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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel