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Set R_BIOC_VERSION env variable used by pak #7

Merged
merged 2 commits into from
Oct 20, 2022
Merged

Set R_BIOC_VERSION env variable used by pak #7

merged 2 commits into from
Oct 20, 2022

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milanmlft
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As mentioned in #6, the Bioc-version can be inconsistent with the one requested after the setup-r-dependencies step. I suspect this is due to the use of pak in setup-r-dependencies, which sets its own package repository settings (see pak::repo_get()) and defaults to Bioc-release, thereby ignoring the configuration done by the setup-bioc step.

This PR sets the environment variable R_BIOC_VERSION environment variable during the setup-bioc step, to ensure that pak will use the requested Bioc-version in subsequent installation steps.

See also r-lib/pak#309 (comment)

@grimbough grimbough merged commit 8ded1d6 into grimbough:main Oct 20, 2022
@milanmlft milanmlft deleted the fix-bioc-version branch October 21, 2022 08:38
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2 participants