In salim-b/pkgpurl: Facilitate Authoring R Packages in the R Markdown File Format
NOTES
-
This file is not included in the source package because of the .nopurl suffix in its
filename.
-
The chunks below have to be manually executed in order to regenerate the package data.
-
Although the datasets below are saved as "internal data" in R/sysdata.rda, they can still be exported and
documented (by documenting the dataset's quoted name in the main .Rmd source file -- which only works when the dataset is also @exported), something
not explicitly mentioned in the book R
Packages. To do so, you first need to manually add the export() directive in the NAMESPACE file since
roxygen2 won't add it automatically.
Define data
default_linters
NOTES:
-
Non-default linters that we tested but dismissed due to annoyance or disagreement include:
nested_pipe_linter (nesting pipes doesn't necessarily have to make the code less-readable, on the contrary!)nonportable_path_linter (requires paths to always be constructed using file.path(), but file.path() emits forward-slashes on all platforms incl.
Windows, so the benefit seems questionable; besides, fs::path() is clearly superior to file.path() anyways)strings_as_factors_linter (unnecessary when the code requires R >= 4.0)
default_linters <- lintr::linters_with_defaults(
absolute_path_linter = lintr::absolute_path_linter(),
any_duplicated_linter = lintr::any_duplicated_linter(),
any_is_na_linter = lintr::any_is_na_linter(),
assignment_linter = lintr::assignment_linter(operator = c("<-", "<<-", "%<>%")),
boolean_arithmetic_linter = lintr::boolean_arithmetic_linter(),
# TODO: set `function_braces = "not_inline"` once lintr 3.2.1+ is released
brace_linter = lintr::brace_linter(allow_single_line = TRUE),
class_equals_linter = lintr::class_equals_linter(),
comparison_negation_linter = lintr::comparison_negation_linter(),
condition_call_linter = lintr::condition_call_linter(),
condition_message_linter = lintr::condition_message_linter(),
conjunct_test_linter = lintr::conjunct_test_linter(allow_filter = "always"),
consecutive_assertion_linter = lintr::consecutive_assertion_linter(),
consecutive_mutate_linter = lintr::consecutive_mutate_linter(),
cyclocomp_linter = lintr::cyclocomp_linter(),
empty_assignment_linter = lintr::empty_assignment_linter(),
expect_comparison_linter = lintr::expect_comparison_linter(),
expect_identical_linter = lintr::expect_identical_linter(),
expect_length_linter = lintr::expect_length_linter(),
expect_named_linter = lintr::expect_named_linter(),
expect_not_linter = lintr::expect_not_linter(),
expect_null_linter = lintr::expect_null_linter(),
expect_s3_class_linter = lintr::expect_s3_class_linter(),
expect_s4_class_linter = lintr::expect_s4_class_linter(),
expect_true_false_linter = lintr::expect_true_false_linter(),
expect_type_linter = lintr::expect_type_linter(),
fixed_regex_linter = lintr::fixed_regex_linter(),
for_loop_index_linter = lintr::for_loop_index_linter(),
function_argument_linter = lintr::function_argument_linter(),
function_return_linter = lintr::function_return_linter(),
if_not_else_linter = lintr::if_not_else_linter(exceptions = NULL),
if_switch_linter = lintr::if_switch_linter(),
ifelse_censor_linter = lintr::ifelse_censor_linter(),
implicit_assignment_linter = lintr::implicit_assignment_linter(),
implicit_integer_linter = lintr::implicit_integer_linter(allow_colon = TRUE),
# DISABLED due to too many false-positives / deviations from RStudio's auto-indent
# cf. https://github.com/r-lib/lintr/issues?q=is%3Aissue+is%3Aopen+indentation_linter
# indentation_linter = lintr::indentation_linter(hanging_indent_style = "always"),
indentation_linter = NULL,
inner_combine_linter = lintr::inner_combine_linter(),
is_numeric_linter = lintr::is_numeric_linter(),
keyword_quote_linter = lintr::keyword_quote_linter(),
length_levels_linter = lintr::length_levels_linter(),
length_test_linter = lintr::length_test_linter(),
lengths_linter = lintr::lengths_linter(),
line_length_linter = lintr::line_length_linter(length = 160L),
list_comparison_linter = lintr::list_comparison_linter(),
literal_coercion_linter = lintr::literal_coercion_linter(),
