* using log directory ‘/srv/hornik/tmp/CRAN_pretest/cleanIVENT.Rcheck’ * using R Under development (unstable) (2025-11-28 r89073) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.5 (1) Debian flang version 21.1.5 (1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘cleanIVENT/DESCRIPTION’ ... OK * this is package ‘cleanIVENT’ version ‘1.0’ * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Wei Qin Tan ’ New submission Possibly misspelled words in DESCRIPTION: de (4:71) Unknown, possibly misspelled, fields in DESCRIPTION: ‘Video’ The Title field should be in title case. Current version is: ‘Tools for Cleaning and Preparing intervention Data for AI Screening’ In title case that is: ‘Tools for Cleaning and Preparing Intervention Data for AI Screening’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cleanIVENT’ can be installed ... [1s/1s] WARNING Found the following significant warnings: Warning: /srv/hornik/tmp/CRAN_pretest/cleanIVENT.Rcheck/00_pkg_src/cleanIVENT/man/split_for_ai.Rd:14: unexpected '}' Warning: /srv/hornik/tmp/CRAN_pretest/cleanIVENT.Rcheck/00_pkg_src/cleanIVENT/man/split_for_ai.Rd:22: unexpected section header '\examples' Warning: /srv/hornik/tmp/CRAN_pretest/cleanIVENT.Rcheck/00_pkg_src/cleanIVENT/man/split_for_ai.Rd:29: unexpected END_OF_INPUT ' See ‘/srv/hornik/tmp/CRAN_pretest/cleanIVENT.Rcheck/00install.out’ for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [2s/2s] NOTE export_results: no visible global function definition for ‘str_replace_all’ export_results: no visible global function definition for ‘write_csv’ load_and_clean: no visible global function definition for ‘read_csv’ load_and_clean: no visible global function definition for ‘relocate’ load_and_clean: no visible global function definition for ‘mutate’ load_and_clean: no visible global function definition for ‘filter’ load_and_clean: no visible binding for global variable ‘Patient Class’ load_and_clean: no visible global function definition for ‘row_number’ load_and_clean: no visible binding for global variable ‘Type (checked)’ load_and_clean: no visible binding for global variable ‘Subtype (checked)’ load_and_clean: no visible binding for global variable ‘Process Related Causes’ load_and_clean: no visible binding for global variable ‘Subtype’ load_and_clean: no visible binding for global variable ‘Response (checked)’ load_and_clean: no visible binding for global variable ‘Response’ split_for_ai: no visible global function definition for ‘filter’ split_for_ai: no visible global function definition for ‘str_detect’ split_for_ai: no visible binding for global variable ‘Type’ split_for_ai: no visible global function definition for ‘mutate’ split_for_ai: no visible binding for global variable ‘S/N’ Undefined global functions or variables: Patient Class Process Related Causes Response Response (checked) S/N Subtype Subtype (checked) Type Type (checked) filter mutate read_csv relocate row_number str_detect str_replace_all write_csv Consider adding importFrom("stats", "filter") to your NAMESPACE file. * checking Rd files ... [0s/0s] WARNING prepare_Rd: ./man/split_for_ai.Rd:14: unexpected '}' prepare_Rd: ./man/split_for_ai.Rd:22: unexpected section header '\examples' prepare_Rd: ./man/split_for_ai.Rd:29: unexpected END_OF_INPUT ' ' checkRd: (-1) split_for_ai.Rd:22-28: Lost braces 22 | \examples{ | ^ * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘split_for_ai’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Bad \usage lines found in Rd file 'export_results.Rd': Step 1: load_and_clean (file, MMMYY) Step 2: split_for_AI(df2) Step 3: export_results(df2, list, MMMYY, prefix = "ivent") Do not omit steps. Bad \usage lines found in Rd file 'load_and_clean.Rd': Step 1: load_and_clean (file, MMMYY) Step 2: split_for_AI(df2) Step 3: export_results(df2, list, MMMYY, prefix = "ivent") Do not omit steps. Bad \usage lines found in Rd file 'split_for_ai.Rd': Step 1: load_and_clean (file, MMMYY) Step 2: split_for_AI(df2) Step 3: export_results(df2, list, MMMYY, prefix = "ivent") Do not omit steps. Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... ERROR Warning: parse error in file 'cleanIVENT-Ex.R': 20:6: unexpected symbol 19: 20: User only ^ ** will not attempt to run examples * checking examples ... SKIPPED * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] ERROR Running ‘testthat.R’ [1s/1s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(cleanIVENT) > > test_check("cleanIVENT") Saving _problems/test-export_results-3.R Saving _problems/test-load_and_clean-12.R Saving _problems/test-split_for_ai-5.R [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-export_results.R:3:3'): export_results writes output files ───── Error in `tibble(Type = "A.", `S/N` = 1)`: could not find function "tibble" ── Error ('test-load_and_clean.R:3:3'): load_and_clean removes SDA/IPD and adds columns ── Error in `write_csv(tibble(`Patient Class` = c("OP", "IPD", "SDA"), Subtype = c("(Re) Started Drug for Untreated Indication - Indication", "Dose or Frequency increased - Efficacy", "Stopped Drug because of duplicate therapy - Safety"), Response = c("Accepted", "Rejected", NA)), tmp)`: could not find function "write_csv" ── Error ('test-split_for_ai.R:2:3'): split_for_AI splits A–D correctly ──────── Error in `tibble(Type = c("A.", "B.", "C.", "D.", "E.", "F.", NA), `S/N` = 1:7)`: could not find function "tibble" [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 4 WARNINGs, 2 NOTEs