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gsource: analyzeData + network refactor + accessor cleanup#361

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jiajic wants to merge 81 commits into
giotto-suite:devfrom
jiajic:gsource
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gsource: analyzeData + network refactor + accessor cleanup#361
jiajic wants to merge 81 commits into
giotto-suite:devfrom
jiajic:gsource

refactor: align setter verbose defaults to NULL (vmsg-respecting)

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GitHub Advanced Security / lintr completed May 24, 2026 in 9s

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Warning: Code scanning may not have found all the alerts introduced by this pull request, because 1 configuration present on refs/heads/dev was not found:

Actions workflow (dev_branch_workflow.yml)

  • ❓  .github/workflows/dev_branch_workflow.yml:lintr

New alerts in code changed by this pull request

  • 151 warnings
  • 82 notes

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Annotations

Check warning on line 99 in R/methods-initialize.R

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Code scanning / lintr

no visible global function definition for '.migrate_nn_net_obj' Warning

no visible global function definition for '.migrate_nn_net_obj'

Check warning on line 953 in R/NN_network.R

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no visible global function definition for 'set_default_feat_type' Warning

no visible global function definition for 'set_default_feat_type'

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no visible global function definition for 'getDimReduction' Warning

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no visible global function definition for 'getExpression' Warning

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no visible global function definition for 't_flex' Warning

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no visible global function definition for 'create_nn_net_obj' Warning

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no visible global function definition for 'vmsg' Warning

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no visible global function definition for 'setNearestNetwork' Warning

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no visible global function definition for 'update_giotto_params' Warning

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no visible global function definition for 't_flex' Warning

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no visible global function definition for 'setGiotto' Warning

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no visible global function definition for 'create_spat_net_obj' Warning

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no visible global function definition for 'create_nn_net_obj' Warning

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no visible global function definition for 'is_present' Warning

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no visible global function definition for 'deprecated' Warning

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no visible global function definition for 'deprecated' Warning

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no visible global function definition for 'is_present' Warning

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no visible global function definition for 'is_present' Warning

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no visible global function definition for 'package_check' Warning

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no visible global function definition for '.init_cell_and_feat_ids' Warning

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no visible global function definition for '.evaluate_nearest_networks' Warning

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no visible global function definition for '.evaluate_spatial_network' Warning

no visible global function definition for '.evaluate_spatial_network'

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no visible global function definition for '.evaluate_spatial_network' Warning

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no visible global function definition for '.gstop' Warning

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