# NOTE: non-base-R fns aren't up for inclusion in default `except` arg, thus we have to customize ourselves
# cf. https://github.com/r-lib/lintr/issues/2109#issuecomment-1842245434
missing_argument_linter = lintr::missing_argument_linter(except = c("alist",
"quote",
"switch",
"extract")),
nested_ifelse_linter = lintr::nested_ifelse_linter(),
nrow_subset_linter = lintr::nrow_subset_linter(),
numeric_leading_zero_linter = lintr::numeric_leading_zero_linter(),
nzchar_linter = lintr::nzchar_linter(),
object_length_linter = lintr::object_length_linter(length = 40L),
object_overwrite_linter = lintr::object_overwrite_linter(packages = "base"),
# TODO: try re-enabling once https://github.com/r-lib/lintr/issues/2252 is fixed
object_usage_linter = NULL,
one_call_pipe_linter = lintr::one_call_pipe_linter(),
outer_negation_linter = lintr::outer_negation_linter(),
paste_linter = lintr::paste_linter(),
pipe_call_linter = lintr::pipe_call_linter(),
pipe_return_linter = lintr::pipe_return_linter(),
print_linter = lintr::print_linter(),
# disabled because being able to use both types of quotes allows to avoid having to escape the respective other quote type
quotes_linter = NULL,
redundant_equals_linter = lintr::redundant_equals_linter(),
redundant_ifelse_linter = lintr::redundant_ifelse_linter(),
regex_subset_linter = lintr::regex_subset_linter(),
rep_len_linter = lintr::rep_len_linter(),
repeat_linter = lintr::repeat_linter(),
routine_registration_linter = lintr::routine_registration_linter(),
sample_int_linter = lintr::sample_int_linter(),
scalar_in_linter = lintr::scalar_in_linter(),
sort_linter = lintr::sort_linter(),
sprintf_linter = lintr::sprintf_linter(),
stopifnot_all_linter = lintr::stopifnot_all_linter(),
string_boundary_linter = lintr::string_boundary_linter(),
system_file_linter = lintr::system_file_linter(),
terminal_close_linter = lintr::terminal_close_linter(),
todo_comment_linter = lintr::todo_comment_linter(),
# disabled since RStudio's built-in `StripTrailingWhitespace` proj opt ignores .Rmd code chunks
trailing_whitespace_linter = NULL,
undesirable_function_linter = lintr::undesirable_function_linter(symbol_is_undesirable = FALSE),
undesirable_operator_linter = lintr::undesirable_operator_linter(op = c(lintr::default_undesirable_operators,
"->" = "Makes it harder to see in code where an object is defined.")),
unnecessary_concatenation_linter = lintr::unnecessary_concatenation_linter(),
unnecessary_lambda_linter = lintr::unnecessary_lambda_linter(),
# TODO: re-enable once lintr 3.2.1+ is released
# unnecessary_nesting_linter = lintr::unnecessary_nesting_linter(),
unnecessary_placeholder_linter = lintr::unnecessary_placeholder_linter(),
unreachable_code_linter = lintr::unreachable_code_linter(),
which_grepl_linter = lintr::which_grepl_linter(),
yoda_test_linter = lintr::yoda_test_linter()
)
funky_config
funky_config <-
funky::ptype_config |>
tibble::add_row(key = "add_copyright_notice",
default_value = list(TRUE),
description = paste0("Whether or not to add a **copyright notice** at the beginning of the generated `.R` files as recommended by e.g. the ",
"[GNU licenses](https://www.gnu.org/licenses/gpl-howto.html). The notice consists of the name and description of the ",
"program and the word `Copyright (C)` followed by the release years and the name(s) of the copyright holder(s), or if ",
"not specified, the author(s). The year is always the current year. All the other information is extracted from the ",
"package's `DESCRIPTION` file.")) |>
tibble::add_row(key = "add_license_notice",
default_value = list(TRUE),
description = paste0("Whether or not to add a **license notice** at the beginning of the generated `.R` files as recommended by e.g. the ",
"[GNU licenses](https://www.gnu.org/licenses/gpl-howto.html). The license is determined from the package's ",
"`DESCRIPTION` file and currently only the [`AGPL-3.0-or-later` ",
"license](https://spdx.org/licenses/AGPL-3.0-or-later.html) is supported.")) |>
tibble::add_row(key = "gen_pkgdown_ref",
default_value = list(TRUE),
description = paste0("Whether or not to overwrite [pkgdown](https://pkgdown.r-lib.org/)'s [reference ",
"index](https://pkgdown.r-lib.org/reference/build_reference.html#reference-index) in the configuration file ",
"`_pkgdown.yml` with an auto-generated one based on the main input file as described in [pkgpurl::gen_pkgdown_ref()]."))
