Running ‘BanffIT_Run_Script.R’ [204s/237s]
Running the tests in ‘tests/BanffIT_Run_Script.R’ failed.
Complete output:
  > # # loading dataset
  > # library(banffIT)
  > # library(fs)
  > # library(dplyr)
  > # library(rlang)
  > # library(tools)
  > # library(readr)
  > # library(stringr)
  > # library(lubridate)
  > # library(tidyr)
  > # library(fabR)
  > # library(madshapR)
  > # library(crayon)
  > # library(Rmonize)
  > # library(janitor)
  > #
  > # input_file = "tests/CHUQ_for_test_3.csv"
  > # output_folder = 'tests'
  > # language = 'label:en'
  > # option_filter = quote(adequacy == 1)
  > # detail = TRUE
  > # include_banff_dictionary = TRUE
  > 
  > library(banffIT)
  > 
  > input_file = system.file("extdata", "banff_example.xlsx", package = "banffIT")
  > 
  > banff_launcher(
  +   input_file = input_file,
  +   output_folder = 'tests',
  +   language = 'label:en',
  +   option_filter = adequacy == 1,
  +   detail = TRUE)
  Welcome to the Banff diagnosis helper.
  
  Press [enter] to continue or [esc] to quit.
  
  
  
  [1/6] - Import data
  
  [2/6] - Evaluation of 'banff_example'
  
  [3/6] - Add diagnosis to each observation of'banff_example'
  
  [4/6] - Generate labels for each variable of 'banff_example'
  Processing of : patient_id
  Processing of : center
  Processing of : biopsy_id
  Processing of : sc_date_bx
  Processing of : date_tx
  Processing of : type_bx
  Processing of : adequacy
  Processing of : fixation_ff
  Processing of : fixation_paraffin
  Processing of : fixation_elec
  Processing of : fixation_rna
  Processing of : microscopy
  Processing of : c4d_if
  Processing of : c4d_ihc
  Processing of : dsa
  Processing of : hist_dsa
  Processing of : i_score
  Processing of : t_score
  Processing of : v_score
  Processing of : g_score
  Processing of : ptc_score
  Processing of : ti_score
  Processing of : cg_score
  Processing of : mm_score
  Processing of : cv_score
  Processing of : ci_score
  Processing of : ct_score
  Processing of : ah_score
  Processing of : glomeruli
  Processing of : arteries
  Processing of : bk
  Processing of : gs
  Processing of : i_ifta_score
  Processing of : atma
  Processing of : ctma
  Processing of : atn
  Processing of : agn
  Processing of : cgn
  Processing of : infec
  Processing of : cni
  Processing of : ain
  Processing of : ptld
  Processing of : sptcbmml
  Processing of : leuscint
  Processing of : monofibneoint
  Processing of : newaif
  Processing of : othi_ifta
  Processing of : genetx
  Processing of : hist_aamr
  Processing of : hist_camr
  Processing of : hist_tcmr
  Processing of : adequacy_calculated
  Processing of : c4d
  Processing of : nogn
  Processing of : ifta
  Processing of : aamr11.1
  Processing of : aamr11.2
  Processing of : aamr12
  Processing of : aamr13
  Processing of : aamr14
  Processing of : aamr1
  Processing of : aamr21
  Processing of : aamr22.1
  Processing of : aamr22.2
  Processing of : aamr22.3
  Processing of : aamr2
  Processing of : aamr
  Processing of : susp_aamr
  Processing of : c4dneg_aamr
  Processing of : susp_c4dneg_aamr
  Processing of : dsaneg_aamr
  Processing of : susp_activeaamr
  Processing of : hist_dsa1
  Processing of : hist_dsa2
  Processing of : hist_dsa_calculated
  Processing of : hist_tcmr1
  Processing of : hist_tcmr2
  Processing of : hist_tcmr3
  Processing of : hist_tcmr_calculated
  Processing of : camr11
  Processing of : camr12
  Processing of : camr13
  Processing of : camr1
  Processing of : activeabmr
  Processing of : camr
  Processing of : susp_camr
  Processing of : c4dneg_camr
  Processing of : susp_c4dneg_camr
  Processing of : dsaneg_camr
  Processing of : chractabmr
  Processing of : susp_chractabmr
  Processing of : hist_camr1
  Processing of : hist_camr2
  Processing of : hist_camr_calculated
  Processing of : hist_aamr1
  Processing of : hist_aamr2
  Processing of : hist_aamr_calculated
  Processing of : chrabmr3
  Processing of : chrabmr
  Processing of : c4d_only
  Processing of : final_abmr
  Processing of : final_susp_abmr
  Processing of : final_abmr_verified
  Processing of : diag_code_1
  Processing of : diag_code_2
  Processing of : diag_code_2_final_abmr
  Processing of : diag_code_2_final_susp_abmr
  Processing of : diag_code_3
  Processing of : diag_code_4_active
  Processing of : diag_code_4_chronic
  Processing of : diag_code_5
  Processing of : diag_code_bk
  Processing of : diag_code_ptld
  Processing of : diag_code_cni
  Processing of : diag_code_atn
  Processing of : diag_code_cgn
  Processing of : diag_code_agn
  Processing of : diag_code_infec
  Processing of : diag_code_ain
  
  [5/6] - Assessment of the the annotated 'banff_example'
  
  - DATA DICTIONARY ASSESSMENT: data_dict --------------
      Assess the standard adequacy of naming
      Assess the uniqueness and presence of variable names
      Assess the presence of possible duplicated columns
      Assess the presence of duplicated rows
      Assess the presence of empty rows in the data dictionary
      Assess the presence of empty column in the data dictionary
      Assess the presence of categories not in the data dictionary
      Assess the `valueType` column in 'Variables'
      Assess the completion of `label` column in 'Variables'
      Assess presence and completion of `label` column in 'Categories'
      Assess the logical values of missing column in Categories
      Generate report
  
    - WARNING MESSAGES (if any): --------------------------------------------
  
  - DATASET ASSESSMENT: banff_example --------------------------
      Assess the standard adequacy of naming
      Assess the presence of variable names both in dataset and data dictionary
      Assess the presence of possible duplicated variable in the dataset
      Assess the presence of possible duplicated participants
      Assess the presence of unique value columns in dataset
      Assess the presence of empty rows in the dataset
      Assess the presence all empty variable in the dataset
      Assess the Categories comparison in dataset and data dictionary
      Assess the `valueType` comparison in dataset and data dictionary
      Generate report
  
    - WARNING MESSAGES (if any): -------------------------------------------------
      
  Error: The dataset and/or the data dictionary contain errors.
  
  Useful tip: Use dataset_evaluate(dataset, data_dict) to get a full assessment of
  your dataset
  Execution halted