[Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor depenencies and cant be installed.

[Gábor Csárdi]

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.xyz using 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-bounces using r-project.org> on behalf of Steve Lianoglou <slianoglou using gmail.com>
> Date: Wednesday, February 28, 2024 at 10:46 AM
> To: Ruff, Sergej <Sergej.Ruff using tiho-hannover.de>
> Cc: bioc-devel using r-project.org <bioc-devel using 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.Ruff using 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 <stvjc using channing.harvard.edu>
> > Gesendet: Mittwoch, 28. Februar 2024 15:20:49
> > An: Ruff, Sergej
> > Cc: bioc-devel using 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.Ruff using tiho-hannover.de
> > <mailto:Sergej.Ruff using 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 using r-project.org<mailto:Bioc-devel using 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 using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel