issues.md

❯ checking R code for possible problems ... [11s/10s] NOTE
  .filter_transciptome: no visible binding for global variable
    'tempus_ensembl_id'
  .filter_transciptome: no visible binding for global variable
    'gene_symbol'
  .tbl_cnv: no visible binding for global variable 'n_reads'
  .tbl_cnv: no visible global function definition for 'STRING_AGG'
  .tbl_diagnosis: no visible global function definition for 'date_diff'
  .tbl_diagnosis_dates: no visible binding for global variable
    'clinical_status'
  .tbl_diagnosis_dates: no visible binding for global variable
    'primary_diagnosis_date_indexed'
  .tbl_full_cohort: no visible binding for global variable 'patient_id'
  .tbl_full_cohort: no visible binding for global variable
    'sample_family_id'
  .tbl_full_cohort: no visible binding for global variable
    'dna_analysis_id'
  .tbl_full_cohort: no visible binding for global variable
    'rna_analysis_id'
  .tbl_rna_analysis: no visible binding for global variable
    'run_date_indexed'
  .tbl_sample: no visible binding for global variable 'classification'
  .tbl_sample: no visible binding for global variable
    'sample_tissue_site'
  .tbl_sample: no visible binding for global variable 'is_liquid_assay'
  .tbl_sample_care_plan: no visible global function definition for
    'date_diff'
  .tbl_sample_line_of_therapy: no visible global function definition for
    'date_diff'
  .tbl_sample_stage: no visible global function definition for
    'date_diff'
  .tbl_smoking_status: no visible binding for global variable
    'assessment_type_canonical_name'
  .tbl_smoking_status: no visible binding for global variable
    'effective_date_time_indexed'
  .tbl_snv_indel: no visible binding for global variable
    'variant_type_code'
  .tbl_snv_indel: no visible binding for global variable 'chrom_pos_1'
  .tbl_snv_indel: no visible binding for global variable 'reference'
  .tbl_snv_indel: no visible binding for global variable 'alternative'
  .tbl_snv_indel: no visible global function definition for 'REPLACE'
  exclude_artifact_fusions: no visible binding for global variable
    'Gene2'
  exclude_artifact_fusions: no visible binding for global variable
    'gene_x'
  exclude_artifact_fusions: no visible binding for global variable
    'gene_y'
  get_cnv: no visible binding for global variable 'patient_id'
  get_cnv: no visible binding for global variable 'sample_family_id'
  get_cnv: no visible binding for global variable 'dna_analysis_id'
  get_cnv: no visible binding for global variable 'gene_symbol'
  get_cnv: no visible binding for global variable 'copy_number'
  get_diagnosis: no visible binding for global variable
    'sample_family_id'
  get_diagnosis: no visible binding for global variable
    'tmo_diagnosis_concept_code'
  get_diagnosis: no visible binding for global variable 'preferred_by'
  get_diagnosis: no visible binding for global variable 'concept_id'
  get_diagnosis: no visible binding for global variable 'literal_form'
  get_diagnosis: no visible binding for global variable 'patient_id'
  get_diagnosis: no visible binding for global variable 'path_to_root'
  get_diagnosis: no visible binding for global variable
    'diagnosis_display'
  get_diagnosis: no visible binding for global variable
    'histology_display'
  get_diagnosis: no visible binding for global variable
    'diagnosis_label_preferred'
  get_fusion: no visible binding for global variable
    'rna_fusion_reportable'
  get_fusion: no visible binding for global variable 'rearr_num_reads'
  get_fusion: no visible binding for global variable
    'dna_fusion_filtered'
  get_fusion: no visible binding for global variable 'molecular_source'
  get_fusion: no visible binding for global variable 'table_source'
  get_fusion: no visible binding for global variable 'chr_pos_x'
  get_medication_rollups: no visible binding for global variable
    'patient_id'
  get_medication_rollups: no visible binding for global variable
    'ordered_administered_flag'
  get_medication_rollups: no visible binding for global variable
    'care_plan_id'
  get_medication_rollups: no visible binding for global variable
    'source_system_canonical_name'
  get_medication_rollups: no visible binding for global variable
    'therapy_group_order'
  get_medication_rollups: no visible binding for global variable
    'medication_concept_canonical_name'
  get_medication_rollups: no visible binding for global variable
    'effective_date_start_indexed'
  get_medication_rollups: no visible binding for global variable
    'effective_date_start_year_indexed'
