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Code Review
This pull request migrates the gDRcore package from the qs dependency to qs2, which includes updating the package version, dependencies in the DESCRIPTION file, and file extensions for intermediate data storage. The review feedback focuses on improving the robustness of the implementation by ensuring that the availability of the qs2 package is verified before use—since it is a suggested dependency—and by refining the regular expression used for file matching to be more precise and anchored.
j-smola
reviewed
Apr 13, 2026
- pipeline_helpers.R: update save_intermediate_data and read_intermediate_data docstrings from qs to qs2 - utils.R: update add_intermediate_data title from qs to qs2
bczech
approved these changes
Apr 14, 2026
darsoo
approved these changes
Apr 16, 2026
j-smola
approved these changes
Apr 17, 2026
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Description
What changed?
Related JIRA issue: GDR-3351
Replaced all usage of the archived
qspackage withqs2:qs::qread()→qs2::qs_read()qs::qsave()→qs2::qs_save().qsto.qs2Why was it changed?
The
qspackage was archived on CRAN on January 17, 2026 and will not be included in Bioconductor 3.23.The
qs2package is its official successor with an incompatible binary format.Checklist for sustainable code base
Logistic checklist