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Code Review
This pull request updates the gDRtestData package to version 1.9.2, migrating test data files from the .qs format to .qs2. The changes include updates to the package description, dependencies, and the NEWS.md file. However, the migration appears incomplete as internal logic in R/get_test_datasets.R still references the .qs extension, which will lead to incorrect dataset naming.
| Date: 2026-04-13 | ||
| Description: R package with internal dose-response test data. Package provides functions to generate | ||
| input testing data that can be used as the input for gDR pipeline. It also contains qs files | ||
| input testing data that can be used as the input for gDR pipeline. It also contains qs2 files |
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The migration to qs2 appears to be incomplete. While the package description and dependencies have been updated, the utility function get_test_dataset_paths() in R/get_test_datasets.R still contains hardcoded logic for the .qs extension. Specifically, line 37 uses gsub(".qs", "", ...) which will fail to correctly strip the new .qs2 extension, resulting in incorrect dataset names (e.g., 'small2' instead of 'small'). Additionally, the docstring on line 7 of that file still refers to 'qs files'. Please update R/get_test_datasets.R to handle the new file format correctly.
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Please, update documentation with devtools::document(). Also, update README.md
- README.md: update testdata description from qs to qs2 format
Done. |
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Description
What changed?
Related JIRA issue: GDR-3351
Migrated all test data binary files from
.qs(archived) to.qs2format.Files were converted inside the rplatform container via
qs::qread()+qs2::qs_save().Why 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