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> 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
