NEWS.md
When processing cross package markdown links (e.g. [pkg::fun()]), roxygen2 now looks up the file it needs to link to, instead of linking to the topic, to avoid “Non-file package-anchored links” R CMD check warnings.
R6 methods and re-exported functions are always sorted in the C locale; this ensures they’re always sorted the same way in every environment (#1077).
roxygen2 now supports inline markdown code and code chunks inside Rd tags. In particular in \out{} (#1115).
roxygen2 now supports inline markdown code and also code chunks, using the same notation as the knitr package. For example:
#' This manual was generated at: `r Sys.time()`.
#' ...
#' `mtcars` is a data frame with `r ncol(mtcars)` columns, here
#' is a summary of them:
#'
#' ```{r}
#' summary(mtcars)
#' ```See vignette("rd-formatting") for details.
roxygen2 now keeps using Windows (CR LF) line endings for files that already have CR LF line endings, and uses LF for new files (#989).
Auto-generated package documentation can now handle author ORCID comments containing full url (#1040).
Hyperlinks to R6 methods are also added in the PDF manual (#1006).
Empty annotations (alternate text) for figures added via markdown are now omitted. This caused issues when generating pkgdown web sites (#1051).
Roxygen metadata can now have a packages element, giving a character vector of package names to load. This makes it easier to use extension package that provide new tags for existing roclets (#1013). See ?load_options for more details.
@evalNamespace() works again (#1022).
@description NULL and @details NULL no longer fail; instead, these tags are ignored, except for @description NULL in package level documentation, where it can be used to suppress the auto-generated Description section (#1008).
Multiple @format tags are now combined (#1015).
The warning for @section titles spanning multiple lines now includes a hint that you’re missing a colon (@maelle, #994).
Can now document objects created with delayedAssign() by forcing evaluation at documentation time (#1041)
\example{} escaping has been improved (again!) so that special escapes within strings are correctly escaped (#990).@includeRmd has now an optional second argument, the top level section the included file will go to. It defaults to the details section (#970). Code chunks are now evaluated in a child of the global environment (#972).
@inheritParams does a better job of munging links.
Links of the form \link[=topic]{text} are now automatically converted to \link[pkg:topic]{text} when inherited from other packages (#979).
Internal has_topic() helper has a better implementation; this means that links should no longer be munged unnecessarily (#973).
\example{} escaping has been considerably simplified (#967), and is now documented in escape_example().
In \usage{}, S3/S4 methods are no longer double-escaped (#976).
Markdown tables with cells that contain multiple elements (e.g. text and code) are now rendered correctly (#985).
Markdown code blocks containing operators and other special syntax (e.g. function, if, +) now converted to \code{} not \verb{} (#971).
roxygen2 can now document R6 classes (#922). See vignette("rd") for details.
Rd comments (%) are now automatically escaped. You will need to replace any existing uses of \% with % (#879).
Markdown headings are supported in tags like @description, @details, and @return (#907, #908). Level 1 headings create a new top-level \section{}. Level 2 headings and below create nested \subsections{}.
Markdown tables are converted to a \tabular{} macro (#290). roxygen2 supports the GFM table syntax which looks like this:
Markdown code (`foofy`) is converted to to either \code{} or \verb{}, depending on whether it not it parses as R code. This better matches the description of \code{} and \verb{} macros, solves a certain class of escaping problems, and should make it easier to include arbitrary “code” snippets in documentation without causing Rd failures (#654).
Markdown links can now contain formatting, e.g. [*mean*][mean] will now generate \link[=mean]{\emph{mean}}.
Use of unsupported markdown features (e.g. blockquotes, inline HTML, and horizontal rules) generates informative error messages (#804).
The default formatting for function usage that spans multiple lines has now changed. Previously, the usage was wrapped to produce the smallest number of lines, e.g.:
parse_package(path = ".", env = env_package(path), registry = default_tags(), global_options = list())
Now it is wrapped so that each argument gets its own line (#820):
parse_package( path = ".", env = env_package(path), registry = default_tags(), global_options = list() )
If you prefer the old behaviour you can put the following in your DESCRIPTION:
Roxygen: list(old_usage = TRUE)roxygen2 now provides three strategies for loading your code (#822):
load_pkgload(), the default, uses pkgload. Compared to the previous release, this now automatically recompiles your package if needed.
load_source() attaches required packages and source()s all files in R/. This is a cruder simulation of package loading than pkgload (and e.g. is unreliable if you use S4 extensively), but it does not require that the package be compiled. Use if the default strategy (used in roxygen2 6.1.0 and above) causes you grief.
load_installed() assumes you have installed the package. This is best used as part of a bigger automated workflow.
You can override the default either by calling (e.g.) roxygenise(load_code = "source")) or by setting the load option in your DESCRIPTION: Roxygen: list(load = "source").
