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

[Ruff, Sergej]

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

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