Wed, 01 Feb 2023

RInside 0.2.18 on CRAN: Maintenance

A new release 0.2.18 of RInside arrived on CRAN and in Debian today. This is the first release in ten months since the 0.2.17 release. RInside provides a set of convenience classes which facilitate embedding of R inside of C++ applications and programs, using the classes and functions provided by Rcpp.

This release brings a contributed change to how the internal REPL is called: Dominick found the current form more reliable when embedding R on Windows. We also updated a few other things around the package.

The list of changes since the last release:

Changes in RInside version 0.2.18 (2023-02-01)

  • The random number initialization was updated as in R.

  • The main REPL is now running via 'run_Rmainloop()'.

  • Small routine update to package and continuous integration.

My CRANberries also provides a short report with changes from the previous release. More information is on the RInside page. Questions, comments etc should go to the rcpp-devel mailing list off the Rcpp R-Forge page, or to issues tickets at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Mon, 30 Jan 2023

#39: Faster Feedback Systems – A Continuous Integration Example

Welcome to the 39th post in the relatively randomly recurring rants, or R4 for short. Today’s post picks up where the previous post #38: Faster Feedback Systems started. As we argued in #38, the need for fast feedback loops is fairly universal and widespread. Fairly shortly after we posted #38, useR! 2022 happened and one presentation had the key line

Waiting 1-24 minutes for a build to finish can be a massive time suck.

which we would like to come back to today. Furthermore, the unimitable @b0rk had a fabulous tweet just weeks later stating the same point debugging strategy: shorten your feedback loop as a key in a successful debugging strategy.

So in sum: shorter is better. Nobody likes to wait. And shorter i.e. faster is a key and recurrent theme in the R4 series. Today we have a fairly nice illustration of two aspects we have stressed before:

  • Fewer dependencies makes for faster installation time (apart from other desirable robustness aspects); and

  • Using binaries makes for faster installation time as it removes the need for compilations.

The combined effects can be staggering as we show below. The example is motivated by a truly “surprising” (we are being generous here) comment we received as an aside when discussing the eternal topic of whether R users do, or do not, have a choice when picking packages, or approaches, or verses. To our surprise, we were told that “packages are not substitutable”. Which is both demonstrably false (see below) and astonishing as it came from an academic. I.e. someone trained and paid to abstract superfluous detail away and recognise and compare ‘core’ features of items under investigation. Truly stunning. But I digress.

CRAN by now has many packages, slowly moving in on 20,000 in total, and is a unique success we commented-on time and time before. By now many packages shadow or duplicate each other, reinvent one another, or revise/review. One example is the pair of packages accessing PostgreSQL databases. There are several, but two are key. The older one is RPostgreSQL which has been around since Sameer Kumar Prayaga wrote it as a Google Summer of Code student in 2008 under my mentorship. The package has now been maintained well (if quietly) for many years by Tomoaki Nishiyama. The other entrant is more recent, though not new, and is RPostgres by Kirill Müller and others. We will for the remainder of this post refer to these two as the tiny and the tidy version as either can been as being a representative of a certain ‘verse’.

The aforementioned comment on non-substitutability struck us as eminently silly, so we set out to prove just how absurd it really is. So about a year ago we set up pair of GitHub repos with minimal code in a pair we called lim-tiny and lim-tidy. Our conjecture was (and is!) that less is more – just as post #34 titled Less Is More argued with respect to package dependencies. Each of the repos just does one thing: a query to a (freely accessible but remote) PostgreSQL database. The tiny version just retrieves a data frame using only the dependencies needed for RPostgreSQL namely DBI and nothing else. The tidy version retrieves a tibble and has access to everything else that comes when installing RPostgres: DBI, dplyr, and magrittr – plus of course their respective dependencies. We were able to let the code run in (very default) GitHub Actions on a weekly schedule without intervention apart from one change to the SQL query when the remote server (providing public bioinformatics data) changed its schema slighly, plus one update to the action yaml code version. No other changes.

