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Enable package installation from GitHub, Bioconductor and local directory. #509

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merged 6 commits into from
Nov 13, 2023

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@jakubnowicki jakubnowicki commented Nov 8, 2023

Changes

Closes #508

How to test

In a rhino project:

  1. Try to install a package from GitHub (e.g. rhino::pkg_install("Appsilon/shiny.i18n")).
  2. Try to install multiple packages from GitHub in one step (e.g. `rhino::pkg_install(c("Appsilon/shiny.i18n", "Appsilon/data.validator"))).
  3. Try to install a specific version of a package (e.g. `rhino::pkg_install("shiny.router@0.3.0"))
  4. Try to install a package from Bioconductor (e.g. `rhino::pkg_install("bioc::Biobase"))
  5. Try to remove packages.

For each step, verify if the packages were installed, added to renv.lock, and added to dependencies.R.

@jakubnowicki jakubnowicki changed the title Enable package installation from GitHub, Bioconductor and local. Enable package installation from GitHub, Bioconductor and local directory. Nov 8, 2023
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codecov-commenter commented Nov 9, 2023

Codecov Report

Merging #509 (0cab5a8) into main (b032a3c) will increase coverage by 1.79%.
The diff coverage is 53.84%.

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

@@            Coverage Diff             @@
##             main     #509      +/-   ##
==========================================
+ Coverage   16.03%   17.82%   +1.79%     
==========================================
  Files           9        9              
  Lines         393      404      +11     
==========================================
+ Hits           63       72       +9     
- Misses        330      332       +2     
Files Coverage Δ
R/dependencies.R 26.47% <53.84%> (+26.47%) ⬆️

@jakubnowicki jakubnowicki force-pushed the fix/installation-from-github branch from 3ec2c2a to 458c725 Compare November 9, 2023 09:28
@jakubnowicki jakubnowicki requested a review from vibalre November 9, 2023 13:55
@jakubnowicki jakubnowicki marked this pull request as ready for review November 9, 2023 13:56
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Performed all the tests.
I can confirm that pkg_install() adds correct packages in dependencies.R and renv.lock for packages from different sources, e.g. github, Bioconductor, and local.
pkg_remove() also removes the packages accordingly.

@jakubnowicki jakubnowicki merged commit 091f967 into main Nov 13, 2023
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@jakubnowicki jakubnowicki deleted the fix/installation-from-github branch November 13, 2023 07:30
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Cannot install more than one github package with rhino::pkg_install
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