High-Performance Open-Source Archive
now ‘’ is handled by toRd.bibentryExtra (previously
was in Rdpack).
don’t interpret ‘’ if the leading slash is escaped.
export bibstyle_JSSextra - not exported in
v2.4.
modified the bibentryExtra method for
toRd to process \slash.
improved handling of latex accents and Unicode combining characters.
removed the deprecated register_JSSextra.
direct of
readBib() is planned for rbibutils v3.0 (from
FALSE to TRUE). For most users
direct = TRUE is superior (better handling of maths,
additional capabilities). If you really want
direct = FALSE, please state that explicitly in the call to
readBib().now rbibutils gives warnings when it encounters undefined bibtex
names (see @string bibtex macro), fixes issue#10. Such
strings are used for consistent naming of journals, for example. The
name is inserted in the output when undefined (previously this was done
silently).
consolidated append_type between the bibtex related
formats. Internal, but fixed a bug causing technical reports to be
converted to MISC when converting from isi and biblatex to
bibtex.
added completion for bibentryExtra objects. Useful
for interactive use. For example in an R session if be is a
bibentryExtra object, typing be$bi then the
‘Tab’ key will be completed to be$bibtype. Also,
be$ then ‘Tab’ will provide a choice from the available
completions. This should work also in RStudio, whereever it provides
completion.
corrected some typo’s in the draft vignette.
now using bibentrydirectout_write also in
‘bibentryout.c’. bibentryout_write was not in sync with
changes in bibentrydirectout_write.
refactored bibstyle_JSSextra; new function
bibstyle_JSSextraLongNames in preparation of removing
bibstyles ‘JSSRd’ and ‘JSSRdLongNames’ from Rdpack.
now bibstyle ‘JSSextra’ doesn’t change the ‘JSS’ style (the fix in v2.3 didn’t resolve this completely).
some long standing unnoticed bugs or shortcomings of the
processing in readBib() and convert() in the
case direct = FALSE have been fixed.
the class of the object returned by readBibentry(),
readBib(), and bibtexImport() is now always
c("bibentryExtra", "bibentry") (unless argument
fbibentry is supplied). Previously
"bibentryExtra" was added only when there were bib items
with non-standard type and extra = TRUE. An option to
return just "bibentry" may be considered.
non-standard bibtypes are lowercased.
consolidated the subsetting operators for ‘bibentryExtra’ objects and the documentation for them.
new function bibentryExtra() creates ‘bibentryExtra’
objects. It accepts arbitrary Bibtex entry types and takes the same
arguments as bibentry().
the default bib style for the bibentryExtra method
for format() is now “JSSextra”.
refactored and streamlined writeBibentry() (the
original version didn’t use the format method).
new generic function as.bibentryExtra.
new ‘bibentryExtra’ method for c().
bib style “JSSextra” now knows how to render ‘online’ bibtype. It is a biblatex (not bibtex) field but very useful these days.
bib style “JSSextra” now knows how to render a few more non-standard bib types.
print(be, style = "R"), where be is an
object from class “bibentryExtra” no longer includes the, effectively,
internal for rbibutils field
truebibtype.
first draft of a vignette.
now bibstyle ‘JSSextra’ creates a new environment for its stuff. Previously it was accidentally adding its objects directly in the ‘JSS’ style’s environment, causing the two to be equivalent.
fixed a bug in format.bibentryExtra() which caused
writeBibentry() to misbehave when
style = "Rstyle".
fixed [<- sub-assignment to ‘bibentryExtra’
objects.
when style = "latex", style “JSSextra” was failing
to print bibentries with types InBook and InCollection, due to a typo
(redundant comma) in the code.
a number of minor bugs were fixed.
\l.
Previously the character following it was enclosed in braces, which was
harmless in most cases but the superfluous braces could cause trouble in
special circumstances. Did the same for the uppercase version,
\L, which was missing from the code.person().const char * to
char * in v2.2.12, causing CRAN warnings on some
platforms.Bugfix: readBib with
texChars = "Rdpack" which converts \'i to
\'\i was wrapping \'\i in braces in ‘author’
and related fields only. Failure to do so in other fields was making the
output invalid when \'i was followed by alphabetical
character(s). Fixes issue#7 reopened by @EricMarcon.
Note that option "Rdpack" for argument
texChars is mainly for internal use which compensates for R
not recognising \'i as an accented character, see the news
items for v2.2.5 and v2.2.4 and the bug report about
tools:::latexToUtf8 at R
bugs.
partial internal refactoring of C code to avoid duplication.
C code, changed sprintf calls to use
snprintf to fix CRAN warnings.C code.new argument fbibentry for readBib and
readBibentry for specification of a function for generation
of bib objects. It should have the same arguments as the default
utils::bibentry() but doesn’t need to be vectorised, since
readBibentry() generates one bibentry call for
each reference.
readBib now parses correctly LaTeX accents like
\a'o. These are officially defined only for LaTeX’s
tabbing environment as replacements for \'o,
etc., but seem accepted by LaTeX outside these environments. Also,
Bibtex converts them to the standard ones when writing
.bbl files and R’s bib processing functions know about
them.
a bug in ads export was causing a test to fail on
platforms with char equivalent to
unsigned char. Reported by @nileshpatra, who also identified the
cause. Fixes issue#8 on github.
readBibentry with extra = TRUE now
parses (almost) any syntactically correct bib entries. In particular, it
accepts arbitrary bib types and doesn’t throw errors for bibentries
missing fields required by bibtex for the standard bibtex types. For
example, biblatex entries typically have date, not
year.
readBib with direct = TRUE and
texChars set to "convert" or
"export" was not processing mathematical expressions
properly. Now fixed.
argument texChars of readBib gets new
possible value, “Rdpack”. This is like the default, “keep”, but in
addition it converts \'i to \'\i. This is
related to issue #7, see below the fix in v2.2.4 for details. This is
mainly for internal use.
improved the messages from error handling when creating bibentry
objects. The fix is in readBibentry but users typically see
them when calling readBib.
fixed an error which caused bibConvert to segfault
when importing nbib files.
readBibentry (and hence readBib) were
printing some error messages that were actually handled.
stopped converting \'\i' to \'i. They
are equivalent but there is no reason to do this. Also, at the time of
writing R’s tools::latexToUtf8 converts the former but not
the latter, while Biber seems to convert the latter but not the former,
see https://bugs.r-project.org/show_bug.cgi?id=18208 . So, users of the
bib file may have specific reasons to use one or the other.
names consisting of just one part, family, were missing processing of escaped characters (issue #5).
Pubmed XML was sometimes giving a handful of
references for files with tens or hundreds of them. Now fixed, see issue
#4, reported by Rafael Santamaría. (The function reading the file was
implicitly assuming that the end of each reference is on a line by
itself and was silently ignoring text on the same line after the end of
reference tag. Reference files from online databases often have no new
lines at all, except for the XML header.)new convenience function charToBib takes input from
a character vector rather than a file. By default it assumes that the
input is in bibtex format and dispatches to
readBib. If an input format is specified it calls
bibConvert.
new S3 class bibentryExtra, inheriting from
bibentry, provides support for non-standard types
(potentially arbitrary) of bibtex entries. Suitable methods are defined
for printing, converting and manipulating (e.g., subsetting and
assignment) bibentryExtra objects. The initial
implementation is incomplete and under development.
readBib() gets a new argument extra. If
it is set to TRUE and non-standard types of entries are
encountered in the input bibtex file, then the class of the result is
set to bibentryExtra. See also the note about
bibentryExtra.
readBib gets new argument, macros, for
specification of file(s) containing Bibtex macros (such as abbreviations
for names of journals). These files are read in before file(s) specified
by file.
readBib with direct = TRUE now accepts
non-syntactic field names, e.g. containing -. (This is
irrelevant when direct = FALSE since in that case
nonstandard fields are ignored and standard fields do not contain
unusual characters.)
internal structures for bibtex macros, such as
@string were not cleared at the end of calls and were
accumulating from multiple invocations of conversions from bibtex and
biblatex. Now fixed.
now references with missing cite keys in bibtex input are accepted (previously such references were dropped). Dummy cite keys are inserted.
now @preamble entry in bibtex is ignored silently.