  get_medication_rollups: no visible binding for global variable
    'effective_date_end_indexed'
  get_medication_rollups: no visible binding for global variable
    'care_plan_start_date'
  get_medication_rollups: no visible binding for global variable
    'effective_date_end_year_indexed'
  get_medication_rollups: no visible binding for global variable
    'last_start_date'
  get_medication_rollups: no visible binding for global variable
    'end_date_last'
  get_medication_rollups: no visible binding for global variable
    'end_year_last_start'
  get_medication_rollups: no visible binding for global variable
    'last_end_year'
  get_medication_rollups: no visible binding for global variable
    'effective_date_end_precision'
  get_medication_rollups: no visible binding for global variable
    'care_plan_end_date'
  get_medication_rollups: no visible binding for global variable
    'care_plan_end_year'
  get_medication_rollups: no visible binding for global variable
    'care_plan_end_date_precision'
  get_medication_rollups: no visible binding for global variable
    'care_plan_therapy_group_order'
  get_medication_rollups: no visible binding for global variable
    'care_plan_start_date_precision'
  get_medication_rollups: no visible binding for global variable
    'care_plan_treatment'
  get_medication_rollups: no visible binding for global variable
    'care_plan_class_group_name'
  get_medication_rollups: no visible binding for global variable
    'care_plan_class_name'
  get_medication_rollups: no visible binding for global variable
    'care_plan_treatment_intent'
  get_medication_rollups: no visible binding for global variable
    'care_plan_curated_line_of_therapy'
  get_medication_rollups: no visible binding for global variable
    'care_plan_start_year'
  get_medication_rollups: no visible binding for global variable
    'flag_start_after_end'
  get_medication_rollups: no visible binding for global variable
    'complete_therapy_group_order'
  get_medication_rollups: no visible binding for global variable
    'complete_care_plan_dates'
  get_medication_rollups: no visible binding for global variable
    'complete_care_plan_start_dates'
  get_medication_rollups: no visible binding for global variable
    'complete_care_plan_start_years'
  get_patient_diagnosis_dates: no visible binding for global variable
    'patient_id'
  get_progression_events: no visible binding for global variable
    'patient_id'
  get_response_assessment: no visible binding for global variable
    'patient_id'
  get_smoking_status: no visible binding for global variable
    'sample_family_id'
  get_smoking_status: no visible binding for global variable 'patient_id'
  get_smoking_status: no visible binding for global variable
    'sample_collection_date'
  get_smoking_status: no visible binding for global variable
    'effective_date_time_indexed'
  get_smoking_status: no visible binding for global variable
    'days_sample_from_smoking_status'
  Undefined global functions or variables:
    Gene2 REPLACE STRING_AGG alternative assessment_type_canonical_name
    care_plan_class_group_name care_plan_class_name
    care_plan_curated_line_of_therapy care_plan_end_date
    care_plan_end_date_precision care_plan_end_year care_plan_id
    care_plan_start_date care_plan_start_date_precision
    care_plan_start_year care_plan_therapy_group_order
    care_plan_treatment care_plan_treatment_intent chr_pos_x chrom_pos_1
    classification clinical_status complete_care_plan_dates
    complete_care_plan_start_dates complete_care_plan_start_years
    complete_therapy_group_order concept_id copy_number date_diff
    days_sample_from_smoking_status diagnosis_display
    diagnosis_label_preferred dna_analysis_id dna_fusion_filtered
    effective_date_end_indexed effective_date_end_precision
    effective_date_end_year_indexed effective_date_start_indexed
    effective_date_start_year_indexed effective_date_time_indexed
    end_date_last end_year_last_start flag_start_after_end gene_symbol
    gene_x gene_y histology_display is_liquid_assay last_end_year
    last_start_date literal_form medication_concept_canonical_name
    molecular_source n_reads ordered_administered_flag path_to_root
    patient_id preferred_by primary_diagnosis_date_indexed
    rearr_num_reads reference rna_analysis_id rna_fusion_reportable
    run_date_indexed sample_collection_date sample_family_id
    sample_tissue_site source_system_canonical_name table_source
    tempus_ensembl_id therapy_group_order tmo_diagnosis_concept_code
    variant_type_code