insert_bib (and a related test) to
handle that.fixed issues causing ‘lost braces’ (actually, superfluous braces)
NOTEs from checks in R-devel occuring with some accented LaTeX
characters. These NOTEs are not yet activated on CRAN but if/when they
do, developers using Rd macros \insertRef and
\insertCite can eliminate them by building their packages
with Rdpack (>= 2.6) and rbibutils (>= 2.2.16). Thanks to
Sebastian Meyer for tracing down the issues.
fixed a Sweave expression in ‘man/predefined.Rd’ to
not emit unnecessary braces (see the note above).
Rd macros insertCite and friends were calling
\insert_citeOnly() with argument key instead
of keys. This was not an error since partial matching is ok
here but not good practice. Fixes issue #28 reported by Marcel
Ramos.
changed the saved value in “tests/testthat/dummyArticle.rds” used in ‘test-bib.R’ with a value obtained with R-devel r84896 n previu versins of R there wasasuperfluous final ’ .’).
in some cases when square brackets were requested, rather than
round ones, \insertCiteOnly was using closing round
parenthesis.
in some cases \insertCiteOnly was not handling well
the last cite when it was followed by free text.
new Rd macro \insertCited{} works like
\insertAllCited but empties the references list after
finishing its work. This means that the second and subsequent
\insertCited in the same help page will list only citations
done since the preceding \insertCited. Prompted by issue
#27 to allow separate references lists for each method and the class in
R6 documentation.
It is no longer necessary to remove backslashes from
\& and similar in bibtex files (e.g. in “John Wiley
& Sons”). The backslash was appearing in the rendered pdf manual but
R-devel’s checks started to warn about it recently with something like
checkRd: (-1) pcts-package.Rd:287: Escaped LaTeX specials: \&
(starting June 2022). This could be avoided by removing the superfluous
backslash in the bib file but this is annoying since this is proper
syntax for the latter. Concerned packages should rebuild the tarball
with Rdpack (>= 2.4) or remove the offending backslashes from their
bib files. (addresses issue #26)
\insertCite, two or more accented Latin
characters were rendered with superfluous curly braces, see issue#25
(reported by Manuel López-Ibáñez) and
https://stat.ethz.ch/pipermail/r-devel/2022-April/081604.html.Rdpack and
could require Rdpack >= 2.3 to ensure that users
installing their package don’t do that accidentally with
Rdpack 2.2.\doi Rd macros resulted in warnings from
R-devel’s checks for packages that use Rdpack built with the released
versions of R. This fixes it. (fixes #24)Rdmacro \insertCite gets a new feature allowing to
drop parentheses for parenthesised citations, analogous to natbib’s
\citealp in latex. This makes it possible to use markup
around the citations outside the arguments of the macro. This fixes
github issue #23 by @ms609.
updated vignette “Inserting_bibtex_references” and other documentation.
the pkgdown site now has a Search button on the
navigation bar.
fixed a test that was failing with versions of rbibutils before v2.1.1 (issue reported by Andreas Tille).
if the version of rbibutils is greater than v2.2.5, parsing bib
files with rbibutils::readBib now uses
texChars = "Rdpack". This ensures proper rendering of
\'i in references (by converting \'i to
\'\i which base R renders correctly). For detailed
discussion of this see issue GeoBosh/bibutils#7 and NEWS.md in rbibutils
v2.2.4 and v2.2.5.
Rdmacros generating references now drop the URL
field if a doi field generating the same URL is present.
This avoids repetition of the URL since rendering the doi
field produces the URL anyway.
now references with identical authors are sorted by year.
fixed rebib() to process doi’s properly.
now checks on github (using github actions) are done on the three major platforms for the following versions of R: release, devel, oldrel, and 3.3.
now a warning (rather than error) is issued if package ‘testthat’ is not available for tests.
now bibtex files are parsed with option
direct = TRUE when the version of rbibutils is
>= ‘2.1.2’. This fixes GeoBosh/rbibutils#3 for Rdpack users (although
that needs fixing also for direct = FALSE).
In viewRd, the default for the help type now is
options("help_type") (previously the default was
"text").
for roxygen2 users, added a note in README and
Rdpack-package.Rd not to indent by exactly four spaces
\insertAllCited{} relative to @references when
markdown mode is activated. This is to avoid it being translated by
roxygen2 as verbatim (\preformatted) text, see
issue (#18).
moved package gbRd to Suggests.
fixed uses of in several examples (necessitated by a change in R-devel circa February 2021).
dramatic speed up of processing of bibliography references, most
noticeable for users with large number of help pages and large
REFERENCES.bib. (prompted by Kisung You, issue
#17)
amended the warning message from bibliography macros to mention duplicated keys.
added entry for rbibutils in
REFERENCES.bib.
corrected wrong citation of rbibutils.
bibtex from Suggests and
elsewhere.imported rbibutils and made suitable adjustments to
the code.
moved bibtex to Suggests (since
bibtex has been orphaned for several years).
gbutils,
which is not among the dependencies of Rdpack. This was
raising a NOTE on one of the CRAN testing machines.viewRd() now loads also Rd macros declared by the
package to which the rendered Rd file belongs. Previously only macros
from Rdpack were loaded but now there is at least one other
package, mathjaxr, which defines Rd macros.
moved grDevices to Suggests.
edited some documentation files.
in documentation of S4 classes, such as
"classname-class.Rd", reprompt() was sometimes
inserting entries for slots already listed in the Slots section. The
same bug was causing the new slots not to be reported properly to the
user.
in some cases reprompt() failed to process properly
\S4method entries in the Usage section of Rd files. Now
fixed.
reprompt() now handles \S4method
statements for replacement methods. As for other functions and methods
(S3 and S4), it is sufficient to put a declaration with empty argument
list in the Usage section and reprompt() will insert the
correct formal arguments for the method (they may be different from
those of the generic).
reprompt() now gives a more helpful error message
when type is invalid.
corrected some minor typo’s in the documentation.
README and the documentation of reprompt() and
Rdpack-package now give more details on
reprompt()ing replacement functions.
README.md and README.org now give the correct
install.packages instruction for CRAN (pull request #10
from @katrinleinweber).
some examples were leaving a stray file,
dummyfun.Rd, after R CMD check.
Updated the vignette about \insertFig,
\printExample and \runExamples, to reflect the
lifting in R 3.6.0 of some limitations of Rd processing in
previous R versions.
Vignette ‘Inserting BibTeX references’ now includes a section on bibliography styles. This section was previously only in README.
The fix in Rdpack 0.10-3 (see below) for an issue introduced in
R-devel in Oct 2018 will be made permanent, at least for now. This fix
resolves also a similar issue in package pkgdown, see the
discussion at https://github.com/GeoBosh/Rdpack/issues/9 for details and
further links.
\insertAllCited{} to appear in a single paragraph in the
html rendering of the Rd documentation.added pkgdown site to DESCRIPTION.
README and the vignette about evaluated examples now state that
R-devel no longer gives warnings about \Sexpr not being a
top level section. This means that macro runExamples which
creates section ‘Examples’ containing code and results of evaluation
will be useable in CRAN packages.
new function Rdo_fetch() gets the Rd object
representing a help page from an installed or source package. It works
also for packages under devtool’s developer’s mode
The site created with pkgdown contains fewer errors now. (Note that the documentation builds without error with R’s tools).
Started moving tests from my local setup to testthat.
now REFERENCES.bib is read-in using the declared
encoding for the corresponding package. If there is no declared
encoding, “UTF-8” is assumed.
Now macros \insertCite and
\insertCiteOnly use the correct results=rd
instead of results=Rd. This was not catched by
Rs building tools but caused errors when processed with
pkgdown::build_site(). Fixes issue#8. Also fixes
r-lib/pkgdown#784. Thanks to Jay Hesselberth for
uncovering this.
now references produced by the citation macros for BibTeX entries
of type @book and @incollection treat field
‘series’ similarly to other BibTeX styles, including JSS (issue#7 raised
by Kisung You). Note that even though the underlying base R tools are
based on JSS, they treat this field differently.
Bugfix: now Rd macro \printExample evaluates the
expressions in the correct environment.
help page of get_usage() gets a fairly complete
Details section with numerous evaluated examples.
now run_examples() escapes % by
default, before returning the text. This is needed for text that is to
be included in an Rd file. It can be turned off by setting the new
argument escape to FALSE.
now reprompt() gives a more informative error
message if an Rd file describes a non-existent S4 class. This is not
captured by Rs tools. It can happen during development if a
class is removed.
now reports printed by reprompt() about methods
documented in Usage sections, but no longer existing, are more readable.
This is due to a new print method for (the mostly internal) class
“f_usage”.
Many features of Rdpack are best demonstrated on a package. The
new package RdpackTester under ./inst/examples now makes
this easier.
now the help page “predefined.Rd” does not print some tables
twice in the pdf manual. (This was due to using
\if{latex}{}{} instead of \ifelse{latex}{}{}
for those tables.)
also in “predefined.Rd”, removed illegal use of vertical bars (in
column specifications of tabular environments) from the pure LaTeX code
in the \ifelse clause(s) and wrapped them in
\out{}.
in “get_sig_text.Rd”, replace help() with
utils::help() to avoid warnings from more stringent
R CMD check. Similarly, in “Rdpack-package.Rd” replace
packageDescription() with
utils::packageDescription(). This may be needed in
\Sexpr’s more generally (TODO: check if
these would still be needed if the symbols are imported by the
package.)
