Skip to contents

Install packages

Source: vignettes/install_packages.Rmd
install_packages.Rmd

To be able to test your package as a developer you can install your package using the MolgenisArmadillo. There are a few preconditions in other to use the install_packages function.

  • Make sure you have the superuser role.
  • The Armadillo needs to run in development mode

Login

You first need to login to the Armadillo (as superuser)

armadillo.login("https://armadillo.dev.molgenis.org",
      "https://armadillo-minio.dev.molgenis.org")
#> Error in armadillo.login("https://armadillo.dev.molgenis.org", "https://armadillo-minio.dev.molgenis.org"): unused argument ("https://armadillo-minio.dev.molgenis.org")

Install packages

If you want to install a package on the Armadillo Rserver you can execute the following endpoint. The selected profile is always default if none is specified.

armadillo.install_packages("data/packages/MolgenisArmadillo_1.1.0.9000.tar.gz")
#> Error in httr::upload_file(path): file.exists(path) is not TRUE

In order to install the packages on a specific profile you can specify the profile.

armadillo.install_packages("data/packages/MolgenisArmadillo_1.1.0.9000.tar.gz", profile = "exposome")

You can install multiple packages as well by specifying a vector

armadillo.install_packages(c("data/packages/MolgenisArmadillo_1.1.0.9000.tar.gz", "data/packages/dsBase_6.1.0.9000.tar.gz"))

Whitelist packages

To be able to use new packages in the Armadillo you need to add them to the whitelist. You can do this by executing the following method.

armadillo.whitelist_packages("MolgenisArmadillo")
#> Error in armadillo.whitelist_packages("MolgenisArmadillo"): could not find function "armadillo.whitelist_packages"

You are able to whilist mulitple packages as well using the following line:

armadillo.whitelist_packages(c("MolgenisArmadillo", "dsBase"))
#> Error in armadillo.whitelist_packages(c("MolgenisArmadillo", "dsBase")): could not find function "armadillo.whitelist_packages"