Write data
Save all the small data objects as a single internal file R/sysdata.rda. Note that when documenting them, they must be explicitly @exported to be available
to package users.
usethis::use_data(default_linters,
funky_config,
internal = TRUE,
overwrite = TRUE,
compress = "xz",
version = 3L)
salim-b/pkgpurl documentation built on June 2, 2025, 8:26 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
NOTES
-
This file is not included in the source package because of the
.nopurlsuffix in its filename. -
The chunks below have to be manually executed in order to regenerate the package data.
-
Although the datasets below are saved as "internal data" in
R/sysdata.rda, they can still be exported and documented (by documenting the dataset's quoted name in the main.Rmdsource file -- which only works when the dataset is also@exported), something not explicitly mentioned in the book R Packages. To do so, you first need to manually add theexport()directive in the NAMESPACE file since roxygen2 won't add it automatically.
Define data
default_linters
NOTES:
-
Non-default linters that we tested but dismissed due to annoyance or disagreement include:
nested_pipe_linter(nesting pipes doesn't necessarily have to make the code less-readable, on the contrary!)nonportable_path_linter(requires paths to always be constructed usingfile.path(), butfile.path()emits forward-slashes on all platforms incl. Windows, so the benefit seems questionable; besides,fs::path()is clearly superior tofile.path()anyways)strings_as_factors_linter(unnecessary when the code requires R >= 4.0)
default_linters <- lintr::linters_with_defaults( absolute_path_linter = lintr::absolute_path_linter(), any_duplicated_linter = lintr::any_duplicated_linter(), any_is_na_linter = lintr::any_is_na_linter(), assignment_linter = lintr::assignment_linter(operator = c("<-", "<<-", "%<>%")), boolean_arithmetic_linter = lintr::boolean_arithmetic_linter(), # TODO: set `function_braces = "not_inline"` once lintr 3.2.1+ is released brace_linter = lintr::brace_linter(allow_single_line = TRUE), class_equals_linter = lintr::class_equals_linter(), comparison_negation_linter = lintr::comparison_negation_linter(), condition_call_linter = lintr::condition_call_linter(), condition_message_linter = lintr::condition_message_linter(), conjunct_test_linter = lintr::conjunct_test_linter(allow_filter = "always"), consecutive_assertion_linter = lintr::consecutive_assertion_linter(), consecutive_mutate_linter = lintr::consecutive_mutate_linter(), cyclocomp_linter = lintr::cyclocomp_linter(), empty_assignment_linter = lintr::empty_assignment_linter(), expect_comparison_linter = lintr::expect_comparison_linter(), expect_identical_linter = lintr::expect_identical_linter(), expect_length_linter = lintr::expect_length_linter(), expect_named_linter = lintr::expect_named_linter(), expect_not_linter = lintr::expect_not_linter(), expect_null_linter = lintr::expect_null_linter(), expect_s3_class_linter = lintr::expect_s3_class_linter(), expect_s4_class_linter = lintr::expect_s4_class_linter(), expect_true_false_linter = lintr::expect_true_false_linter(), expect_type_linter = lintr::expect_type_linter(), fixed_regex_linter = lintr::fixed_regex_linter(), for_loop_index_linter = lintr::for_loop_index_linter(), function_argument_linter = lintr::function_argument_linter(), function_return_linter = lintr::function_return_linter(), if_not_else_linter = lintr::if_not_else_linter(exceptions = NULL), if_switch_linter = lintr::if_switch_linter(), ifelse_censor_linter = lintr::ifelse_censor_linter(), implicit_assignment_linter = lintr::implicit_assignment_linter(), implicit_integer_linter = lintr::implicit_integer_linter(allow_colon = TRUE), # DISABLED due to too many false-positives / deviations from RStudio's auto-indent # cf. https://github.com/r-lib/lintr/issues?q=is%3Aissue+is%3Aopen+indentation_linter # indentation_linter = lintr::indentation_linter(hanging_indent_style = "always"), indentation_linter = NULL, inner_combine_linter = lintr::inner_combine_linter(), is_numeric_linter = lintr::is_numeric_linter(), keyword_quote_linter = lintr::keyword_quote_linter(), length_levels_linter = lintr::length_levels_linter(), length_test_linter = lintr::length_test_linter(), lengths_linter = lintr::lengths_linter(), line_length_linter = lintr::line_length_linter(length = 160L), list_comparison_linter = lintr::list_comparison_linter(), literal_coercion_linter = lintr::literal_coercion_linter(), # NOTE: non-base-R fns aren't up for inclusion in default `except` arg, thus we have to customize ourselves # cf. https://github.com/r-lib/lintr/issues/2109#issuecomment-1842245434 