We measure the time a standard continuous integration run takes in total using the default GitHub Action setup in the tidy case (which relies on RSPM/PPM binaries, caching, …, and does not rebuild from source each time), and our own r-ci script (introduced in #32 for CI with R. It switched to using r2u during the course of this experiment but already had access to binaries via c2d4u – so it is always binaries-based (see e.g. #37 or #13 for more). The chart shows the evolution of these run-times over the course of the year with one weekly run each.

tiny vs tidy ci timing impact chart

This study reveals a few things:

  • “Yes, Veronica, we have a choice”: one year of identical results retrieving a data set via SQL from a PostgreSQL server. We can often choose between alternative packages to get (or process) our data.
  • There is a Free Lunch (TM) here: RPostgreSQL consistently dominates RPostgres when measured in CI run-time for the same task.
  • While there is (considerable) variability (likely stemming from heterogenous setups at GitHub Action) the tiny approach is on average about twice as fast as the tidy approch.
  • You do have a choice. Would you rather wait x minutes for CI, or 2x?

The key point there is that while the net-time to fire off a single PostgreSQL is likely (near-)identical, the net cost of continuous integration is not. In this setup, it is about twice the run-time simply because ‘Less Is More’ which (in this setup) comes out to about being twice as fast. And that is a valid (and concrete, and verifiable) illustration of the overall implicit cost of adding dependencies to creating and using development, test, or run-time environments.

Faster feedback loops make for faster builds and faster debugging. Consider using fewer dependencies, and/or using binaries as provided by r2u.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sun, 29 Jan 2023

RcppTOML 0.2.2 on CRAN: Now with macOS-on-Intel Builds

Just days after a build-fix release (for aarch64) and still only a few weeks after the 0.2.0 release of RcppTOML and its switch to toml++, we have another bugfix release 0.2.2 on CRAN also bringing release 3.3.0 of toml++ (even if we had large chunks of 3.3.0 already incorporated).

TOML is a file format that is most suitable for configurations, as it is meant to be edited by humans but read by computers. It emphasizes strong readability for humans while at the same time supporting strong typing as well as immediate and clear error reports. On small typos you get parse errors, rather than silently corrupted garbage. Much preferable to any and all of XML, JSON or YAML – though sadly these may be too ubiquitous now. TOML is frequently being used with the projects such as the Hugo static blog compiler, or the Cargo system of Crates (aka “packages”) for the Rust language.

The package was building fine on Intel-based macOS provided the versions were recent enough. CRAN, however, aims for the broadest possibly reach of binaries and builds on a fairly ancient macOS 10.13 with clang version 10. This confused toml++ into (wrongly) concluding it could not build when it in fact can. After a hint from Simon that Apple in their infinite wisdom redefines clang version ids, this has been reflected in version 3.3.0 of toml++ by Mark so we should now build everywhere. Big thanks to everybody for the help.

The short summary of changes follows.

Changes in version 0.2.2 (2023-01-29)

  • New toml++ version 3.3.0 with fix to permit compilation on ancient macOS systems as used by CRAN for the Intel-based builds.

Courtesy of my CRANberries, there is a diffstat report for this release. More information is on the RcppTOML page page. Please use the GitHub issue tracker for issues and bugreports.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Wed, 25 Jan 2023

RcppTOML 0.2.1 on CRAN: Small Build Fix for Some Arches

Two weeks after the release of RcppTOML 0.2.0 and the switch to toml++, we have a quick bugfix release 0.2.1.

TOML is a file format that is most suitable for configurations, as it is meant to be edited by humans but read by computers. It emphasizes strong readability for humans while at the same time supporting strong typing as well as immediate and clear error reports. On small typos you get parse errors, rather than silently corrupted garbage. Much preferable to any and all of XML, JSON or YAML – though sadly these may be too ubiquitous now. TOML is frequently being used with the projects such as the Hugo static blog compiler, or the Cargo system of Crates (aka “packages”) for the Rust language.

