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pharmaR / regulatory-r-repo-wg

Package consensus for regulated industries
https://pharmar.github.io/regulatory-r-repo-wg
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Repo acceptance testing #75

Open dgkf opened 4 months ago

dgkf commented 4 months ago

Depends on #74

Once we have an updated PACKAGES file, we can test to see how effective this solution is for pulling packages.

Note that this style of repository requires the use of pak (which I think has special handling for the downloadURL field. I expect that we can still use the available.packages filter functions, but we should test this out.

yannfeat commented 3 months ago

Created https://github.com/pharmaR/repos/blob/feature/riskscore/.Rprofile, following the example of https://github.com/dgkf/rvalhub-repo-filters-mvp/tree/main. I have added a function that mocks pak::pkg_install, as the original doesn't filter with available.packages, and it was mentioned that utils::install.packages doesn't currently work with our repo. I don't think my solution is 100% solid, as I am not sure that dependences are filtered as well, but this is a start. I have successfully tested this code by first creating a new folder in the repo for my OS that contained 2 packages, one with a risk score > 0.66, the other < 0.66. Then, after changing the risk threshold to 0.66, the following happens, which is the desired behavior: image The Coverage metric is absent from the PACKAGE file, which is why I had to simplify the filter created by @dgkf.

dgkf commented 3 months ago

@yannfeat - I think the pak::pkg_install might be unnecessary. The available_packages_filters option should limit the packages that are provided by available.packages. Assuming pak::pkg_install uses available.packages() internally, the filter will automatically be applied at that stage.

Mocking install.packages was only used in that demo to inject a oysteR scan of the packages to be installed for security vulnerabilities.

Otherwise, this looks great. I'm glad you had success using the filters with the repos solution!!

yannfeat commented 3 months ago

@yannfeat - I think the pak::pkg_install might be unnecessary. The available_packages_filters option should limit the packages that are provided by available.packages. Assuming pak::pkg_install uses available.packages() internally, the filter will automatically be applied at that stage.

Mocking install.packages was only used in that demo to inject a oysteR scan of the packages to be installed for security vulnerabilities.

Otherwise, this looks great. I'm glad you had success using the filters with the repos solution!!

@dgkf pak::pkg_install didn't filter automatically when I tried it. I don't think it is using install.packages.