I believe that devtools just uses remotes under the hood, so it should work.
Shian On 29 Feb 2024, at 11:42, Ruff, Sergej <sergej.r...@tiho-hannover.de> wrote: Does it apply only to the remotes package or also to devtools::install_git function? Sergej ________________________________ Von: Shian Su <s...@wehi.edu.au> Gesendet: Donnerstag, 29. Februar 2024 01:39:18 An: Ruff, Sergej Cc: bioc-devel@r-project.org Betreff: [EXTERN] Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor depenencies and cant be installed. Sorry if this is spam, I think my last message got bounced because my mail client converted the GitHub link into a nice jpg. As you mentioned, you can just add biocViews: Software to your DESCRIPTION: https://github.com/r-lib/remotes/issues/477. If you need further explanation then the code is here: https://github.com/r-lib/remotes/blob/b9091cc471ea59471d10981330a868402e1b7bd9/install-github.R#L687-L694 Adding the field causes remotes to add BioC to the repo list when installing dependencies. I think it's worth doing so your users can use remotes if they want and not have to install/use other installation managers. Shian On 29 Feb 2024, at 11:24, Ruff, Sergej <sergej.r...@tiho-hannover.de> wrote: Thank you, I am still wondering why everyone on the internet mentions adding "biocView" to the DESCRIPTIOn-File. I couldn´t find a source for that but everyone on Biostart, Stackoverflow or any other forum keeps mentioning adding biocView. What does adding biocView do if anything? When should I add BiocView to the DESCRIPTION-File? ________________________________ Von: Gábor Csárdi <csardi.ga...@gmail.com<mailto:csardi.ga...@gmail.com>> Gesendet: Mittwoch, 28. Februar 2024 19:32:40 An: Martin Morgan Cc: Steve Lianoglou; Ruff, Sergej; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Betreff: Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor depenencies and cant be installed. While the remotes package still works, https://github.com/r-lib/pak is now a better alternative. It also comes with built-in Bioconductor support: pak::pkg_install("klausjung-hannover/bootGSEA") Gabor On Wed, Feb 28, 2024 at 4:52 PM Martin Morgan <mtmorgan....@gmail.com> wrote: Actually BiocManager delegates to remotes, and remotes is only a 'Suggests', so the user needs to have both remotes and BiocManager pkgs <- c("remotes", "BiocManager") pkgs <- setdiff(pkgs, rownames(installed.packages()) install.packages(pkgs) and then BiocManager::install("<github_id>/<pkg_name>") or remotes::install_github("<github_id>/<pkg_name>", repos = BiocManager::repositories()) The `setdiff()` isn't really quite good enough because it wouldn't install an updated version of BiocManager or remotes… From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Steve Lianoglou <slianog...@gmail.com> Date: Wednesday, February 28, 2024 at 10:46 AM To: Ruff, Sergej <sergej.r...@tiho-hannover.de> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor depenencies and cant be installed. As was already mentioned, your easiest path forward is to first ask your users to install the {BiocManager} package from CRAN, then use that to install your package. As it is, you are already asking your end users to install {devtools} (really {remotes}) first in order to install your package anyway, ie: Instead of asking them to do this: R> install.packages("remote") R> remotes::install_github("klausjung-hannover/bootGSEA") You should instead ask them to: R> install.packages("BiocManager") R> BiocManager::install("klausjung-hannover/bootGSEA") HTH, -steve On Feb 28, 2024 at 6:22:48 AM, "Ruff, Sergej" <sergej.r...@tiho-hannover.de> wrote: library(devtools) install_github("klausjung-hannover/bootGSEA") This command was used. Does it mean, I just need to provide instructions to use Biocmanager:install() for teh End-users? I want to make the installation process as smooth as possible. Meaning there should be no need to install something else ideally. ________________________________ Von: Vincent Carey <st...@channing.harvard.edu> Gesendet: Mittwoch, 28. Februar 2024 15:20:49 An: Ruff, Sergej Cc: bioc-devel@r-project.org Betreff: [EXTERN] Re: [Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed. What command was used? BiocManager::install should resolve the dependencies whereas straight use of install.packages would not. On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej <sergej.r...@tiho-hannover.de <mailto:sergej.r...@tiho-hannover.de>> wrote: Hello, I have an R package on Github that uses Bioconductor dependencies: https://github.com/klausjung-hannover/bootGSEA/blob/main/DESCRIPTION One reviewer recently sent me a message that he can´t install the package. Itried installing the package on a new device and got the following error: Installing package into ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is unspecified) ERROR: dependencies ‘topGO’, ‘ReactomePA’, ‘org.Mm.eg.db’ are not available for package ‘bootGSEA’ * removing ‘/home/sergejruff/R/x86_64-pc-linux-gnu-library/4.3/bootGSEA’ Warning messages: 1: packages ‘org.Mm.eg.db’, ‘ReactomePA’, ‘topGO’ are not available for this version of R Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 2: In i.p(...) : installation of package ‘/tmp/Rtmpnq6hVG/filed7528253e49/bootGSEA_1.0.tar.gz’ had non-zero exit status The CRAN dependencies install fine but Bioconductor packages refuse to install. Is there a way to solve the problem? I use the following command: library(devtools) install_github("klausjung-hannover/bootGSEA") I read that I should use biocView to the description file, but i couldn´t find a good source where someone explains why thats right or what biocView does? Could someone help me with my problem and explain if adding Biocview helps and more importantly why? Best, Sergej [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel The information in this e-mail is intended only for th...{{dropped:22}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
