It looks like a permission denied ERROR. Perhaps R was installed as root and
you do not have access to write to the default R install directory. You should
install to a directory you do have write permissions by setting a lib argument
or by setting the .libPaths()
Lori Shepherd - Kern
Hello,
I tried using biocManager:install but it doesnt seem to work. I am using Ubuntu
and I get the following error when installing
installing to /usr/lib/R/library/00LOCK-survival/00new/survival/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package
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
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
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