NEWS.md

In klmr/roxydoxy: Documentation for non-package R code

roxygen2 6.0.0.9000

• Automatically generating a usage section for an infix function containing "<-" no longer removes "<-" from the function name (#554).

roxygen2 6.0.0

Markdown

• Most fields can now be written using Markdown markup instead of the traditional Rd language. You can turn on Markdown globally by adding Roxygen: list(markdown = TRUE) to DESCRIPTION. The @md / @noMd tags turn Markdown parsing on / off for the given block. See vignette("markdown") for more details (#364, #431, #499, #506, #507), by @gaborcsardi

Improved inheritance

• New @inheritDocParams allows you to automatically generate parameter documentation for ... for the common case where you pass ... on to another function (#512). Because you often override some arguments, it comes with a flexible specification for argument selection:

  • @inheritDotParams foo takes all parameters from foo()
  • @inheritDotParams foo a b e:h takes parameters a, b, and all parameters between e and h
  • @inheritDotParams foo -x -y takes all parameters except for x and y.

  The documentation generated is similar to the style used in ?plot and will eventually be incorporated in to RStudio's autocomplete.

• New @inherit generalises @inheritParams, and allows to you inherit parameters, return, references, title, description, details, sections, and seealso. The default @inherit my_fun will inherit all, you can document an object entirely by specifying only the @inherit tag. Alternatively, you can select specific tags to inherit with @inherit my_fun return params (#384).

• New @inheritSection fun title allows you to inherit the contents of a single section from another topic (#513).

• @inheritParams now works recursively, so that you can inherit parameters from a function that inherited its paramters from somewhere else. It also better handles \dots as an alias for ... (#504).

Minor improvements and bug fixes

Tags

• @aliases are no longer sorted alphabetically, but instead match the order of their usage. This gives you more control in pkgdown.

• @describeIn now escapes special characters in function names (#450).

• @family see alsos are added in the same order they appear, not alphabetically (#315). Fixed an issue where .s were sometimes added between words within a @family tag (#477, @kevinushey).

• @author is rendered after @seealso.

• @example gives a nice warning message if you accidentally use it instead of @examples (#494). Multiple @examples sections are merged (#472, @krlmlr).

• Roxygen will no longer write out topics that don't have a name or title, and will instead generate a warning. This makes it easier to detect if you've accidentally used @rdname with an incorrect value (#474).

S3

• Non-primitive, internal S3 generics (e.g. 'rbind', 'cbind') are now properly detected as S3 generics. (#488, @kevinushey)

• Ensure that functions with S3 class are still treated as functions (#455).

• S3 method declarations via R.methodS3::setMethodS3() and function declarations via R.oo::setConstructorS3() are now supported (@HenrikBengtsson, #525).

S4

• You can now document setClassUnion()s (#514).

• The default alias for S4 method now re-addeds trailing ANY signatures that are sometimes dropped (#460).

• Back references are now wrapped over multiple lines, if long (#493, @LiNk-NY).

Other

• "_PACKAGE" documentation now generates a default @seealso combining the URL and BugReport fields, and a default @author field generated from the Authors@R field (#527). It now works from roxygenise(); before it only worked from devtools::document() (#439, @krlmlr).

• Manually created NAMESPACE or documentation files are never overwritten, even if using roxygen2 for the first time (@krlmlr, #436).

• Changes to DESCRIPTION (i.e. Collate: and RoxygenNote) now use the desc package. This will minimise spurious changes (#430).

• default_data_format() has been renamed to object_format().

• New roclet_find() provides a more flexible way to specify roclets: as roclet name (e.g. "rd_roclet"), in an package ("foo::roclet_bar"), or with options ("foo::roclet_bar(baz = TRUE)").

• The usage of replacement functions uses non-breaking spaces so that <- will never get put on its own line (#484).

• Roxygen now parses nonASCII documentation correctly (as long as UTF-8 encoded or specified Encoding in DESCRIPTION) (#532, @shrektan), and ignores files listed in .Rbuildignore (#446, @fmichonneau).

Extending roxygen2

• Deprecated register.preref.parser() and register.preref.parsers() have been removed. register_tags() has also been removed in favour of a new roclet_tags() generic.

• roclet() (the constructor), roclet_tags(), roclet_process() roclet_output(), roc_clean() and now exported making it possible to create roclets in other packages. Helper functions roxy_tag() and roxy_tag_warning() are also exported.

• new_roclet() is no longer exported - use roclet() instead.

roxygen2 5.0.1

• Use ls(), not names() to list elements of environment: fixes R 3.1.0 incompatibility (#422, @kevinushey).

