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Hi, I agree that the email handshake is the best approach (and very reasonable to expect it). I thought that maybe in cases like this there was a waiting period and/or multiple attempts to contact the maintainer and someone...

Dear Bioconductor team, Bioconductor packages can be installed via install.packages when they are a dependency of another package if there is in the DESCRIPTION file a "biocViews:" section (see https://github.com/r-lib/devtools/issues/700# issuecomment-235127291...

Dear list, I'm trying to get some details from repositories with available.packages. However, despite being included on the DESCRIPTION files they are not available. ap <- utils::available.packages(fields = "Additional_repositories", filters = c("CRAN", "duplicates"), ignore_repo_cache...

Hi Tim, I think there is a mentorship program for cases like this (I am not sure if it still accepts mentees): https://www.bioconductor.org/developers/new-developer-program/ I also recommend the book the Bioconductor community wrote to...

Hi Stefano, About 1) you can document internal functions but remove them from the index if you use #' @keywords internal tag. See the vignette of roxygen2 https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html under Other tags...

Hi, I am trying to push some changes from my machine to the svn repository of Bioconductor. Since the start of the package I've been using git, so I have prior history before submitting to Bioconductor. And I made...

Hi Xin Yu, You seem to be using the symbol ? somewhere on the documentation, looking at the repository on GitHub I only found that symbol on two comments: https://github.com/whirlsyu/EnMCB/blob/6124a5a237a94d42d935720dc1bf8a44b11f6966/R/metricMCB.R#L239 https...

Hi Kristian, I think the threshold was decided because it matches CRAN's, but it could be modified. But let's check the numbers regarding this threshold: Approximately 20% of Bioconductor packages are affected with this threshold (see code below...

Dear Duncan, Thank you for your answer. I checked again and made a mock package that removes a file with .onDetach. The file was not removed upon uninstalling the package. Llu?s On Thu, 2 Jan 2025 at 17:23...

I have recently faced a similar warning. This is when a link to a help page of another package is broken (there is not such help page). Although those could be false positives: mclapply help page does exists in parallel...

Dear Lori, In light of the time burden that the Bioconductor core team has: Does this project for "a maintainer validity check " require specific permissions or internal expertise? Could someone from the community contribute or help to get it done...

Some people is lost even when and how many updates are and differences between different packages. See this question for instance ( https://www.biostars.org/p/287871/) Compared to CRAN or PyPi, which don't have release cycles, Bioconductor workflow...

Dear R-devel, I read with interest the recent blog post on how R will have parallel downloads, on blog.r-project.org (https://blog.r-project.org/2024/12/02/faster-downloads/index.html). Thanks Tomas! The blog mentions...

Dear Scott, I'll reply within the content: On Tue, 27 May 2025 at 21:12, Scott McLoud <mclouds at ohsu.edu> wrote: > Hello Lluis, > > Dear Llu?s, > > > > *How is this specific palette different from other palettes existing on > CRAN...

Dear all, Short problem: I am a trying to sync my new package BioCor git repository with the Bioconductor svn repository. But I am failing when I do git svn dcommit. Long history of the problem I did some changes...

Adding a different project to this discussion: Recently at the R repository working group a project to provide them for multiple distributions and toolchain was presented. See the documentation about what do they (Patrick Schratz) share: https://docs.r-package...

Dear all, I've recently changed my Mac and I am trying to reinstall my commonly used R-packages. I'm having troubles with a package called LaplacesDemon. This package is no more in the CRAN list and the developers...

Hi, How are the datasets loaded in the first place? If it uses readRDS you set the name. If you use load or data it returns the name of the objects loaded: (data("datasets")) ## "obj1", "obj2", "obj3", "obj4" If there...

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...

Thanks Lori, I see this is handled differently (not sure how frequently). I hope that developers have enough time so that users aren't impacted (much). On Wed, 2 Apr 2025 at 13:20, Kern, Lori <Lori.Shepherd at roswellpark...