Changes in R

We present important changes in the development version of R (referred to as R-devel, to become R 4.2) and give a summary of the new search engine interfaced by RSiteSearch(). Some statistics on bug tracking activities in 2021 are also provided.

1 R-devel selected changes

R 4.2.0 is due to be released around April 2022. The following gives a selection of the most important changes in R-devel, which are likely to appear in the new release.

Native UTF-8 support and other changes on Windows

R on Windows now uses UTF-8 as the native encoding. This feature requires recent Windows 10 or newer (or Windows Server 2022 or newer). On older systems, a (non-Unicode) system locale encoding will be used as in earlier versions of R. With this feature, it is now possible to work with characters not representable in the locale encoding (e.g., with Asian characters on European locales). Previously, such characters could only be used with considerable care needed to prevent their mis-representation or undesirable substitution. It is now possible to use Unicode characters even in Rterm, the console front-end for R.

To make this possible, R switched to the Universal C Runtime (UCRT), which is the new C library on Windows and has to be installed manually on Windows 8.1 and older. The switch required a new toolchain targeting UCRT. All code linked statically to R or R packages has to be rebuilt. Therefore, a new toolchain bundle, Rtools42, has been created which includes a recent GCC 10 compiler toolchain targeting 64-bit UCRT and a set of pre-compiled static libraries for R packages. R and CRAN use this new toolchain for R-devel (to become R 4.2.0). Older versions of R will still use older toolchains. As from 4.2, R on Windows will no longer support 32-bit builds. Rtools42, containing only the 64-bit toolchain, is one step simpler to install for users than the earlier toolchain bundle.

The change so far required updates of over 100 CRAN packages and several of their Bioconductor dependencies. As these packages have a very large number of reverse dependencies (packages depending recursively on them), R gained support for automated installation-time patching of packages, so that packages can be quickly patched and their reverse dependencies tested, giving package authors more time to incorporate the updates. This feature is experimental and may be removed in the future.

R allows package authors to maintain the same package sources for R 4.2 (Rtools42) and R 4.1 (Rtools40) by supporting Makevars.ucrt and other make/configuration files with extension .ucrt which are used by R 4.2 in preference of their existing .win variants, but ignored by older versions of R. Both toolchain bundles can coexist on the same machine.

The work on the toolchain and on testing CRAN packages has lead to the discovery of new bugs in GCC: invalid unwind tables causing crashes (GCC PR#103274), inconsistency in option handling related to unwind tables (GCC PR#103465) and lack of support for UCRT/C99 format strings (GCC PR#95130). Additional bugs were found that turned out to be fixed already in later versions of GCC, but required a back-port (GCC PR#101238, GCC PR#100402). Thanks to MinGW-W64 developer Martin Storsjo and GCC developers Eric Botcazou and Martin Liska for their help with identifying and resolving the issues. The Rtools42 toolchain bundle includes patches for these and other, smaller, issues.

Following the philosophy that disruptive changes for users and package authors should be rare, this seemed a good time to change also the default personal library location. Now it is a subdirectory of the Local Application Data directory (usually a hidden directory C:\\Users\\username\\AppData\\Local). This is to follow Windows conventions, but also to avoid problems users experienced with various cloud backup/syncing services enabled by default for the personal directory (usually C:\\Users\\username\\Documents). For the very same reason, the default installation location for user-only installation has been changed to C:\\Users\\username\\AppData\\Local\\Programs.

Additional bug fixes (e.g., for handling previously untested code paths involving characters not representable in system locale encoding) and improvements (e.g., removal of workarounds no longer needed with UCRT) are being added following testing and reports from package authors and are to appear in R 4.2.

More details on the changes in R for Windows and on what is required from package authors are available in Tomas Kalibera et al. blog post and material linked from there.

Graphics changes

Support for isolated groups, compositing operators, affine transformations, and stroking and filling paths has been added to the R graphics engine. The existing support for masks has also been expanded to include luminance masks. An R-level interface for these new features has been added to the grid graphics package. See Paul Murrell’s blog post for more details. The changes to the R graphics engine mean that packages that provide graphics devices, such as the ragg package, will need to be reinstalled.

Hash tables

Hash tables are data structures used to efficiently map keys to values. Keys can be simple, such as strings or symbols, or more complex objects, such as environments. Hash tables can be thought of as generalizations of environments that allow more general key objects, though without the notion of a parent table. Like environments, and unlike most objects in R, hash tables are mutable.

Hash tables have been used internally in R for many years, in particular in match(), unique(), and duplicate(), to improve the efficiency of these functions. R-devel now provides an R level interface to the hash table infrastructure used in these functions. The R level interface is provided in package utils. New hash tables are created by hashtab(); entries are created or modified by sethash(), and values are retrieved with gethash(). More details are available in the help page for hashtab(). The R level interface is based loosely on hash table support in Common Lisp.

A C level interface will eventually be made available in the C API as well. The details are still under development. Comparison of keys typically is based on identical(), but can also be based on the memory addresses of keys. Address-equality based tables are most likely to be useful at the C level. For address-based hash tables it may be useful to provide a weak version in which keys are not protected from garbage collection and entries are scheduled for removal once keys are determined to no longer be reachable.

