NEWS.md

rbibutils 2.3.0.9000

TODO: edit this section before release

• WARNING: A change of the default for argument direct of readBib() is planned for rbibutils v3.0 (from FALSE to TRUE). If you really want direct = FALSE, please state that explicitly. Note that for most users direct = TRUE is superior (better handling of maths, additional capabilities). Still, direct = FALSE has some features that may be desirable for some applications.

  :TODO: the documentation needs improving to describe the above.

• added completion for bibentryExtra objects. Useful for interactive use. For example in an R session if be is a bibentryExtra object, typing be$bi then '' will be completed to be$bibtype. Also, be$ then '' 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.

• some long standing unnoticed bugs or shortcomings of the processing in readBib() and convert() in the case direct = FALSE have been fixed.

  :TODO: argument texChars is not supported when direct = FALSE but maybe after these fixes it can be done.

rbibutils 2.3

New and improved features

• 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.

Bug fixes

• 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.

rbibutils 2.2.16

• fixed processing of the Polish suppressed-l \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.

rbibutils 2.2.15

• adapted some tests to a change in R-devel circa r84986.

rbibutils 2.2.14

• fixed a couple of tests in 'test-convert.R' which started failing (ca. R svn rev 84760) due to an R-devel change in person().

rbibutils 2.2.13

• Bugfix: the declaration of the return value of a C function was accidentally changed from const char * to char * in v2.2.12, causing CRAN warnings on some platforms.

rbibutils 2.2.12

• 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.

rbibutils 2.2.11

• in C code, changed sprintf calls to use snprintf to fix CRAN warnings.

rbibutils 2.2.10

• fixed warnings about deprecated function declarations without prototypes in C code.

rbibutils 2.2.9

• fixed wrong markup of an item in this file (for v2.2.4) causing bad rendering and a NOTE from CRAN.

rbibutils 2.2.8

• 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.

rbibutils 2.2.7

• fixed bug in isi output occuring in v2.2.5 and 2.2.6 and revealed by gss/ASAN check.

rbibutils 2.2.6 (not on CRAN)

• fixed memory leaks in nbib output in biblatex input occuring in v2.2.5.

rbibutils 2.2.5

• 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.

rbibutils 2.2.4

• 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).

rbibutils 2.2.3

• fixed memory issues from valgrind in v2.2.2 thanks to patch supplied by Bill Dunlap.

rbibutils 2.2.2

• import of 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.)

rbibutils 2.2.1

• fixed problems revealed by valgrind.

rbibutils 2.2

• 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.

rbibutils 2.1.1

• 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).

rbibutils 2.1

• 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).

rbibutils 2.0

• 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.

rbibutils 1.4

• 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.

rbibutils 1.3

• 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.

rbibutils 1.2.1 (not on CRAN)

• improved processing of URL field when converting to bibentry.

rbibutils 1.2 (not on CRAN)

• fixed inBook processing.

• fixed encoding bug introduced in v1.1.

• fixed misterous loss of $s and curly braces in certain circumstances.

rbibutils 1.1.0

• 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.

rbibutils 1.0.3

• 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.

rbibutils 1.0.2

• completed the copyright credits in DESCRIPTION (there were contributors not mentioned anywhere except in the C source files they contributed).

rbibutils 1.0.1 (not on CRAN)

• clarified the copyright holders in DESCRIPTION.

rbibutils 1.0.0 (not on CRAN)

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.