From 88551b1ea0a5cd799ec5fd0cf76f5645382938c7 Mon Sep 17 00:00:00 2001 From: hansvancalster Date: Wed, 21 Jan 2026 15:27:40 +0100 Subject: [PATCH 1/2] update protocolhelper and checklist --- renv.lock | 49 ++++++++++++++++++++++++++----------------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/renv.lock b/renv.lock index aff543a3..49d445e1 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.5.0", + "Version": "4.5.1", "Repositories": [ { "Name": "CRAN", @@ -675,11 +675,11 @@ }, "checklist": { "Package": "checklist", - "Version": "0.4.2", + "Version": "0.5.2", "Source": "GitHub", "Type": "Package", "Title": "A Thorough and Strict Set of Checks for R Packages and Source Code", - "Authors@R": "c( person(\"Thierry\", \"Onkelinx\", , \"thierry.onkelinx@inbo.be\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-8804-4216\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Els\", \"Lommelen\", , \"els.lommelen@inbo.be\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3481-5684\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Hans\", \"Van Calster\", , \"hans.vancalster@inbo.be\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8595-8426\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Research Institute for Nature and Forest (INBO)\", , , \"info@inbo.be\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Thierry\", \"Onkelinx\", , \"thierry.onkelinx@inbo.be\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-8804-4216\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Els\", \"Lommelen\", , \"els.lommelen@inbo.be\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3481-5684\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Hans\", \"Van Calster\", , \"hans.vancalster@inbo.be\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8595-8426\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Research Institute for Nature and Forest (INBO)\", , , \"info@inbo.be\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"https://ror.org/00j54wy13\")) )", "Description": "An opinionated set of rules for R packages and R source code projects.", "License": "GPL-3", "URL": "https://inbo.github.io/checklist/, https://github.com/inbo/checklist, https://doi.org/10.5281/zenodo.4028303", @@ -700,7 +700,7 @@ "hunspell", "jsonlite", "knitr", - "lintr (>= 3.2.0)", + "lintr (>= 3.3.0)", "pkgdown (>= 2.0.7)", "R6", "rcmdcheck", @@ -716,6 +716,7 @@ "curl", "cyclocomp", "mockery", + "pak", "renv", "roxygen2", "rstudioapi", @@ -730,16 +731,16 @@ "Encoding": "UTF-8", "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "SystemRequirements": "Pandoc (>= 1.17.2)", - "Author": "Thierry Onkelinx [aut, cre] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Hans Van Calster [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd]", + "Author": "Thierry Onkelinx [aut, cre] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Hans Van Calster [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd] (ROR: )", "Maintainer": "Thierry Onkelinx ", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "inbo", "RemoteRepo": "checklist", "RemoteRef": "main", - "RemoteSha": "6af592f5617c6f4e0a695d65375170c833a5c017" + "RemoteSha": "3cb091bae8fba959b28c7ddd0eab08bee3813c3c" }, "cli": { "Package": "cli", @@ -2755,10 +2756,10 @@ }, "lintr": { "Package": "lintr", - "Version": "3.2.0", + "Version": "3.3.0-1", "Source": "Repository", "Title": "A 'Linter' for R Code", - "Authors@R": "c( person(\"Jim\", \"Hester\", , role = \"aut\"), person(\"Florent\", \"Angly\", role = \"aut\", comment = \"fangly\"), person(\"Russ\", \"Hyde\", role = \"aut\"), person(\"Michael\", \"Chirico\", email = \"michaelchirico4@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kun\", \"Ren\", role = \"aut\"), person(\"Alexander\", \"Rosenstock\", role = \"aut\", comment = \"AshesITR\"), person(\"Indrajeet\", \"Patil\", , \"patilindrajeet.science@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-1995-6531\", Twitter = \"@patilindrajeets\")) )", + "Authors@R": "c( person(\"Jim\", \"Hester\", , role = \"aut\"), person(\"Florent\", \"Angly\", role = \"aut\", comment = c(GitHub = \"fangly\")), person(\"Russ\", \"Hyde\", role = \"aut\"), person(\"Michael\", \"Chirico\", email = \"michaelchirico4@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kun\", \"Ren\", role = \"aut\"), person(\"Alexander\", \"Rosenstock\", role = \"aut\", comment = c(GitHub = \"AshesITR\")), person(\"Indrajeet\", \"Patil\", email = \"patilindrajeet.science@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-1995-6531\")), person(\"Hugo\", \"Gruson\", role = \"aut\", comment = c(ORCID = \"0000-0002-4094-1476\")) )", "Description": "Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.", "License": "MIT + file LICENSE", "URL": "https://lintr.r-lib.org, https://github.com/r-lib/lintr", @@ -2767,7 +2768,7 @@ "R (>= 4.0)" ], "Imports": [ - "backports (>= 1.4.0)", + "backports (>= 1.5.0)", "cli (>= 3.4.0)", "codetools", "digest", @@ -2776,6 +2777,7 @@ "rex", "stats", "utils", + "xfun", "xml2 (>= 1.0.0)", "xmlparsedata (>= 1.0.5)" ], @@ -2797,14 +2799,14 @@ ], "VignetteBuilder": "knitr", "Config/Needs/website": "tidyverse/tidytemplate", - "Config/Needs/development": "pkgload, cli, testthat, patrick", + "Config/Needs/development": "pkgload, testthat, patrick", "Config/testthat/edition": "3", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", - "Collate": "'make_linter_from_xpath.R' 'xp_utils.R' 'utils.R' 'AAA.R' 'T_and_F_symbol_linter.R' 'absolute_path_linter.R' 'actions.R' 'addins.R' 'any_duplicated_linter.R' 'any_is_na_linter.R' 'assignment_linter.R' 'backport_linter.R' 'boolean_arithmetic_linter.R' 'brace_linter.R' 'cache.R' 'class_equals_linter.R' 'commas_linter.R' 'commented_code_linter.R' 'comparison_negation_linter.R' 'condition_call_linter.R' 'condition_message_linter.R' 'conjunct_test_linter.R' 'consecutive_assertion_linter.R' 'consecutive_mutate_linter.R' 'cyclocomp_linter.R' 'declared_functions.R' 'deprecated.R' 'duplicate_argument_linter.R' 'empty_assignment_linter.R' 'equals_na_linter.R' 'exclude.R' 'expect_comparison_linter.R' 'expect_identical_linter.R' 'expect_length_linter.R' 'expect_lint.R' 'expect_named_linter.R' 'expect_not_linter.R' 'expect_null_linter.R' 'expect_s3_class_linter.R' 'expect_s4_class_linter.R' 'expect_true_false_linter.R' 'expect_type_linter.R' 'extract.R' 'fixed_regex_linter.R' 'for_loop_index_linter.R' 'function_argument_linter.R' 'function_left_parentheses_linter.R' 'function_return_linter.R' 'get_source_expressions.R' 'ids_with_token.R' 'if_not_else_linter.R' 'if_switch_linter.R' 'ifelse_censor_linter.R' 'implicit_assignment_linter.R' 'implicit_integer_linter.R' 'indentation_linter.R' 'infix_spaces_linter.R' 'inner_combine_linter.R' 'is_lint_level.R' 'is_numeric_linter.R' 'keyword_quote_linter.R' 'length_levels_linter.R' 'length_test_linter.R' 'lengths_linter.R' 'library_call_linter.R' 