Some architectures, aarch64 included, got confused over ‘float16’ which is of course a tiny two-byte type nobody should need. After consulting with Mark we concluded to (at least for now) simply override this excluding the use of ‘float16’.

The short summary of changes follows.

Changes in version 0.2.1 (2023-01-25)

  • Explicitly set -DTOML_ENABLE_FLOAT16=0 to permit compilation on some architectures stumbling of the type.

Courtesy of my CRANberries, there is a diffstat report for this release. More information is on the RcppTOML page page. Please use the GitHub issue tracker for issues and bugreports.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sun, 22 Jan 2023

Rcpp 1.0.10 on CRAN: Regular Update

rcpp logo

The Rcpp team is thrilled to announce the newest release 1.0.10 of the Rcpp package which is hitting CRAN now and will go to Debian shortly. Windows and macOS builds should appear at CRAN in the next few days, as will builds in different Linux distribution and of course at r2u. The release was prepared a few days ago, but given the widespread use at CRAN it took a few days to be processed. As always, our sincere thanks to the CRAN maintainers Uwe Ligges and Kurt Hornik. This release continues with the six-months cycle started with release 1.0.5 in July 2020. As a reminder, we do of course make interim snapshot ‘dev’ or ‘rc’ releases available via the Rcpp drat repo and strongly encourage their use and testing—I run my systems with these versions which tend to work just as well, and are also fully tested against all reverse-dependencies.

Rcpp has become the most popular way of enhancing R with C or C++ code. Right now, around 2623 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 252 in BioConductor. On CRAN, 13.7% of all packages depend (directly) on CRAN, and 58.7% of all compiled packages do. From the cloud mirror of CRAN (which is but a subset of all CRAN downloads), Rcpp has been downloaded 67.1 million times.

This release is incremental as usual, preserving existing capabilities faithfully while smoothing our corners and / or extending slightly. Of particular note is the now fully-enabled use of the ‘unwind’ protection making some operations a little faster by default; special thanks to Iñaki for spearheading this. Kevin and I also polished a few other bugs off as detailed below.

The full list of details follows.

Changes in Rcpp release version 1.0.10 (2023-01-12)

  • Changes in Rcpp API:

    • Unwind protection is enabled by default (Iñaki in #1225). It can be disabled by defining RCPP_NO_UNWIND_PROTECT before including Rcpp.h. RCPP_USE_UNWIND_PROTECT is not checked anymore and has no effect. The associated plugin unwindProtect is therefore deprecated and will be removed in a future release.

    • The 'finalize' method for Rcpp Modules is now eagerly materialized, fixing an issue where errors can occur when Module finalizers are run (Kevin in #1231 closing #1230).

    • Zero-row data.frame objects can receive push_back or push_front (Dirk in #1233 fixing #1232).

    • One remaining sprintf has been replaced by snprintf (Dirk and Kevin in #1236 and #1237).

    • Several conversion warnings found by clang++ have been addressed (Dirk in #1240 and #1241).

  • Changes in Rcpp Attributes:

    • The C++20, C++2b (experimental) and C++23 standards now have plugin support like the other C++ standards (Dirk in #1228).

    • The source path for attributes received one more protection from spaces (Dirk in #1235 addressing #1234).

  • Changes in Rcpp Deployment:

    • Several GitHub Actions have been updated.

Thanks to my CRANberries, you can also look at a diff to the previous release. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page. Bugs reports are welcome at the GitHub issue tracker as well (where one can also search among open or closed issues); questions are also welcome under rcpp tag at StackOverflow which also allows searching among the (currently) 2932 previous questions.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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BH 1.81.0-1 oon CRAN: New Upstream, New Library, sprintf Change

Boost

Boost is a very large and comprehensive set of (peer-reviewed) libraries for the C++ programming language, containing well over one hundred individual libraries. The BH package provides a sizeable subset of header-only libraries for (easier, no linking required) use by R. It is fairly widely used: the (partial) CRAN mirror logs (aggregated from the cloud mirrors) show over 32.6 million package downloads.