• @export again allows trailing new line (#415).

• Fixed bug in @noRd, where usage would cause error (#418).

roxygen2 5.0.0

New features

• Roxygen now records its version in a single place: the RoxygenNote field in the DESCRIPTION (#338). This will be the last time an roxygen2 upgrade changes every file in man/.

• You can now easily re-export functions that you've imported from another package:

  ```R

  ' @export

  magrittr::%>% ```

  All imported-and-re-exported functions will be documented in the same file (rexports.Rd), containing a brief descrption and links to the original documentation (#376).

• You can more easily generate package documentation by documenting the special string "_PACKAGE" (@krlmlr, #349):

  ```R

  ' @details Details

  "_PACKAGE" ```

  The title and description will be automatically filled in from the DESCRIPTION.

• New tags @rawRd and @rawNamespace allow you to insert raw (unescaped) in Rd and the NAMESPACE (this is useful for conditional imports). @evalRd() is similar, but instead of literal Rd, you give it R code that produces literal Rd code when run. This should make it easier to experiment with new types of output (#385).

• Roxygen2 now parses the source code files in the order specified in the Collate field in DESCRIPTION. This improves the ordering of the generated documentation when using @describeIn and/or @rdname split across several .R files, as often happens when working with S4 (#323, #324).

Minor features and bug fixes

• The contents of documented functions are now also parsed for roxygen comments. This allows, e.g., documenting a parameter's type close to where this type is checked, or documenting implementation details close to the source, and simplifies future extensions such as the documentation of R6 classes (#397, @krlmlr).

• Data objects get a simpler default @format that describes only the object's class and dimensions. The former default, generated by generated by str(), didn't usually produce useful output and was quite slow. The new S3 generic default_data_format() generates the format and can be overridden to generate a custom format (#410, @krlmlr).

• The roxygen parsers has been completely rewritten in C++ (#295). This gives a nice performance boost and gives:

• Better error messages: you now get the exact the line number of the tag, not just the start of the block.

• The parser has been simplified a little: tags now must always start on a new line. This is recommended practice anyway, and it means that escaping inline @ (with @@) is now optional. (#235)

• Unknown tags now emit a warning, rather than an error.

• @examples no longer complains about non-matching braces inside strings (#329).

• @family now cross-links each manual page only once, instread of linking to all aliases (@gaborcsardi, #283, #367).

• The special @include parser has also been rewritten in C++, giving a performance boost for larger packages (#401). This is particularly important because it's also called from devtools::load_all(). Additionally, a space before @include is no longer necessary (@krlmlr, #342).

• @inheritParams foo::bar ensures that % remains escaped (#313).

• If you document multiple arguments with one @param, (e.g. @param a,b,c) each parameter will get a space after it so it can be wrapped in the generated Rd file (#373).

• @sections with identical titles are now merged together, just like @description and @details. This is useful in conjunction with the @rdname tag. (@krlmlr, #300).

• Automatic @usage is now correctly generated for functions with string arguments containing "\"" (#265).

• load_options() is now exported so devtools::document() doesn't have to run update_collate() twice (#395).

• update_collate() only rewrites the Collate entry in the DESCRIPTION file when it changes (#325, #723).

• An empty NAMESPACE file is written if it is maintained by roxygen2 (@krlmlr, #348).

• Data that is not lazy-loaded can be documented (@krlmlr, #390).

Internal changes

• register.preref.parser() and register.preref.parsers() have been deprecated - please use register_tags() instead.

• Parser callbacks registered with register_tags() are now called for fields parsed from the "introduction" (the text before the first tag) (@gaborcsardi, #370).

roxygen2 4.1.1

• Formatting of the Authors@R field in the DESCRIPTION file is now retained (@jranke, #330).

• The collate roclet falls back to base::strwrap() when generating the collate field. This makes roxygen2 compatible with the next version of stringr.

• New "vignette" roclet. This vignette automatically rebuilds all out of date vignettes (#314).

• An off-by-one error in the C++ Roxygen preparser was fixed.

• The new @backref tag makes it possible to override the sourceref for R code generators like Rcpp (@krlmlr, #291, #294).

roxygen2 4.1.0

• The source of the documentation is added to autogenerated .Rd files.

• If there are no @include tags, roxygen2 leaves the collate field alone. This makes it easier to convert an existing project that uses a predefined collate, but if you start with @include and later remove them, you'll need to also remove the collate field (#302, #303).