\eqn{}.new macro \printExample for inclusion of example
computations in narrative sections, such as Details. The
code is evaluated and printed similarly to R sessions but
the code is not prefixed and the output is prefixed with comment
symbols, eg.
2+2
##: 4new experimental macro \runExamples for use as top
level section in an Rd file as a replacement of section
\examples. \runExamples{code} evaluates the
code and creates section \examples containing the code and
the results (similarly to \printExample). So,
\runExamples{2 + 2} produces
\examples{
2 + 2
##: 4
}The generated section examples is processed by R’s
documentation tools (almost) as if it was there from the
outset.
new experimental macro \insertFig to create a figure
with R code and include it in the documentation. The
related macro \makeFig just creates a graphics file, which
can be included with the standard Rd command
\figure.
new vignette gives a brief description of the new macros.
\insertRef and
\insertAllCited (see below) - in the rendered
News on CRAN the backslashed words had disappeared.\insertRef and \insertAllCited macros
now support bibstyles for formatting references (feature
requested by Jamie Halliday, issue#5). Use
Rdpack (>= 0.8) in Imports: to use this
feature. Currently only long author names are supported but complete
support for styles can be added trivially if requested.
updates to the documentation, in particular the bulk of Rdpack-package.Rd was from 2011!
improvements to handling of free form citations in textual mode:
(bugfix) now the whole citation is not parenthesised in textual mode,
the handling for textual mode was incomplete in that additional text after the citation was not put inside the parentheses along with the year.
updates to the documentation.
fix a bug in Rdo_locate_core_section().
consolidated the changes introduced since the previous CRAN
release of Rdpack (it was 0.5-5) in preparation for the next release.
Users of the new macros for citation can use
Rdpack (>=0.7) in the Imports: field of
file “DESCRIPTION” to ensure that they are available.
comprehensive overhaul of handling of errors and warnings during
processing of references and citations. In particular, such errors
should (in most cases) produce only warnings during
R CMD build and R CMD INSTALL, and not prevent
the package from being built and installed.
Unresolved BibTeX keys produce warnings during building and installation of the package, but not errors. Dummy entries are inserted in the documentation explaining what was amiss (currently with ‘author’ A Adummy).
new Rd macros for citations
\insertCite inserts citation(s) for one or more keys
and records the keys for \insertAllCited (see
below).
\insertCiteOnly is similar to
\insertCite but does not record the keys.
\insertNoCite records the keys but does not produce
a citation.
\insertAllCited prints a bibliography including all
references recorded by \insertCite and
\insertNoCite.
new entries in this file will use markdown syntax.
updates to the documentation.
get_bibentries() gets a new argument “everywhere”.
When is is TRUE, the default, unescaped percents are escaped in all
bibtex fields, otherwise the replacement is done only in field
“URL”.
removed several print() statements which were
accidentally left in the code in v. 0.5-6.
updated help page of get_bibentries() and included
examples.
cleaned up the imports in NAMESPACE.
insert_ref() and Rd macro \insertRef
should now work ok in the presence of percent encoded symbols in URL
field of a BibTeX entry. Closes issue “Unexpected END_OF_INPUT error
(URL parsing?)”, see Rdpack issue 3,
raised by jdnewmil.
get_bibentries() now takes care of percent encoded
symbols in URLs. It now returns an object from class “bibentryRd”, which
inherits from “bibentry” but has its own print method which escapes or
unescapes the percent signs in URLs depending on the requested output
style. This was also reported by by jdnewmil in issue#3 referenced
above.
get_bibentries() now tries to load the
bib file from the development directory of argument
“package”, in case it is in development mode under “devtools”. (Even
though the search is with system.file(), which
devtools replaces with its own version, the bib file still
needs to be looked for in “inst/”, i.e. it is not in the root directory
as is the case in installed packages.)
Streamlined the help page of reprompt() and
Rdpack-package.
new argument, edit, in reprompt() opens
the Rd file after updating it.
new function ereprompt()
(e' for _edit_)* opensreprompt()with suitable defaults to replace the original Rd file and open it in an editor, otherwise equivalent toreprompt()`.
now if infile does not exist,
reprompt(), and hence ereprompt(), strips the
directory part, finds the root of the package directory, and looks for
the file under man/ (this uses package
rprojroot’). In particular, if the working directory is
anywhere under the package root, infile can be simply the
name of the Rd file, without path.
now README.md is generated from README.org. I changed the layout and amended the information in it.
