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Remove lookup-refs, vbump dependencies + add Remotes #403

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merged 4 commits into from
Feb 4, 2025
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@m7pr m7pr commented Jan 30, 2025

Part of https://github.com/insightsengineering/coredev-tasks/issues/609

From now on, we will provide development dependencies in

Remotes: repo/project@branch

format, so it's explicitly visible in the DESCRIPTION file and can be handled by pak::install, renv::install and remotes::install.

With development dependencies specified in CJ Pipelines configuration, this connection was hidden, and it was hard to install the package from the main branch (or any other branch) locally from user's machine.

@m7pr m7pr added the core label Jan 30, 2025
@m7pr m7pr requested review from pawelru and llrs-roche January 30, 2025 12:33
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github-actions bot commented Jan 30, 2025

Unit Tests Summary

 1 files  15 suites   8s ⏱️
56 tests 43 ✅ 13 💤 0 ❌
94 runs  81 ✅ 13 💤 0 ❌

Results for commit 95aca7d.

♻️ This comment has been updated with latest results.

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I could install the package without further problems from this branch using only remotes (to test the new Remotes field). The logs show it picked packages from github.

But somehow it installed packages from Bioconductor 3.18. While current version is 3.20 (just noting this but I think it is unrelated to the PR but might confuse or cause problems for the users):

remotes::install_github("insightsengineering/teal.modules.hermes@remove_lookups")
...
https://bioconductor.org/packages/3.18/bioc/src/...'
...
Downloading GitHub repo insightsengineering/teal@HEAD
....
Done

@llrs-roche llrs-roche self-assigned this Jan 31, 2025
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m7pr commented Jan 31, 2025

@llrs-roche what is your version of R locally? R local version is tied to Bioconductor version. I think if you R is old, then you'll pick up from the old Bioconductor during the installation?

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llrs-roche commented Jan 31, 2025

Yes, but my R version is 4.4.2 which matches where Bioconductor 3.20 is meant to be used. It could be a problem on my local setup too

Signed-off-by: Marcin <[email protected]>
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m7pr commented Feb 3, 2025

cc @pawelru @llrs-roche I vbumped teal.widgets to it's version released on CRAN

@m7pr m7pr enabled auto-merge (squash) February 4, 2025 13:23
@m7pr m7pr merged commit 3206e9c into main Feb 4, 2025
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@m7pr m7pr deleted the remove_lookups branch February 4, 2025 13:33
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