• Protected a dir() with sort_c() - If you'd noticed an inconsistency in ordering between devtools::document() and devtools::check() this was the cause of that.

• Fixed broken regular expression that caused problems with stringr 1.0.0.

• The Authors@R field in DESCRIPTION is now longer wrapped(@krlmlr, #284).

• @describeIn with plain functions now correctly includes the function name and can be applied to data documentation. (@jimhester, #285, #288).

• Works again when called from Rscript and methods is not loaded (@krlmlr, #305).

roxygen2 4.0.2

• If you don't use @exports or other namespace directives, your namespace file will not be touched (#276).

• Methods no longer automatically attempt to inherit parameters from their generic. It's too fraught with difficulty (#261).

• Roxygen now understands what to do with setReplaceMethod() (#266).

• Parameter documentation is ordered according to the order of the formals, if possible (@krlmlr, #63).

• Export is_s3_method().

• Roxygen no longer fails when run in non-UTF-8 locales on windows.

roxygen2 4.0.1

• Explicit updateRoxygen() is no longer needed - roxygenize() does the right thing the first time it is run.

• Exporting a S4 generic works (#246).

• roxygenise() no longer complains about absense of wrap field because it's so unlikely that anyone wants the old behaviour (#245).

roxygen2 4.0.0

Roxygen2 4.0.0 is a major update to roxygen2 that makes provides enhanced error handling and considerably safer default behaviour. Now, roxygen2 will never overwrite a file that it did not create. This means that before you run it for the first time, you'll need to run roxygen2::upgradeRoxygen(). That will flag all existing files as being created by roxygen2.

New features

• Six vignettes provide a comprehensive overview of using roxygen2 in practice. Run browseVignettes("roxygen2") to access.

• @describeIn makes it easier to describe multiple functions in one file. This is especially useful if you want to document methods with their generic, or with a common class, but it's also useful if you want to document multiple related functions in one file (#185).

• @field documents the fields on a reference class (#181). It works the same way as @slot for S4 classes.