'line_length_linter.R' 'lint.R' 'linter_tag_docs.R' 'linter_tags.R' 'lintr-deprecated.R' 'lintr-package.R' 'list_comparison_linter.R' 'literal_coercion_linter.R' 'make_linter_from_regex.R' 'matrix_apply_linter.R' 'methods.R' 'missing_argument_linter.R' 'missing_package_linter.R' 'namespace.R' 'namespace_linter.R' 'nested_ifelse_linter.R' 'nested_pipe_linter.R' 'nonportable_path_linter.R' 'shared_constants.R' 'nrow_subset_linter.R' 'numeric_leading_zero_linter.R' 'nzchar_linter.R' 'object_length_linter.R' 'object_name_linter.R' 'object_overwrite_linter.R' 'object_usage_linter.R' 'one_call_pipe_linter.R' 'outer_negation_linter.R' 'package_hooks_linter.R' 'paren_body_linter.R' 'paste_linter.R' 'path_utils.R' 'pipe_call_linter.R' 'pipe_consistency_linter.R' 'pipe_continuation_linter.R' 'pipe_return_linter.R' 'print_linter.R' 'quotes_linter.R' 'redundant_equals_linter.R' 'redundant_ifelse_linter.R' 'regex_subset_linter.R' 'rep_len_linter.R' 'repeat_linter.R' 'return_linter.R' 'routine_registration_linter.R' 'sample_int_linter.R' 'scalar_in_linter.R' 'semicolon_linter.R' 'seq_linter.R' 'settings.R' 'settings_utils.R' 'sort_linter.R' 'source_utils.R' 'spaces_inside_linter.R' 'spaces_left_parentheses_linter.R' 'sprintf_linter.R' 'stopifnot_all_linter.R' 'string_boundary_linter.R' 'strings_as_factors_linter.R' 'system_file_linter.R' 'terminal_close_linter.R' 'todo_comment_linter.R' 'trailing_blank_lines_linter.R' 'trailing_whitespace_linter.R' 'tree_utils.R' 'undesirable_function_linter.R' 'undesirable_operator_linter.R' 'unnecessary_concatenation_linter.R' 'unnecessary_lambda_linter.R' 'unnecessary_nesting_linter.R' 'unnecessary_placeholder_linter.R' 'unreachable_code_linter.R' 'unused_import_linter.R' 'use_lintr.R' 'vector_logic_linter.R' 'which_grepl_linter.R' 'whitespace_linter.R' 'with.R' 'with_id.R' 'xml_nodes_to_lints.R' 'xml_utils.R' 'yoda_test_linter.R' 'zzz.R'", + "RoxygenNote": "7.3.3", + "Collate": "'make_linter_from_xpath.R' 'xp_utils.R' 'utils.R' 'AAA.R' 'T_and_F_symbol_linter.R' 'absolute_path_linter.R' 'actions.R' 'addins.R' 'all_equal_linter.R' 'any_duplicated_linter.R' 'any_is_na_linter.R' 'assignment_linter.R' 'backport_linter.R' 'boolean_arithmetic_linter.R' 'brace_linter.R' 'cache.R' 'class_equals_linter.R' 'coalesce_linter.R' 'commas_linter.R' 'commented_code_linter.R' 'comparison_negation_linter.R' 'condition_call_linter.R' 'condition_message_linter.R' 'conjunct_test_linter.R' 'consecutive_assertion_linter.R' 'consecutive_mutate_linter.R' 'cyclocomp_linter.R' 'declared_functions.R' 'deprecated.R' 'download_file_linter.R' 'duplicate_argument_linter.R' 'empty_assignment_linter.R' 'equals_na_linter.R' 'exclude.R' 'expect_comparison_linter.R' 'expect_identical_linter.R' 'expect_length_linter.R' 'expect_lint.R' 'expect_named_linter.R' 'expect_not_linter.R' 'expect_null_linter.R' 'expect_s3_class_linter.R' 'expect_s4_class_linter.R' 'expect_true_false_linter.R' 'expect_type_linter.R' 'extract.R' 'fixed_regex_linter.R' 'for_loop_index_linter.R' 'function_argument_linter.R' 'function_left_parentheses_linter.R' 'function_return_linter.R' 'get_source_expressions.R' 'ids_with_token.R' 'if_not_else_linter.R' 'if_switch_linter.R' 'ifelse_censor_linter.R' 'implicit_assignment_linter.R' 'implicit_integer_linter.R' 'indentation_linter.R' 'infix_spaces_linter.R' 'inner_combine_linter.R' 'is_lint_level.R' 'is_numeric_linter.R' 'keyword_quote_linter.R' 'length_levels_linter.R' 