issue when setting up and running the example data about armor

[sorjuela]

Hi @pikkaa215,

Yes, we also see this same issue in the latest GitHub Action only for ubuntu https://github.com/csoneson/ARMOR/actions/runs/755054578

The problem seems to be in the installation of RSQLite, which is also reported as an issue in their repo: r-dbi/RSQLite#367

We are trying to figure out a solution. Thanks for reporting :)

Stephany

[fhaertner]

Hey,

in the meantime, until the issue is resolved, you can install an older version of RSQLite. In the 'scripts/install_pkgs.R' file just add the following lines in the usePackage() function before the other packages are installedd with BiocManager:

`

Install the other packages

install.packages("remotes", repos = "http://cran.rstudio.com/",
                     lib = .libPaths()[1])
remotes::install_version("RSQLite", version = "2.2.5", dependencies = TRUE,
					repos = "http://cran.rstudio.com/", lib = .libPaths()[1],
					Ncpus = as.integer(ncores))

isInstalled <- pkgs %in% installed.packages(lib.loc = .libPaths()[1])[, 1]
BiocManager::install(pkgs[!isInstalled],
                     update = FALSE, dependencies = TRUE,
                     lib = .libPaths()[1], Ncpus = as.integer(ncores))`

You can also have a look here:
https://stackoverflow.com/questions/67279457/error-with-r-package-biomart-and-this-dependency-rsqlite

[csoneson]

Thanks, and sorry for the lack of updates here, we're still working on clearing our Ubuntu/conda GitHub Actions run. Actually I had hoped that RSQLite version 2.2.7 would solve the issues that were present in version 2.2.6 (and thus would not require manually installing version 2.2.5)... 🤔

[sorjuela]

Hi,

We have a workaround for this issue in the fixbuilderror branch: https://github.com/csoneson/ARMOR/tree/fixbuilderror which should work now for ubuntu machines. Please let us know if this solves your issue, or if you need help using this branch.

[pikkaa215]

Yes. That solved my problem. Thanks!