Previously it was also dropped but with a message about unrecognised
type, which was confusing.
export arXiv:XXX and similar as https (some were
still exported as http). Fixes GeoBosh/Rdpack#21, reported
by Kisung You.
unsuported conversions for some formats were accepted with unpredictable results. Informative messages are printed now.
improved handling of byte order marks (BOM) for utf8 output. This was causing problems to tests of this package on Windows since on Linux BOMs are not emitted (I haven’t figured what causes the difference - the code is not OS dependent).
improved handling of corner cases in bibtex input, especially for
readBib with direct = TRUE.
now a warning (rather than error) is issued if package ‘testthat’ is not available for tests.
readBib now has a default for the encoding, so it
would usually be called just with one argument (the filename).
readBib can now convert bibtex files directly (i.e.,
without first converting to XML intermediate) to bibentry R objects.
This can be requested by setting the new argument direct to
TRUE.
readBib gets argument texChars to
control whether or not to convert TeX sequences representing characters
(such as accented Latin characters) to normal characters in the output
encoding. There is an option also to convert charaters to the
corresponding TeX sequences.
readBib now accepts encodings as for
bibConvert.
readBib now processes field key in
bibtex files. (This field is optional, used by some bibtex styles for
sorting.)
bug fixes and improvements.
removed field LazyData from DESCRIPTION as there is
no data directory (and R-devel now flags it with a NOTE).
there is no longer (unintended) dependence on R >= 3.4. This
was because of the use of R_unif_index. Report and fix due
to Henrik Sloot (#1).
completely reimplemented the conversion to bibentry
- now this is done entirely in C and it now has the same
speed as the conversions to other bibliograthy formats.
removed xml2 from the imports - it is no longer
needed now that the conversion to bibentry is done in
C.
new functions readBibentry and
writeBibentry for reading from and writing bibentries to R
source files.
now errors when reading bibentry files are turned into warnings with suitable messages.
new function writeBib for writing bibtex
files.
fixed erroneous processing of PhD thesis bib entries with some
values of field type. (reported by Kisung You for
GeoBosh/Rdpack#17)
fixed a compiler warning about a pointer differing in signedness from the expected type (reported by Patrice Kiener).
somehow README.md went missing in v1.3, now
reinstated.
reverted a change in v1.2 which caused trouble with some latex characters.
trimmed white space in cite keys and some others to avoid getting cite keys containing the newline character (possible if the comma after the key is on a new line).
new function readBib for importing bibtex
files.
fixed inBook processing.
fixed encoding bug introduced in v1.1.
fixed misterous loss of $s and curly braces in
certain circumstances.
fixed processing of multiple person names in bibtex import.
mathematical formulas were wrongly exported without dollars in some cases.
stopped printing some messages causing problems to Rdpack.
fixed warnings from clang compilers on CRAN. (These
were about tautology if clauses in
src/adsout.c and default argument promotion of the second
argument in a couple of invocations of va_start in
src/modsout.c).
fixed typo’s in the documentation.
updated the website.
Features of this version:
includes an R port of bibutils libraries (currently
bibutils_6.10).
supports all character encodings available in
bibutils (defaults are UTF-8).
supports all input/output bibliography formats available in
bibutils, including Bibtex, Biblatex, and XML mods
intermediate.
in addition, supports conversions of the above formats from/to
bibentry R source files or rds
objects.
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