Version 1.81.0 of Boost was released in December following the regular Boost release schedule of April, August and December releases. As the commits and changelog show, we packaged it almost immediately and started testing following our annual update cycle which strives to balance being close enough to upstream and not stressing CRAN and the user base too much. The reverse depends check revealed about a handful of packages requiring changes or adjustments which is a pretty good outcome given the over three hundred direct reverse dependencies. So we opened issue #88 to coordinate the issue over the winter break during which CRAN also closes (just as we did before), and also send a wider ‘PSA’ tweet as a heads-up. Our sincere thanks to the two packages that already updated, and the four that likely will soon. Our thanks also to CRAN for reviewing the package impact over the last few days since I uploaded the package earlier this week.

There are a number of changes I have to make each time in BH, and it is worth mentioning them. Because CRAN cares about backwards compatibility and the ability to be used on minimal or older systems, we still adjust the filenames of a few files to fit a jurassic constraints of just over a 100 characters per filepath present in some long-outdated versions of tar. Not a big deal. We also, and that is more controversial, silence a number of #pragma diagnostic messages for g++ and clang++ because CRAN insists on it. I have no choice in that matter. Next, and hopefully this time only, we also found and replaced a few remaining sprintf uses and replaced them with snprintf. Many of the Boost libraries did that, so I hope by the next upgrade for Boost 1.84.0 next winter this will be fully taken care of. Lastly, and also only this time, we silenced a warning about Boost switching to C++14 in the next release 1.82.0 in April. This may matter for a number of packages having a hard-wired selection of C++11 as their C++ language standard. Luckily our compilers are good enough for C++14 so worst case I will have to nudge a few packages next December.

This release adds one new library for url processing which struck us as potentially quite useful. The more detailed NEWS log follows.

Changes in version 1.81.0-1 (2023-01-17)

  • Upgrade to Boost 1.81.0 (#87)

  • Added url (new in 1.81.0)

  • Converted remaining sprintf to snprintf (#90 fixing #89)

  • Comment-out gcc warning messages in three files

Via my CRANberries, there is a diffstat report relative to the previous release.

Comments and suggestions about BH are welcome via the issue tracker at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sat, 21 Jan 2023

RcppSimdJson 0.1.9 on CRAN: New Upstream

The RcppSimdJson package was just updated to release 0.1.9.

RcppSimdJson wraps the fantastic and genuinely impressive simdjson library by Daniel Lemire and collaborators. Via very clever algorithmic engineering to obtain largely branch-free code, coupled with modern C++ and newer compiler instructions, it results in parsing gigabytes of JSON parsed per second which is quite mindboggling. The best-case performance is ‘faster than CPU speed’ as use of parallel SIMD instructions and careful branch avoidance can lead to less than one cpu cycle per byte parsed; see the video of the talk by Daniel Lemire at QCon.

This release updates the underlying simdjson library to version 3.0.1, settles on C++17 as the language standard, exports a worker function for direct C(++) access, and polishes a few small things around the package and tests.

The NEWS entry for this release follows.

Changes in version 0.1.9 (2023-01-21)

  • The internal function deseralize_json is now exported at the C++ level as well as in R (Dirk in #81 closing #80).

  • simdjson was upgraded to version 3.0.1 (Dirk in #83).

  • The package now defaults to C++17 compilation; configure has been retired (Dirk closing #82).

  • The three main R access functions now use a more compact argument check via stopifnot (Dirk).

Courtesy of my CRANberries, there is also a diffstat report for this release. For questions, suggestions, or issues please use the issue tracker at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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RcppFastFloat 0.0.4 on CRAN: New Upstream

A new release of RcppFastFloat arrived on CRAN yesterday. The package wraps fast_float, another nice library by Daniel Lemire. For details, see the arXiv paper showing that one can convert character representations of ‘numbers’ into floating point at rates at or exceeding one gigabyte per second.

