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 <st...@channing.harvard.edu>
Gesendet: Mittwoch, 28. Februar 2024 15:20:49
An: Ruff, Sergej
Cc: bioc-devel@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.r...@tiho-hannover.de<mailto:sergej.r...@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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