• You can now document objects defined elsewhere (like datasets) by documenting their name as a string (#221). For example, to document an dataset called mydata, you can do:

  ```R

  ' Mydata set

  '

  ' Some data I collected about myself

  "mydata" ```

• Roxygen2 now adds a comment to all generated files so that you know they've been generated, and should not be hand edited.

• Roxygen2 no longer wraps the text in Rd files by default, i.e. the default option is wrap = FALSE now. To override it, you have to specify a field Roxygen: list(wrap = TRUE) in DESCRIPTION (#178).

• Roxygenise automatically deletes out-of-date Rd files in man/.

Improved error handling

• Roxygen2 will never overwrite a file that was not generated by roxygen2. This means that the first time you use this version of roxygen, you'll need to delete all existing Rd files. roxygenise() gains a clean argument that will automatically remove any files previously created by roxygen2.

• Parsing is stricter: many issues that were previously warnings are now errors. All errors should now give you the line number of the roxygen block associated with the error.

• Every input is now checked to make sure that you have matching braces (e.g. every { has a matching }). This should prevent frustrating errors that require careful reading of .Rd files (#183).

• @section titles and @export tags can now only span a single line to prevent common bugs.

• @S3method is deprecated - just use @export (#198).

• Namespace tags now throw parsing errors if you give them bad inputs (#220).

• Better error message if you try to document something other than NULL, an assignment, a class, a generic or a method (#194).

Bug fixes and minor improvements

• Better parsing of non-syntactic function names in other packages when used in @inheritParams (#236).

• Deprecated arguments to roxygenise() (roxygen.dir, copy.package, overwrite, unlink.target) removed.

• Remove unneeded codetools and tools dependencies.

• Bump required Rcpp version to 0.11.0, and remove custom makefiles.

• Non-syntactic argument names (like _x) are now surrounded by back-ticks in the usage (#191).

• The internal parsers are no longer part of the public roxygen2 interface.

• Usage statements in generated roxygen statements non-longer contain non-ASCII characters and will be wrapped if long (#180).

• By default, reference classes now only document their own methods, not their methods of parents (#201).

• Default aliases always include the original name of the object, even if overridden by @name. This also means that A <- setClass("A") will get two aliases by default: A and A-class (#202). Use @aliases NULL to suppress default alias.

• Non-syntactic class names (like <-) are now escaped in the usage section of S4 methods (#205).

• Eliminated two more cases where wrapping occured even when wrap = FALSE.

roxygen2 3.1.0

Documentation for reference classes

It's now possible to document reference classes, using the "docstring" convention described in ?setRefClass. If you want to provide a short paragraph description of what a method does, make the first component of the message a string containing the description, e.g.:

setRefClass("A", methods = list(
  f = function(a, b) {
    "Take numbers \code{a} and \code{b} and add them together"
    a + b
  }
))

Unlike the documentation for R functions, the documentation for methods can be quite succinct.

Roxygen adopts the convention that documented methods are public, and will be listed in the man page for the object. Undocumented methods are private and will not be shown in the documentation. The methods for all superclasses are also listed, so that you don't need to flip through multiple pages of documentation to understand what you can do with an object. All documented methods will be placed in a bulleted list in a section titled "Methods", the method usage will be automatically prepended to the docstring.

Minor fixes and improvements

• Fixes for Rcpp 0.11.0 compatibility.

• roxygenise() now invisible returns a list of all files generated by individual roclets. This is useful for tools that want to figure out if there are extra files in the man/ directory.

• is_s3_generic() now recognises group generics (#166).

• Don't try and add parameters for data objects (#165).

• Sort output of families using C locale (#171).

• @family now escapes function names in references (#172).

roxygen2 3.0.0

Roxygen2 now fully supports S4 and RC (reference classes) - you should no longer need to manually add @alias or @usage tags for S4 classes, methods and generics, or for RC classes.

• The default usage definitions are much better, generating the correct usage for data sets (#122), S3 methods (without additional @method tag), S4 generics, S4 methods, and for replacement (#119) and infix functions. Backslashes in function arguments in are correctly escaped. Usage statements also use a more sophisticated line wrapping algorithm so that they should cause fewer problems with the R CMD check line limit. (#89, #125).

• S4 classes, S4 methods, and RC classes are given better default topics, and the file names corresponding to those topics are shorter.

• S4 methods will automatically inherit parameter documentation from their generic.

• @slot name description allows you to document the slots of a S4 class.

S3 support has also been improved: roxygen2 now figures out whether a function is a S3 method or generic. (In the rare cases it does so incorrectly, use @method to manually describe the generic and class associated with a method). This means you can remove existing uses of @method, and can replace @S3method with @export.

Roxygen now has support for package specific options through the Roxygen field in the DESCRIPTION. The value of the field should be R code that results in a list. Currently only wrap and roclet values are supported:

• Turn off Rd re-wrapping with adding Roxygen: list(wrap = FALSE)

• Change the default roclets by specifying Roxygen: list(roclets = c("collate", "rd"))

Roxygen 3.0 also includes a number of minor fixes and improvements:

• Infix functions are now escaped correctly in the NAMESPACE. (Thanks to @crowding, #111)

• roxygenise() now works more like devtools::document() and only ever works in the current directory. The arguments roxygen.dir, overwrite, copy.package and unlink.target have been deprecated due to potential data loss problems.

• The collate roclet is no longer a roclet: it processes R files using custom code (only statically, not dynamically) and is designed to be executed before the code is sourced. Run update_collate() to update the Collate directive based on @include tags - if there are none present, a collate directive will not be generated.

• @useDynLib now works with more possible specifications - if you include a comma in the tag value, the output will be passed as is. This means that @useDynLib mypackage, .registration = TRUE will now generate useDynLib(mypackage, .registration = TRUE) in the NAMESPACE. (#124)

