Package: banffIT Check: tests New result: ERROR Running ‘BanffIT_Run_Script.R’ [153s/153s] 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 Package: Rmonize Check: examples New result: ERROR Running examples in ‘Rmonize-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dataschema_evaluate > ### Title: Generate an assessment report for a DataSchema > ### Aliases: dataschema_evaluate > > ### ** Examples > > { + + # use Rmonize_DEMO provided by the package + + library(dplyr) + library(madshapR) # data_dict_filter + + dataschema <- + Rmonize_DEMO$`dataschema - final` %>% + data_dict_filter("name == 'adm_unique_id'") + + dataschema_evaluate(dataschema) + + } Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Some changes to functions in the current version of madshapR may require updates of existing code. To see which functions have changed, please see https://cran.r-project.org/web/packages/madshapR/news/news.html Error in data_dict_evaluate(dataschema, taxonomy, as_data_dict_mlstr = TRUE) : unused argument (as_data_dict_mlstr = TRUE) Calls: dataschema_evaluate Execution halted Package: Rmonize Check: R code for possible problems New result: NOTE dataschema_evaluate: possible error in data_dict_evaluate(dataschema, taxonomy, as_data_dict_mlstr = TRUE): unused argument (as_data_dict_mlstr = TRUE) harmonized_dossier_evaluate: possible error in dataset_evaluate(dataset = pooled_harmonized_dataset, data_dict = dataschema, taxonomy = taxonomy, as_data_dict_mlstr = as_dataschema_mlstr): unused argument (as_data_dict_mlstr = as_dataschema_mlstr) Package: Rmonize Check: whether package can be installed New result: WARNING Found the following significant warnings: Note: possible error in 'data_dict_evaluate(dataschema, ': unused argument (as_data_dict_mlstr = TRUE) Note: possible error in 'dataset_evaluate(dataset = pooled_harmonized_dataset, ': unused argument (as_data_dict_mlstr = as_dataschema_mlstr) See ‘/home/hornik/tmp/CRAN_recheck/Rmonize.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’.