missing_argument_linter = lintr::missing_argument_linter(except = c("alist", "quote", "switch", "extract")), nested_ifelse_linter = lintr::nested_ifelse_linter(), nrow_subset_linter = lintr::nrow_subset_linter(), numeric_leading_zero_linter = lintr::numeric_leading_zero_linter(), nzchar_linter = lintr::nzchar_linter(), object_length_linter = lintr::object_length_linter(length = 40L), object_overwrite_linter = lintr::object_overwrite_linter(packages = "base"), # TODO: try re-enabling once https://github.com/r-lib/lintr/issues/2252 is fixed object_usage_linter = NULL, one_call_pipe_linter = lintr::one_call_pipe_linter(), outer_negation_linter = lintr::outer_negation_linter(), paste_linter = lintr::paste_linter(), pipe_call_linter = lintr::pipe_call_linter(), pipe_return_linter = lintr::pipe_return_linter(), print_linter = lintr::print_linter(), # disabled because being able to use both types of quotes allows to avoid having to escape the respective other quote type quotes_linter = NULL, redundant_equals_linter = lintr::redundant_equals_linter(), redundant_ifelse_linter = lintr::redundant_ifelse_linter(), regex_subset_linter = lintr::regex_subset_linter(), rep_len_linter = lintr::rep_len_linter(), repeat_linter = lintr::repeat_linter(), routine_registration_linter = lintr::routine_registration_linter(), sample_int_linter = lintr::sample_int_linter(), scalar_in_linter = lintr::scalar_in_linter(), sort_linter = lintr::sort_linter(), sprintf_linter = lintr::sprintf_linter(), stopifnot_all_linter = lintr::stopifnot_all_linter(), string_boundary_linter = lintr::string_boundary_linter(), system_file_linter = lintr::system_file_linter(), terminal_close_linter = lintr::terminal_close_linter(), todo_comment_linter = lintr::todo_comment_linter(), # disabled since RStudio's built-in `StripTrailingWhitespace` proj opt ignores .Rmd code chunks trailing_whitespace_linter = NULL, undesirable_function_linter = lintr::undesirable_function_linter(symbol_is_undesirable = FALSE), undesirable_operator_linter = lintr::undesirable_operator_linter(op = c(lintr::default_undesirable_operators, "->" = "Makes it harder to see in code where an object is defined.")), unnecessary_concatenation_linter = lintr::unnecessary_concatenation_linter(), unnecessary_lambda_linter = lintr::unnecessary_lambda_linter(), # TODO: re-enable once lintr 3.2.1+ is released # unnecessary_nesting_linter = lintr::unnecessary_nesting_linter(), unnecessary_placeholder_linter = lintr::unnecessary_placeholder_linter(), unreachable_code_linter = lintr::unreachable_code_linter(), which_grepl_linter = lintr::which_grepl_linter(), yoda_test_linter = lintr::yoda_test_linter() )
funky_config
funky_config <- funky::ptype_config |> tibble::add_row(key = "add_copyright_notice", default_value = list(TRUE), description = paste0("Whether or not to add a **copyright notice** at the beginning of the generated `.R` files as recommended by e.g. the ", "[GNU licenses](https://www.gnu.org/licenses/gpl-howto.html). The notice consists of the name and description of the ", "program and the word `Copyright (C)` followed by the release years and the name(s) of the copyright holder(s), or if ", "not specified, the author(s). The year is always the current year. All the other information is extracted from the ", "package's `DESCRIPTION` file.")) |> tibble::add_row(key = "add_license_notice", default_value = list(TRUE), description = paste0("Whether or not to add a **license notice** at the beginning of the generated `.R` files as recommended by e.g. the ", "[GNU licenses](https://www.gnu.org/licenses/gpl-howto.html). The license is determined from the package's ", "`DESCRIPTION` file and currently only the [`AGPL-3.0-or-later` ", "license](https://spdx.org/licenses/AGPL-3.0-or-later.html) is supported.")) |> tibble::add_row(key = "gen_pkgdown_ref", default_value = list(TRUE), description = paste0("Whether or not to overwrite [pkgdown](https://pkgdown.r-lib.org/)'s [reference ", "index](https://pkgdown.r-lib.org/reference/build_reference.html#reference-index) in the configuration file ", "`_pkgdown.yml` with an auto-generated one based on the main input file as described in [pkgpurl::gen_pkgdown_ref()]."))
Write data
Save all the small data objects as a single internal file R/sysdata.rda. Note that when documenting them, they must be explicitly @exported to be available
to package users.
usethis::use_data(default_linters, funky_config, internal = TRUE, overwrite = TRUE, compress = "xz", version = 3L)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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