'length_test_linter.R' 'lengths_linter.R' 'library_call_linter.R' 'line_length_linter.R' 'lint.R' 'linter_tag_docs.R' 'linter_tags.R' 'lintr-deprecated.R' 'lintr-package.R' 'list2df_linter.R' 'list_comparison_linter.R' 'literal_coercion_linter.R' 'make_linter_from_regex.R' 'matrix_apply_linter.R' 'methods.R' 'missing_argument_linter.R' 'missing_package_linter.R' 'namespace.R' 'namespace_linter.R' 'nested_ifelse_linter.R' 'nested_pipe_linter.R' 'nonportable_path_linter.R' 'shared_constants.R' 'nrow_subset_linter.R' 'numeric_leading_zero_linter.R' 'nzchar_linter.R' 'object_length_linter.R' 'object_name_linter.R' 'object_overwrite_linter.R' 'object_usage_linter.R' 'one_call_pipe_linter.R' 'outer_negation_linter.R' 'package_hooks_linter.R' 'paren_body_linter.R' 'paste_linter.R' 'path_utils.R' 'pipe_call_linter.R' 'pipe_consistency_linter.R' 'pipe_continuation_linter.R' 'pipe_return_linter.R' 'print_linter.R' 'quotes_linter.R' 'redundant_equals_linter.R' 'redundant_ifelse_linter.R' 'regex_subset_linter.R' 'rep_len_linter.R' 'repeat_linter.R' 'return_linter.R' 'routine_registration_linter.R' 'sample_int_linter.R' 'scalar_in_linter.R' 'semicolon_linter.R' 'seq_linter.R' 'settings.R' 'settings_utils.R' 'sort_linter.R' 'source_utils.R' 'spaces_inside_linter.R' 'spaces_left_parentheses_linter.R' 'sprintf_linter.R' 'stopifnot_all_linter.R' 'string_boundary_linter.R' 'strings_as_factors_linter.R' 'system_file_linter.R' 'terminal_close_linter.R' 'todo_comment_linter.R' 'trailing_blank_lines_linter.R' 'trailing_whitespace_linter.R' 'tree_utils.R' 'undesirable_function_linter.R' 'undesirable_operator_linter.R' 'unnecessary_concatenation_linter.R' 'unnecessary_lambda_linter.R' 'unnecessary_nesting_linter.R' 'unnecessary_placeholder_linter.R' 'unreachable_code_linter.R' 'unused_import_linter.R' 'use_lintr.R' 'vector_logic_linter.R' 'which_grepl_linter.R' 'whitespace_linter.R' 'with.R' 'with_id.R' 'xml_nodes_to_lints.R' 'xml_utils.R' 'yoda_test_linter.R' 'zzz.R'", "Language": "en-US", "NeedsCompilation": "no", - "Author": "Jim Hester [aut], Florent Angly [aut] (fangly), Russ Hyde [aut], Michael Chirico [aut, cre], Kun Ren [aut], Alexander Rosenstock [aut] (AshesITR), Indrajeet Patil [aut] (, @patilindrajeets)", + "Author": "Jim Hester [aut], Florent Angly [aut] (GitHub: fangly), Russ Hyde [aut], Michael Chirico [aut, cre] (ORCID: ), Kun Ren [aut], Alexander Rosenstock [aut] (GitHub: AshesITR), Indrajeet Patil [aut] (ORCID: ), Hugo Gruson [aut] (ORCID: )", "Maintainer": "Michael Chirico ", "Repository": "CRAN" }, @@ -3664,21 +3666,21 @@ }, "protocolhelper": { "Package": "protocolhelper", - "Version": "0.8.1", + "Version": "0.8.3", "Source": "GitHub", "Title": "Helper Functions to Manage Protocols", - "Authors@R": "c( person(\"Hans\", \"Van Calster\", , \"hans.vancalster@inbo.be\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-8595-8426\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Thierry\", \"Onkelinx\", , \"thierry.onkelinx@inbo.be\", role = \"aut\", comment = c(ORCID = \"0000-0001-8804-4216\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Floris\", \"Vanderhaeghe\", , \"floris.vanderhaeghe@inbo.be\", role = \"aut\", comment = c(ORCID = \"0000-0002-6378-6229\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Els\", \"Lommelen\", , \"els.lommelen@inbo.be\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3481-5684\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Research Institute