I believe that devtools just uses remotes under the hood, so it should work.
Shian
On 29 Feb 2024, at 11:42, Ruff, Sergej wrote:
Does it apply only to the remotes package or also to devtools::install_git
function?
Sergej
Von: Shian Su
Gesendet: Donnerstag,
Does it apply only to the remotes package or also to devtools::install_git
function?
Sergej
Von: Shian Su
Gesendet: Donnerstag, 29. Februar 2024 01:39:18
An: Ruff, Sergej
Cc: bioc-devel@r-project.org
Betreff: [EXTERN] Re: [Bioc-devel] [EXTERN] Re: R package on
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
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
Thank you, solved. Another reminder that Docker containers don't have
access to the ~/.ssh folder. Pushing from the local terminal after
debugging in a container helps.
Thanks,
Mikhail
On Wed, Feb 28, 2024 at 8:42 AM Kern, Lori
wrote:
> Everything looks correct on our configuration. You might
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 wrote:
>
> Actually BiocManager delegates to
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("/")
or
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
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
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
wrote:
> Hello,
>
>
> I have an R package on Github that uses Bioconductor dependencies:
>
>
>
Bioconductor packages need to be installed with BiocManager. If you do
BiocManager::install("klausjung-hannover/bootGSEA") That should also find
Bioconductor package dependencies.
Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of
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
Everything looks correct on our configuration. You might need to add a new ssh
key to your BiocCredentials account. Or since there are multiple keys on your
account already, explicitly state the correct ssh key you would like to use .
Lori Shepherd - Kern
Bioconductor Core Team
Roswell
I'm trying to push fixes for
https://master.bioconductor.org/checkResults/3.19/bioc-LATEST/TADCompare/nebbiolo1-buildsrc.html.
git remote -v
biocg...@git.bioconductor.org:packages/TADCompare.git (fetch)
biocg...@git.bioconductor.org:packages/TADCompare.git (push)
E.g., for git fetch
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