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

[Martin Morgan]

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]]
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> The information in this e-mail is intended only for th...{{dropped:22}}

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