works without suggested packages: in the StepReg results The noSuggests title leads to: https

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

2024-05-16 Thread Uwe Ligges
On 16.05.2024 10:15, Sebastian Meyer wrote: Am 15.05.24 um 00:09 schrieb Lluís Revilla: Hi Junhui, There is a separate log for checking if your package works without suggested packages: in the StepReg results The noSuggests title leads to: https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg

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

2024-05-16 Thread Duncan Murdoch
On 2024-05-16 4:15 a.m., Sebastian Meyer wrote: Am 15.05.24 um 00:09 schrieb Lluís Revilla: Hi Junhui, There is a separate log for checking if your package works without suggested packages: in the StepReg results The noSuggests title leads to: https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepR

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Ivan Krylov via R-package-devel
Dear Zeinab, Welcome to R-package-devel! В Thu, 16 May 2024 03:22:56 + Zeinab Mashreghi пишет: > I recently submitted my R package to CRAN, and I received this note > from the CRAN teams: "checking CRAN incoming feasibility ... NOTE." Without a link to the full error log and, ideally, to t

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Michael Dewey
Dear Zeinab It would help if you gave us more information. What exactly was the NOTE which it gave you? Michael On 16/05/2024 04:22, Zeinab Mashreghi wrote: Hi, I hope this message finds you well. I recently submitted my R package to CRAN, and I received this note from the CRAN teams: "ch

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

2024-05-16 Thread Sebastian Meyer
Am 15.05.24 um 00:09 schrieb Lluís Revilla: Hi Junhui, There is a separate log for checking if your package works without suggested packages: in the StepReg results The noSuggests title leads to: https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out Where you can see that it fails if a user

[R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Zeinab Mashreghi
Hi, I hope this message finds you well. I recently submitted my R package to CRAN, and I received this note from the CRAN teams: "checking CRAN incoming feasibility ... NOTE." When I run R CMD check on my device, I do not encounter any issues, and I am unsure of the specific steps I need to ta