As well as storing roxygen options in the Roxygen field of the DESCRIPTION you can now also store them in man/roxygen/meta.R (#889). The evaluation of this file should produce a named list that maps option names to values.
roxygen now also looks for templates in man/roxygen/templates (#888).
New rd_family_title option: this should be a named list, and is used to overrides the default “Other family:” prefix that @family generates. For example, to override the prefix generated by @family foo place rd_family_title <- list(foo = "Custom prefix: ") in man/roxygen/meta.R (#830, @kevinushey).
Rd comments (%) are automatically escaped in markdown formatted text. This is a backward incompatible change because you will need to replace existing uses of \% with % (#879).
Using @docType package no longer automatically adds -name. Instead document _PACKAGE to get all the defaults for package documentation, or use @name to override the default file name.
@S3method has been removed. It was deprecated in roxygen2 4.0.0 released 2014-05-02, over 5 years ago.
Using the old wrap option will now trigger a warning, as hasn’t worked for quite some time. Suppress the error by deleting the option from your DESCRIPTION.
The process for extending roxygen2 with new tags and new roclets has been completely overhauled, and is now documented in vignette("extending"). If you’re one of the few people who have written a roxygen2 extension, this will break your code - but the documentation, object structure, and print methods are now so much better that I hope it’s not too annoying! Because this interface is now documented, it will not change in the future without warning and a deprecation cycle.
If you have previously made a new roclet, the major changes are:
The previously internal data structures used to represent blocks and tags have been overhauled. They are now documented and stable. See roxy_block() and roxy_tag() for details.
roclet_tags() is no longer used; instead define a roxy_tag_parse() method. For example, if you create a new @mytag tag, it will generate a class of roxy_tag_mytag, and will be parsed by roxy_tag_parse.roxy_tag_mytag() method. The method should return a new roxy_tag() object with the val field set.
This means that the registry argument is no longer needed and has been removed.
rd_section() and roxy_tag_rd() are now exported so that you can more easily extend rd_roclet() with your own tags that generate output in .Rd files.
global_options is no longer passed to all roclet methods. Instead, use roxy_meta_get() to retrieve values stored in the options (#918).
tag_two_part() and tag_words() are now simple functions, not function factories.
tag_markdown_restricted() has been removed because it did exactly the same thing as tag_markdown().
A big thanks goes to @mikldk for starting on the vignette and motivating me to make the extension process much more pleasant (#882).
Empty roxygen2 lines at the start of a block are now silently removed (#710).
Whitespace is automatically trimmed off the RoxygenNote field when comparing the installed version of roxygen2 to the version used to generate the documentation (#802).
Files generated on Windows systems now retain their existing line endings, or use unix-style line endings for new files (@jonthegeek, @jimhester, #840).
roxygen2 now recognises fully qualified S4 functions like methods::setGeneric(), methods::setClass() and methods::setMethod() (#880).
Package documentation now converts ORCIDs into a useful link (#721). The package logo (if found at man/images/logo.png) is now scaled to 120px wide (@peterdesmet, #834).
Documenting an S4 method that has a .local() wrapper no longer fails with an obscure error message (#847).
Functions documented in reexports are now sorted alphabetically by package (#765).
@describeIn can now be used with any combination of function types (#666, #848).
@description and @detail tags are automatically generated from the leading description block, and now have correct line numbers (#917).
@example and @examples are interwoven in the order in which they appear (#868).
In @examples, escaped ' and " in strings are no longer doubly escaped (#873).
@family automatically adds () when linking to functions (#815), and print each link on its own line (to improve diffs).
When @inheriting from external documentation, \link{foo} links are automatically transformed to \link{package}{foo} so that they work in the generated documentation (#635). \href{} links in external inherited are now inserted correctly (without additional {}) (#778).
@inheriting a a function with no arguments no longer throws a confusing error message (#898).
@inheritDotParams automatically ignores arguments that can’t be inherited through ... because they are used by the current function (@mjskay, #885).
@inheritDotParams includes link to function and wraps parameters in \code{} (@halldc, #842).
@inheritDotParams can be repeated to inherit dot docs from multiple functions (@gustavdelius, #767).
@inheritDotParams avoids multiple ... arguments (@gustavdelius, #857).
@inheritParams ignores leading dots when comparing argument names (#862).
@inheritParams warns if there are no parameters that require documentation (#836).
@param containing only whitespce gives a clear warning message (#869).
Multiple @usage statements in a single block now generate a warning. Previously, the first was used without a warning.
Now specifically imports recent version of desc package (>= 1.2.0) to fix various parsing issues (@crsh, #773, #777, #779). Multi-line DESCRIPTION collate directives now correctly parsed on windows (@brodieG, #790).
roxygenise() no longer recompiles packages containing src code (#784).
roxygenise() now stops with an informative error message when run in a directory that’s not the package root (@mikmart, #704).