This release updates the underlying fast_float library version. Special thanks to Daniel Lemire for quickly accomodating a parsing use case we had encode as a test, namely with various whitespace codes. The default in fast_float, as in C++17, is to be more narrow but we enable the wider use case via two #define statements.

Changes in version 0.0.4 (2023-01-20)

  • Update to fast_float 3.9.0

  • Set two #define re-establish prior behaviour with respect to whitespace removal prior to parsing for as.double2()

  • Small update to continuous integration actions

Courtesy of my CRANberries, there is also a diffstat report for this release.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sun, 15 Jan 2023

RcppArmadillo 0.11.4.3.1 on CRAN: Updates

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 1034 packages other packages on CRAN, downloaded 27.6 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper (preprint / vignette) by Conrad and myself has been cited 509 times according to Google Scholar.

This release brings another upstream bugfix interation 11.4.3, released in accordance with the aimed-for monthly release cadence. We had hoped to move away from suppressing deprecation warnings in this release, and had prepared over two dozen patch sets all well as pull requests as documented in issue #391. However, it turns out that we both missed with one or two needed set of changes as well as two other sets of changes triggering deprecation warnings. So we expanded issue #391, and added issue #402 – and prepared another eleven pull requests and patches today. With that we can hopefully remove the suppression of these warnings by an expected late of late April.

The full set of changes (since the last CRAN release 0.11.4.2.1) follows.

Changes in RcppArmadillo version 0.11.4.3.1 (2023-01-14)

  • The #define ARMA_IGNORE_DEPRECATED_MARKER remains active to suppress the (upstream) deprecation warnings, see #391 and #402 for details.

Changes in RcppArmadillo version 0.11.4.3.0 (2022-12-28) (GitHub Only)

  • Upgraded to Armadillo release 11.4.3 (Ship of Theseus)

    • fix corner case in pinv() when processing symmetric matrices
  • Protect the undefine of NDEBUG behind additional opt-in define

Courtesy of my CRANberries, there is a diffstat report relative to previous release. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sat, 14 Jan 2023

RApiDatetime 0.0.8 on CRAN: Maintenance

A new release of our RApiDatetime package is now on CRAN.

RApiDatetime provides a number of entry points for C-level functions of the R API for Date and Datetime calculations. The functions asPOSIXlt and asPOSIXct convert between long and compact datetime representation, formatPOSIXlt and Rstrptime convert to and from character strings, and POSIXlt2D and D2POSIXlt convert between Date and POSIXlt datetime. Lastly, asDatePOSIXct converts to a date type. All these functions are rather useful, but were not previously exported by R for C-level use by other packages. Which this package aims to change.

This release accomodates a CRAN request (as one does) to change (one single) instance of sprintf() to snprintf(). No more, no less.

Changes in RApiDatetime version 0.0.8 (2023-01-14)

  • Update one use of sprint to snprintf

  • Minor edits to DESCRIPTION

Courtesy of my CRANberries, there is are comparisons to the previous release. More information is on the rapidatetime page.

For questions or comments please use the issue tracker off the GitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Thu, 12 Jan 2023

RcppGSL 0.3.13 on CRAN: Mandated Update

A new release 0.3.13 of RcppGSL is now on CRAN. The RcppGSL package provides an interface from R to the GNU GSL by relying on the Rcpp package.

This release contains one change (made at the request of a CRAN email in light of possible future changes for C standard C17 and then C23) and removes a compiler-check from configure.ac. It is both a fair point as our src/Makevars does not actually set a compiler yet also a little … marginal?

The NEWS entry follows:

Changes in version 0.3.13 (2023-01-12)

  • Remove 'AC_PROG_CC' from 'configure.ac' per CRAN wish

Courtesy of CRANberries, a summary of changes in the most recent release is also available.