Other selected changes

• matrix(x, n, m) now warns in more cases where length(x) differs from n * m, as suggested by Abby Spurdle and Wolfgang Huber in February 2021 on the R-devel mailing list. This warning can be turned into an error by setting environment variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check –as-cran does so unless it is already set.
• simplify2array() gains an except argument for controlling the exceptions used by sapply().
• R on Windows now uses the system memory allocator. Doug Lea’s allocator was used since R 1.2.0 to mitigate performance limitations seen with system allocators on earlier versions of Windows.
• R gains more classed errors. Attempting to subset an object that is not subsettable now signals an error of class notSubsettableError, with the non-subsettable object contained in the object field of the error condition. Also, subscript-out-of-bounds and stack-overflow errors are now signaled as errors of class, respectively, subscriptOutOfBoundsError and stackOverflowError.
• New partly experimental Sys.setLanguage() utility, solving the main problem of PR #18055.
• Deparsing no longer remaps attribute names dim, dimnames, levels, names and tsp to historical S-compatible names (which structure() maps back).

2 Bug statistics for 2021

Summaries of bug-related activities over the past year were derived from the database underlying R’s Bugzilla system. Overall, 244 new bugs or requests for enhancements were reported, 220 reports were closed, and 1065 comments (on any report) were added by a total of 115 contributors. This amounts to averages of about two new reports and two closures over three days, and three comments per day. All totals are about 30% lower than in 2020, especially the number of closures. High bug activity in 2020 had largely been driven by dedicated efforts of several contributors in reviewing old reports.

Figure 1: Bug tracking activity by month (left) and weekday (right) in 2021.

Figure 1 shows statistics for the numbers of new reports, closures and comments by calendar month and weekday, respectively, in 2021. The frequency of new reports was relatively stable over the year except for a low in March/April. There tended to be more new reports than closures, but this was reversed in November/December in a revived effort to address old reports. The top 5 components reporters have chosen for their reports were “Low-level”, “Language”, “Documentation”, “Misc”, and “Wishlist”, which is the same set as in 2020. Many reports are suggestions for enhancements and marked as Wishlist but are sometimes also put in a specific component, ideally with severity level “enhancement”.

Bug discussions led to an average of 65 comments each month from January to August 2021, which is less than in the same period of 2020 with an average of 140 comments each month. Comment activity has increased again in late 2021.

Last but not least, from the numbers by weekday in the right panels of Figure 1 we see that the R community is also active during weekends, though at a lower frequency.

3 Relaunch of search.R-project.org

A long time ago, Jonathan Baron (University of Pennsylvania, USA) created an “R Site Search” database and has for many years provided a web service for queries into this database, allowing the community to search help files of CRAN packages, task views, vignettes, and initially also the R-help mail archive. This web service was made available as https://search.R-project.org, with simple and advanced R interfaces provided by, respectively, functions RSiteSearch() in package utils and CRAN package sos (see the corresponding article on “Searching Help Pages of R Packages” in the R Journal).

The next generation of this web service was developed by Gennadiy Starostin and is now hosted at Wirtschaftsuniversität Wien, Austria. In doing so, there were two major changes.

First, the old service was based on the namazu search engine (http://www.namazu.org/), which is no longer actively developed (last release more than ten years old). After careful examination of available open-source alternatives xapian-omega (https://xapian.org/) was chosen as the new search engine, which provides the necessary versatility alongside reasonable complexity. The most notable features of xapian are ranked search, phrase and proximity searching, Boolean search operators, Boolean filters, support for stemming of search terms, and allowing simultaneous update and searching.

For compatibility reasons the server still supports requests in the previously used namazu format (limited to the parameters used by the former search engine). This compatibility feature may be dropped in the future.

In addition to the human-readable output of search results, two other formats are made available: “xml” and “opensearch”. Simply change in the URL FMT=query to either FMT=xml or FMT=opensearch when sending a HTTP GET request to the server. One can tailor search queries using additional parameters, see the query part of the URL in the default form and the xapian-omega documentation.

Second, the covered CRAN content was expanded. Currently, there are eight categories, any combination of which can be searched simultaneously:

• R manuals (currently based on the R-patched development branch)
• Help pages of base packages (also from R-patched)
• CRAN packages (5 categories): general info, news, readme files, vignettes, and help pages
• CRAN task views

Although content of the majority of these categories is available on CRAN to read and explore, two of them, the help pages of base and CRAN packages, are additionally generated for search.R-project.org. As of December 22, 2021, in terms of searchable documents they constitute approximately 400,000 out of 450,000 total (about 89%).

Generating this content was not straightforward. HTML content is preferable to PDF content for browsing search results, but the new R help system works best for dynamic HTML (see the corresponding article in the R Journal), whereas for the search service, using static HTML is more appropriate. The code for generating static HTML needed a bit of tweaking by Deepayan Sarkar and Kurt Hornik, and now can (again) be used to provide help files which are good for both searching and browsing.

In the future, search.R-project.org may be expanded with relevant sources outside of CRAN, e.g., the Bioconductor project. Depending on user feedback, which is always welcome, one can expect other improvements.

4 Acknowledgements

Tomas Kalibera’s work on the article and R development has received funding from the Czech Ministry of Education, Youth and Sports from the Czech Operational Programme Research, Development, and Education, under grant agreement No.CZ.02.1.01/0.0/0.0/15_003/0000421, from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, under grant agreement No. 695412, and from the National Science Foundation award 1925644.

CRAN packages used

sos

CRAN Task Views implied by cited packages

Note

This article is converted from a Legacy LaTeX article using the texor package. The pdf version is the official version. To report a problem with the html, refer to CONTRIBUTE on the R Journal homepage.