Bioc review2

[ncborcherding]

Per comments raised in Bioconductor/Contributions#4143

• Vignette: removed undefined variable references (mouse_tcr_data, contig_list placeholder, ... in custom_ref). Five previously unevaluated chunks now run during build, using tempdir(), scRepertoire::contig_list, the bundled gliph_sce, and a real reference data frame built from gliph_input_data. The three remaining eval = FALSE chunks are limited to BiocManager::install() calls and the optional getGLIPHreference() network download.
• Consolidated duplicated column-type coercion for loops in loadGLIPH(), plotNetwork() and clusterScoring() into a single lapply()-based helper, .coerce_numeric_cols().

[codecov]

Codecov Report

❌ Patch coverage is 77.77778% with 2 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
R/loadGLIPH.R	33.33%	2 Missing ⚠️

Files with missing lines	Coverage Δ
R/clusterScoring.R	83.66% <100.00%> (-0.17%)	⬇️
R/plotNetwork.R	46.23% <100.00%> (-0.14%)	⬇️
R/utils-output.R	100.00% <100.00%> (ø)
R/loadGLIPH.R	57.96% <33.33%> (+0.46%)	⬆️

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