More information is on the RcppGSL page. Questions, comments etc should go to the issue tickets at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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RDieHarder 0.2.5 on CRAN: Mandated Update

An new version 0.2.5 of the random-number generator tester RDieHarder (based on the DieHarder suite developed / maintained by Robert Brown with contributions by David Bauer and myself along with other contributors) is now on CRAN.

This release contains one change (made at the request of a CRAN email in light of possible future changes for C standard C17 and then C23) and removes a compiler-check from configure.ac. It is both a fair point as our src/Makevars does not actually set a compiler yet also a little … marginal?

Thanks to CRANberries, you can also look at the most recent diff.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Wed, 11 Jan 2023

linl 0.0.5 on CRAN: Extended Background Support

A new release of our linl package for writing LaTeX letters with (R)markdown is now on CRAN. linl makes it easy to write letters in markdown, with some extra bells and whistles thanks to some cleverness chiefly by Aaron.

This version add extended header and footer placement support thanks to an included copy of wallpaper.sty as added in a nice PR by Iñaki. As the previous release was well over three years ago, we also enhanced continuous integration in the process. The repository README.md shows some screenshots of input and output files.

The NEWS entry follows:

Changes in linl version 0.0.5 (2023-01-11)

  • Several updates to continuous integration and testing

  • Enhanced placment functionality for images in header and footer via wallpaper.sty and new x and y offset variable (Iñaki Ucar in #30)

Courtesy of CRANberries, there is a comparison to the previous release. More information is on the linl page. For questions or comments use the issue tracker off the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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qlcal 0.0.4 on CRAN: Extended and Updated

The fourth release of the still new-ish qlcal package arrivied at CRAN just now.

qlcal is based on the calendaring subset of QuantLib. It is provided (for the R package) as a set of included files, so the package is self-contained and does not depend on an external QuantLib library (which can be demanding to build). qlcal covers over sixty country / market calendars and can compute holiday lists, its complement (i.e. business day lists) and much more.

This release generalizes the advanceDate() function (similar to what advanceUnits() already had), and updates several calendars along with the upcoming QuantLib 1.29 release. This includes updates for the UK and Australia related to changes in the monarchy, an update for South Africa and the additional of 2023 holidays for China.

Changes in version 0.0.4 (2023-01-11)

  • The advanceDate{} function can now selects a business day convention, a time unit and an end-of-month convention

  • Calendars routines for Australia, China, South Africa, UK, US have been updated to current versions from QuantLib 1.29.

Courtesy of my CRANberries, there is a diffstat report for this release. See the project page and package documentation for more details, and more examples.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Tue, 10 Jan 2023

RcppTOML 0.2.0: TOML 1.0.0 rewrite with toml++

A few years since the last release in late 2020, the RcppTOML package is now back with a new and shiny CRAN release 0.2.0. It is now based on the wonderful toml++ C++17 library by Mark Gillard and gets us (at long last!) full TOML v1.0.0 compliance for use with R.

TOML is a file format that is most suitable for configurations, as it is meant to be edited by humans but read by computers. It emphasizes strong readability for humans while at the same time supporting strong typing as well as immediate and clear error reports. On small typos you get parse errors, rather than silently corrupted garbage. Much preferable to any and all of XML, JSON or YAML – though sadly these may be too ubiquitous now. TOML is frequently being used with the projects such as the Hugo static blog compiler, or the Cargo system of Crates (aka “packages”) for the Rust language.

This package is a rewrite of the internals interfacing the library, and updates the package to using toml++ and C++17. The R interface is unchanged, and a full run of reverse dependencies passed. This involved finding one sole test failure which turned to have been driven by a non-conforming TOML input file which Jianfeng Li kindly fixed at the source making his (extensive) set of tests in package configr pass too. The actual rewrite was mostly done in a one-off repo RcppTomlPlusPlus which can now be considered frozen.

The short summary of changes follows.

