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

Thu Feb 29 01:39:18 CET 2024

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.Ruff using 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.gabor using gmail.com<mailto:csardi.gabor using gmail.com>>
Gesendet: Mittwoch, 28. Februar 2024 19:32:40
An: Martin Morgan
Cc: Steve Lianoglou; Ruff, Sergej; bioc-devel using r-project.org<mailto:bioc-devel using 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.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

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