• inst directory not created by default (#56).

• Explicitly depend on utils and methods packages to make roxygen compatible with Rscript (#72). Import digest package instead of depending on it.

• Always use C locale when sorting NAMESPACE file or tags in .Rd files. This ensures a consistent ordering across systems (#127).

• Templates with extension .r are supported on case-sensitive file systems (#115). Template variables now actually work (#160, thanks to @bronaugh).

• Suppress default aliases, format and usage with @aliases NULL, @format NULL and @usage NULL.

roxygen2 2.2.2

• Correctly use keyword datasets not dataset (Fixes #60)

• Reference classes no longer given incorrect docType (data).

roxygen2 2.2.1

• Use unicode escapes in test files so tests pass on all platforms.

• Work around bug in gsub in C locale by manually specifying Encoding().

roxygen2 2.2

New features

• Package docType will automatically add package alias, if needed. (Fixes #4)

• Data docType will automatically add datasets keyword, default usage, and default format. (Fixes #5). Data docType automatically added to data objects.

• New @encoding tag for manually setting non-ASCII encodings when needed. (Fixes #7)

Bug fixes

• write.description() now tries much harder to respect users' original DESCRIPTION field formatting instead of forcibly re-wrapping certain fields at 60 characters.

• @details and @description now work correctly

• @useDynLib now works correctly:

  @useDynLib packageName routine1 routine2

produces

   useDynLib(packageName, routine1)
   useDynLib(packageName, routine2)

in the NAMESPACE file, instead of separate (wrong) useDynLib statements as before.

• All namespace import directives now behave in the same way as the export directives, producing multiple single directives instead one multiple directive: @importClassesFrom pkg a b now produces importClassesFrom(pkg, a) and importClassesFrom(pkg, b)

• In example files included with @example you can now use infix operators (e.g. %*%) or other things with %, because they will be preceded by a backslash in the Rd file. This behaviour was already in place for examples directly included with @examples.

• Aliases are no longer quoted, and % is escaped with a backslash (Fixes #24). Names also have % escaped (Fixes #50)

• Replacement functions (e.g. foo<-) now get correct usage statements: foo() <- value instead of foo()<-value. (Fixes #38)

• Functions with no arguments now correctly get usage statements (Fixes #35)

• Indentation in examples now preserved (Fixes #27)

• roxygen2 will replace characters that are not valid in filenames with a character substitute, e.g. [] becomes sub, <- becomes set (Fixes #6)

• Usage strings use non-breaking spaces to prevent string default values containing whitespace to be split across multiple lines. This may cause problems in the unlikely event that you have default value containing a non-breaking space (`"\uA0"') (Fixes #21)

• Functions with quoted names now get correct usage statements (Fixes #41)

• Objects that no longer exist are not documented (Fixes #42)

• Errors now display file name and line number of roxygen block to help you find the problem. Thanks to code contributions from Renaud Gaujoux. (Fixes #13)

• Documentation with no untagged text but with @title, @description and @details tags now produces correct output.

roxygen2 2.1

New features

• package dependencies loaded automatically

• added support for the @source tag

Bug fixes

• NAMESPACE file no longer needs to exist

• Collate field in DESCRIPTION no longer needs to exist

• = now recognised as way of assigning functions

• x$y <- function() {...} no longer causes error

• @example no longer added extra new-lines.

• Correct directory normalisation under windows fixes broken test.

• A special thanks goes to Yihui Xie who contributed all of the fixes and improvements (bar one) in this version!

roxygen2 2.0

Major changes

• now works with run-time details to give more accurate output. This requires that the source code that roxygen is documenting be loaded prior to documentation. roxygen will attempt to do so, but you need to ensure required packages are loaded.

  Run-time data fixes some long standing bugs where roxygen couldn't correctly figure out function usage. We are not aware of any cases where you still need to use the @usage tag.

• written in idiomatic R, and uses S3 instead of a homegrown class system.

• roclets build up an internal data structure instead of writing to disk directly. This means that you can now use the @rdname tag to merge documentation for multiple functions into one file, and that only unique namespace directives are written to NAMESPACE (which makes @importFrom much more useful).

• some features have been removed, and may or may not (based on your feedback) be reincluded. These include the callgraph roclet, and R CMD roxygen, which only worked on some systems.

• a templating system: use the @template tag to insert a brew template stored in man-roxygen. Template variables can be set using @templateVar name value and retrieved from within the template with <%= name %>

• extensive use of caching to make repeated runs as fast as possible. To clear caches and guarantee a complete rebuild, use clear_caches().

• parsing of "introduction" (the text before the first tag) has changed. Now the title consists of the first paragraph (i.e. all text before the first empty line), the second paragraph is the description and all others are put in the details. Any component can be overridden with @title, @description and @details as appropriate.

Minor changes

• @name is always output as an alias, even if @aliases are used.

• @export correctly uses @method to generate S3method namespace directive

New tags

• @rdname filename sets the output filename (without extension). Use for functions non-alphanumeric functions (e.g. [<-) or if you want to document multiple functions in one file

• @template templatename includes a documentation template (see above)

• @section Section title: contents includes a section with any title. Don't forget the colon! That separates the title of the section from its contents.

• @description and @details tags allow you to specify description and details components in a template

• @family family name automatically adds see-also cross-references between all functions in a family. A function can belong to multiple families.

• @inheritParams name allows you to inherit the documentation for parameters from another function, either within the current package (function) or in any other installed package (package:function). Currently only supports single inheritance (i.e. you can't inherit from a function that inherits from another function), but you can have multiple @inheritParams tags.

• @format has been implemented; it existed in the roxygen package but was actually ignored

klmr/roxydoxy documentation built on May 20, 2019, 4:09 p.m.