for Nature and Forest (INBO)\", , , \"info@inbo.be\", role = c(\"cph\", \"fnd\")) )", + "Authors@R": "c( person(\"Hans\", \"Van Calster\", , \"hans.vancalster@inbo.be\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-8595-8426\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Thierry\", \"Onkelinx\", , \"thierry.onkelinx@inbo.be\", role = \"aut\", comment = c(ORCID = \"0000-0001-8804-4216\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Floris\", \"Vanderhaeghe\", , \"floris.vanderhaeghe@inbo.be\", role = \"aut\", comment = c(ORCID = \"0000-0002-6378-6229\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Els\", \"Lommelen\", , \"els.lommelen@inbo.be\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3481-5684\", affiliation = \"Research Institute for Nature and Forest (INBO)\")), person(\"Research Institute for Nature and Forest (INBO)\", , , \"info@inbo.be\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"https://ror.org/00j54wy13\")) )", "Description": "Helper functions to manage INBO protocols.", "License": "GPL-3", "URL": "https://inbo.github.io/protocolhelper/, https://github.com/inbo/protocolhelper", "BugReports": "https://github.com/inbo/protocolhelper/issues", "Depends": [ - "R (>= 3.6)" + "R (>= 4.1.0)" ], "Imports": [ "assertthat", "bookdown", - "checklist (>= 0.4.1)", + "checklist (>= 0.5.2)", "cli", "commonmark", "fs", @@ -3690,6 +3692,7 @@ "rmarkdown", "rprojroot", "stringr", + "withr", "xfun", "xml2", "yaml", @@ -3704,7 +3707,6 @@ "png", "reactable", "rlang", - "slickR", "testthat (>= 2.1.0)", "tinytex", "zen4R" @@ -3712,20 +3714,21 @@ "Additional_repositories": "https://inbo.r-universe.dev", "Config/checklist/communities": "inbo", "Config/checklist/keywords": "protocols; R package; Reproducible research; Rmarkdown templates", + "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-GB", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", - "RoxygenNote": "7.3.2", - "SystemRequirements": "Pandoc (>= 2.0.0)", - "Author": "Hans Van Calster [aut, cre] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Thierry Onkelinx [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Floris Vanderhaeghe [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd]", + "RoxygenNote": "7.3.3", + "SystemRequirements": "Pandoc (>= 2.0.0), TeX Live", + "Author": "Hans Van Calster [aut, cre] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Thierry Onkelinx [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Floris Vanderhaeghe [aut] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Els Lommelen [ctb] (ORCID: , affiliation: Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd] (ROR: )", "Maintainer": "Hans Van Calster ", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "inbo", "RemoteRepo": "protocolhelper", "RemoteRef": "main", - "RemoteSha": "1abef67527c4cd5a4ac6d36ffabb7865824771d5" + "RemoteSha": "70c81c3e8053d74e486d9989cc7eb53aa99b2165" }, "ps": { "Package": "ps", From 5a0d291c61a372cf9fb17502b7fadd42a4b289f7 Mon Sep 17 00:00:00 2001 From: hansvancalster Date: Wed, 21 Jan 2026 15:41:37 +0100 Subject: [PATCH 2/2] update gitignore patterns --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 1f3205ff..d67d27d1 100644 --- a/.gitignore +++ b/.gitignore @@ -35,6 +35,9 @@ vignettes/*.pdf *.utf8.md *.knit.md *.log +*.tex +# ignore combined Rmd files (auto-deleted, but persist in case render fails) +source/**/s[fpiao]f_*.Rmd # R Environment Variables .Renviron