* using log directory ‘/srv/hornik/tmp/CRAN_pretest/saferDev.Rcheck’ * using R Under development (unstable) (2026-04-15 r89888) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (3+b1) Debian flang version 21.1.8 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-04-16 15:25:05 UTC * checking for file ‘saferDev/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘saferDev’ version ‘1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/7s] NOTE Maintainer: ‘Gael Millot ’ New submission Found the following (possibly) invalid URLs: URL: From: README.md Message: Empty URL URL: https://opensource.org/licenses/MITgpl-3-0 From: README.md Status: 404 Message: Not Found URL: https://safer-r.github.io/saferDev (moved to https://safer-r.github.io/saferDev/) From: README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. Found the following (possibly) invalid file URIs: URI: yushi.han2000@gmail.com From: man/all_args_here.Rd URI: wanghaiding442@gmail.com From: man/all_args_here.Rd URI: yushi.han2000@gmail.com From: man/dot-all_args_here_fill.Rd URI: wanghaiding442@gmail.com From: man/dot-all_args_here_fill.Rd The Title field should be in title case. Current version is: ‘function and pipeline development’ In title case that is: ‘Function and Pipeline Development’ The Description field should start with a capital letter. * 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 serialization versions ... OK * checking whether package ‘saferDev’ can be installed ... [6s/6s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Author field differs from that derived from Authors@R Author: ‘Haiding Wang [aut, ctb], Yushi Han [aut, ctb], Mia Legras [ctb], Gael Millot [cre, aut, ctb]’ Authors@R: ‘Haiding Wang [aut, ctb], Yushi Han [aut, ctb], Mia Legras [ctb], Gael Millot [cre, aut, ctb] (ORCID: )’ * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.all_args_here_fill’ ‘.base_op_check’ ‘.colons_check_message’ ‘.extract_all_fun_names’ ‘.fun_args_pos’ ‘.functions_detect’ ‘.has_odd_number_of_quotes’ ‘.in_parenthesis_replacement’ ‘.in_quotes_replacement’ ‘.noclean_functions’ ‘.pack_and_function_check’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [11s/11s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [5s/5s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [85s/85s] ERROR Running ‘testthat.R’ [85s/85s] 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(saferDev) > > test_check("saferDev") INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. INSIDE test(), ARGUMENTS ARE MISSING. RESULT EXPORTED IN: ./res.tsv INSIDE test(), ARGUMENTS ARE MISSING. RESULT EXPORTED IN: ./res.tsv AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: INSIDE fun2(), EVERYTHING SEEMS CLEAN. INSIDE fun3(), EVERYTHING SEEMS CLEAN, AS NO ANALYSABLE FUNCTION DETECTED. INSIDE fun7(), EVERYTHING SEEMS CLEAN, AS NO ANALYSABLE FUNCTION DETECTED. INSIDE fun10(), ARGUMENTS ARE MISSING. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: INSIDE fun6(), EVERYTHING SEEMS CLEAN. INSIDE fun12(), ARGUMENTS ARE MISSING. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: INSIDE fun13(), EVERYTHING SEEMS CLEAN. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: RESULT EXPORTED IN: ./res.tsv BUT INSIDE fun4(), EVERYTHING SEEMS CLEAN. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: RESULT EXPORTED IN: ./res.tsv BUT INSIDE fun5(), EVERYTHING SEEMS CLEAN. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: RESULT EXPORTED IN: ./res.tsv BUT INSIDE fun2(), EVERYTHING SEEMS CLEAN. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: RESULT EXPORTED IN: ./res.tsv BUT INSIDE fun2(), EVERYTHING SEEMS CLEAN. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: INSIDE fun14(), EVERYTHING SEEMS CLEAN. INSIDE fun15(), ARGUMENTS ARE MISSING. AFTER RUNNING all_args_here() OF THE saferDev PACKAGE: INSIDE fun16(), EVERYTHING SEEMS CLEAN. INSIDE fun17(), ARGUMENTS ARE MISSING. INSIDE fun18(), ARGUMENTS ARE MISSING. ================ ERROR THE vec5 ARGUMENT MUST BE MODE numeric ================ Saving _problems/test-arg_check-650.R Saving _problems/test-arg_check-657.R ================ ERROR THE vec8 ARGUMENT MUST BE MODE character ================ INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 16 gregexpr matches <- 18 regmatches matched_strings <- 21 sum tempo4 <- a$regmatches(x = text, m = matches)[[1]] ; 24 sub result <- 24 range result <- sub("\\($##", "", matched_strings) ; 26 return INSIDE test(), INTERNAL FUNCTION DETECTED: FUN1 INSIDE test(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 23 roc1 tempo.cat <- base::paste0("INTERNAL ERROR 4 IN ", function.name, " OF THE ", package.name, " PACKAGE\nLENGTHS OF col1 (", base::length( 25 roc4 tempo.cat <- base::paste0("IAGE\nLENGTHS OF roc00() (", base::ks.test( INSIDE base::mean(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 2 UseMethod AFTER RUNNING saferDev::colons_check(). INSIDE colons_check(), EVERYTHING SEEMS CLEAN. AFTER RUNNING saferDev::colons_check(). INSIDE fun2(), EVERYTHING SEEMS CLEAN. AFTER RUNNING saferDev::colons_check(). INSIDE fun3(), EVERYTHING SEEMS CLEAN FOR R BASIC FUNCTIONS. INSIDE fun3(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 1 fun1 function(x){ AFTER RUNNING saferDev::colons_check(). INSIDE fun4(), EVERYTHING SEEMS CLEAN. INSIDE fun6(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 3 print INSIDE fun7(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 3 print INSIDE fun7(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 2 ggplot INSIDE fun8(), SOME :: OR ::: ARE MISSING BEFORE BASIC FUNCTIONS: LINE FUN STRING_BEFORE 2 return AFTER RUNNING saferDev::colons_check(). INSIDE fun_non_base(), EVERYTHING SEEMS CLEAN FOR R BASIC FUNCTIONS. INSIDE fun_non_base(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 2 aes ggplot2::ggplot(mtcars, AFTER RUNNING saferDev::colons_check(). INSIDE fun_custom(), EVERYTHING SEEMS CLEAN FOR R BASIC FUNCTIONS. INSIDE fun_custom(), SOME :: OR ::: ARE MISSING BEFORE OTHER FUNCTIONS: LINE FUN STRING_BEFORE 2 my_helper [1] 1 [1] 1 [1] 1 Saving _problems/test-get_message-361.R Saving _problems/test-get_message-368.R Saving _problems/test-get_message-399.R Saving _problems/test-get_message-447.R [ FAIL 6 | WARN 4 | SKIP 0 | PASS 2310 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-arg_check.R:650:5'): arg_check() ───────────────────────────── Expected `result` to equal `expect`. Differences: Component "problem": 1 element mismatch Component "text": 1 string mismatch ── Failure ('test-arg_check.R:657:5'): arg_check() ───────────────────────────── Expected `result` to equal `expect`. Differences: Component "problem": 1 element mismatch Component "text": 1 string mismatch ── Failure ('test-get_message.R:361:21'): get_message() ──────────────────────── Expected `result` to equal `expected`. Differences: target is NULL, current is character ── Failure ('test-get_message.R:368:17'): get_message() ──────────────────────── Expected `result` to equal `expected`. Differences: target is NULL, current is character ── Failure ('test-get_message.R:399:17'): get_message() ──────────────────────── `get_message(...)` produced unexpected messages. Expected match: `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. Actual values: * `stat_bin()` using `bins = 30`. Pick better value `binwidth`. ── Failure ('test-get_message.R:447:5'): get_message() ───────────────────────── Expected `result` to equal `expected`. Differences: target is NULL, current is character [ FAIL 6 | WARN 4 | SKIP 0 | PASS 2310 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! Paragraph ended before \Rd@code@wrk was complete. \par l.519 * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘saferDev-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 4 NOTEs