The NAMESPACE roclet now works in two passes - it first generates the NAMESPACE containing only import directives because this can be generated without evaluating the code in the package. This alleviates a problem where it was previously possible to get into a state that you could only get out of by carefully editing the NAMESPACE by hand (#372).
@evalRd foo() evaluates foo() defined in the package namespace and inserts the results into the current block (#645). The code should return a character vector with one entry for each line (and they should not start with #').
There are two small limitations to the current implementation:
@md/@noMd status@evalRd does not work inside templates.@evalNamespace does for NAMESPACE what @evalRd does for Rd files: you give it R code that produces a literal entry in NAMESPACE when run. This should make it easier to export functions that are generated by other functions in your package (#531, @egnha).
@inherits can now inherit examples (#588).
vignette("rd") received a thorough updating for current best-practices. The vignette still needs more work so pull requests are greatly appreciated (#650).
roxygenise() uses pkgload::load_all() instead of a home grown solution to simulate package loading (this is needed because roxygen2 uses run-time information to generate the documentation). This should reduce S4 related problems and ensures that devtools::document() and roxygenise() always have exactly the same behaviour (#568, #595).
If an inherited section cannot be found, the warning contains the help page from which that section was requested (#732, @krlmlr).
roxygen2 now always reads and writes using UTF-8 encoding. If used with a package that does not have Encoding: UTF-8 in the DESCRIPTION, you’ll now get a warning (#564, #592).
Roxygen blocks now have an official structure as encoded in roxy_block(). It is a named list containing the tags with attributes providing other metadata.
The parsed argument to roclet_process() have been replaced with separate blocks and env arguments.
New roclet_preprocess() generic makes it possible for roclets to perform actions before code is evaluated.
parse_package(), parse_file() and parse_code() provide an exported API that allows you to use roxygen’s parsing code independently of creating roclets.
All tags (including @alias) are now de-duplicated and consistently sorted. This reduces spurious diffs (#586, @flying-sheep).
@concept now generates one \concept per tag (#611).
The default @description (i.e. the title) is now added much later in the process. That means that @inherit description now works when you have specified a title for the inheritor (#629) and the default description is slightly nicer when merging multiple blocks.
@family automatically adds its value to concepts (#611).
@inherits: The mechanism for extracting inherited Rd does a better job of preserving escapes (#624)
Empty .Rbuildignore now handled correctly (#576).
Stricter regular expression ensures only files ending with .R or .r are parsed for roxygen comments (#625).
Objects with names starting with a dot are now by default documented in files with prefix ‘dot-’.
Roclets can now access global options as designed. This allows templates to use markdown formatting if set globally (#594).
You can now autogenerate package documentation even if you don’t have Authors@R (#606).
Multiple given and/or family names are now supported in the Authors@R field of the DESCRIPTION file (#672, @sgibb).
If a package logo exists (man/figures/logo.png) it will be automatically included in generated package docs (#609).
Usage for data objects now correctly generated, avoiding double escaping other components of usage (#562).
Improvements to markdown translation:
Code in link text is now properly rendered as code (#620, @egnha).
Whitespace between words in link text is now preserved as single space for links of the form [text][fcn] and [text](URL) (#628, #754, #760, @egnha and @jennybc).
% in inline code (#640), code blocks (@nteetor, #699) and links (#724) is now automatically escaped.
Parsing of markdown links has been tweaked to reduce false positives (#555). If you still get a false positive, you can now put \\ in front of the [ to avoid it being converted to a link (#720). Links can no longer be followed by { to avoid spurious matches to Rd commands like \Sexpr{}.
Unsupported markdown features now generate a mildly helpful warning instead of throwing an utterly useless error (#560).
person() now supports all MARC Relator role codes (#662, @publicus).
topic_add_usage() now outputs formatted “Usage” section with max width of 80 characters thanks to a now more flexible wrap_string() (@JoshOBrien, #719).
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 @gaborcsardiNew @inheritDotParams 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 parameters from somewhere else. It also better handles \dots as an alias for ... (#504).
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).
"_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).
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.
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:
#' @export magrittr::`%>%`
All imported-and-re-exported functions will be documented in the same file (rexports.Rd), containing a brief description and links to the original documentation (#376).
You can more easily generate package documentation by documenting the special string "_PACKAGE" (@krlmlr, #349):
#' @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).
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, instead 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).
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).
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).
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).
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.
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 absence of wrap field because it’s so unlikely that anyone wants the old behaviour (#245).
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.
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:
#' 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/.
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).
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 occurred even when wrap = FALSE.
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.
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 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.
Correctly use keyword datasets not dataset (Fixes #60)
Reference classes no longer given incorrect docType (data).
Use unicode escapes in test files so tests pass on all platforms.
Work around bug in gsub in C locale by manually specifying Encoding().
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)
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:
produces
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.
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!
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.