README.* now get links to georgisemacs for an
emacs function to reprompt() the Rd file at point.
viewRd() now works also when the file is from a
package under devtools’ development mode on any platform (e.g. RStudio,
Emacs/ESS, Rgui).
new RStudio add-in Reprompt, contributed by Duncan
Murdoch. If the file being edited in the RStudio’s code editor is an Rd
file it calls reprompt(). If the file is as R source file,
it looks for the help page of a selected object name and works on it if
found, otherwise creates one.
added the version of Rdpack to the abstract of the
vignette. This seems more informative than giving the compilation
date.
now reprompt() doesn’t give spurious warnings about
unknown Rd macros when the Rd file contains user defined Rd macros.
These warnings were harmless and rare, but alarming and
annoying.
fixed a bug in inspect_args() which caused the
warning “In is.na(x) : is.na() applied to non-(list or vector) of
type ‘NULL’” in reprompt(), when the signature of a
function in “Usage” section was empty.
added the github url to DESCRIPTION.
now give a more informative warning if a key is missing from REFERENCES.bib (thanks to Kisung You for suggesting this).
tools::parse_Rd() rather than parse_Rd()
(before this was not necessary since ‘gbRd’ depended on
‘tools’).new function viewRd() parses and shows an Rd file in
a source package.
May be particularly helpful for devtools developers.
revamped the vignette, added additional explanations of possible issues.
new functions makeVignetteReference() and
vigbib() generate Bibtex references for vignettes in a
package.
Added the requirement to Import Rdpack to the
help page of insert_ref(). (It was out of sync with the
vignette.)
Updated Description in DESCRIPTION, which was also out of sync with the vignette.
Bug fix in the vignette: changed \@references to
@references in the roxygen2 example.
Edited and amended vignette “Inserting_bibtex_references”, including:
additional explanation and an example,
requirement to import Rdpack and a mention of travis etc.
paragraph about devtools.
changed the URL for parse_Rd.pdf in REFERENCES.bib to https.
new facility for inserting references from BibTeX files - just put the line:
RdMacros: Rdpackin the DESCRIPTION file of your package and the
references in inst/REFERENCES.bib. Then put
\inserRef{key}{yourpackage} in documentation chunks to
insert item key from the bib file. This works with both
manually created Rd files and roxygen comments, see the documentation
for details.
from now on, put next to versions published on CRAN (as above)
a minor correction in file NEWS.
reprompt() and rebib().don’t export parse_text
corrected bug in reprompt for S4 classes - new slots were not
handled correctly (see slots.R for details).
in reprompt for S4 methods: if the methods documentation describes methods that do not exist, print an informative message for the user. (Such methods are also printed for debugging purposes but in non-user friendly form.)
included methods in Imports: - around
R-devel version 2015-07-01 r68620 not including it triggers
warnings)
new functions .whichtageq and
.whichtagin; replaced most calls to
toolsdotdotdotRdTags with these.
removed toolsdotdotdotRdTags
removed ::: calls from code; copied some functions
from tools to achieve this (see “threedots.R”). Renamed the
functions replacing ::: with dotdotdot.
export by name (not the generic export pattern); preparation for more selective export of functions in the future.
new functions: Rdo_get_argument_names,
Rdo_get_item_labels
dependence bibtex becomes “Imports”.
tools and gbRd remain (for now) “Depends”
since functions from them are used in some examples without
require()’s.
rebib(): now outfile="" can be used to
request overwriting infile. (a small convenience; before
the change, one could do this by giving the outfile and
infile the same values.)
Bug fix: predefined.Rd contained
\tabular environments with vertical bars, |,
in the format specification. This is not documented in “Writing R exts”
but works for LaTeX and remained unnoticed by me and R CMD check.
However, rendering the help page for the objects documented in
“predefined.Rd” gave an error in html and text mode. Package
installation failed only if html was requested at build time.
small changes in the documentation
new major feature: processing references from Bibtex files. The
top user level function is rebib(), which updates section
“references” in an Rd file. promptPackageSexpr() has been
updated to use this feature. inspect_Rdbib() can be used in
programming.
new auxiliary functions for work with bibentry
objects.
new convenience programming functions for Rd objects.
some small bug fixes.
some gaps in the documentation filled.
reprompt() was not handling properly S4 replacement
methods. Changed the parsing of the arguments to rectify this. Some
other functions also needed correction to handle this.Depends field in DESCRIPTION file updated to require R
2.15.0 or later (because of a few uses of paste0() in
recent code).