Changes in version 0.2.0 (2023-01-10)

  • Rewritten in C++17 using toml++ for TOML v1.0.0 compliance

  • Unchanged interface from R, unchanged (and expanded tests)

  • Several small continuous integration upgrades since last release

Courtesy of my CRANberries, there is a diffstat report for this release. More information is on the RcppTOML page page. Please use the GitHub issue tracker for issues and bugreports.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sun, 08 Jan 2023

spdl 0.0.4 on CRAN: Adding Stopwatch

Another quick update to the still new-ish package spdl is now om CRAN, and in Debian. The key focus of spdl is a offering the same interface from both R and C++ for logging by relying on spdlog via my RcppSpdlog package.

This release add support for the stopwatch() facility. One can now instantiate such an object, and referencing it in a log message shows the elapsed time. No more, no less, and it works the same way in R and C++.

The short NEWS entry follows.

Changes in spdl version 0.0.4 (2023-01-08)

  • Add support for stopwatch

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the spdl page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/spdl | permanent link

RVowpalWabbit 0.0.18: Maintenance

A new maintenance release, now at version 0.0.18, of the RVowpalWabbit package arrived on CRAN. It improves several sprintf() calls by changing them to snprintf() (though there is a remaining one creeping in from a linked-to library).

As noted before, there is a newer package rvw based on the excellent GSoC 2018 and beyond work by Ivan Pavlov (mentored by James and myself) so if you are into VowpalWabbit from R go check it out.

CRANberries provides a summary of changes to the previous version. More information is on the RVowpalWabbit page. Issues and bugreports should go to the GitHub issue tracker.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rvowpalwabbit | permanent link

Sat, 07 Jan 2023

RcppSpdlog 0.0.12 on CRAN: Added Stopwatch

Version 0.0.12 of RcppSpdlog is now on CRAN and in Debian. RcppSpdlog bundles spdlog, a wonderful header-only C++ logging library with all the bells and whistles you would want that was written by Gabi Melman, and also includes fmt by Victor Zverovich.

This release adds support for the stopwatch object, a simple container around a std::chrono object. It makes (simple) time measurements of routines and code segments trivially easy. Instantiate a stopwatch object, and ‘formatting’ it in a logging string displays elapsed time. And given that the whole mojo of RcppSpdlog (and its sibbling package spdl) is to make use easy in both R and C++ we can do this nicely and consistently in both languages. The vignette has an added section with a concrete example.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.12 (2023-01-07)

  • Addeed support for 'stopwatch' object allowing for simple timing (from both C++ and R) via the logging framework.

  • The ‘spdlog’ logging pattern is documented via a reference.

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog page, or the package documention site.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Tue, 20 Dec 2022

RcppDE 0.1.7 on CRAN: Several Updates

The first fresh release of our RcppDE package in over four years (!!) is now on CRAN.

RcppDE is a “port” of DEoptim, a popular package for derivative-free optimisation using differential evolution optimization, from plain C to C++. By using RcppArmadillo the code becomes a lot shorter and more legible. Our other main contribution is to leverage some of the excellence we get for free from using Rcpp, in particular the ability to optimise user-supplied compiled objective functions which can make things a lot faster than repeatedly evaluating interpreted objective functions as DEoptim does (and which, in fairness, most other optimisers do too). The gains can be quite substantial.

This release brings two helpful patches from Max Coulter who spotted two distinct areas for improvement, based on how DEoptim how changed in recent years. I updated a number of aspects of continuous integration since the last release, and also streamlined and simplified the C++ interface (and in doing so also squashed a bug or two).

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppDE page, or the repository.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Wed, 14 Dec 2022

spdl 0.0.3 on CRAN: Adding File Logger

A second update to the still-new package spdl is now om CRAN, and in Debian. The key focus of spdl is a offering the same interface from both R and C++ for logging by relying on spdlog via my RcppSpdlog package.

This release add support for a simple filesetup() initialiser to direct logging output to a file. For now the console logger and the file logger are exclusive, if there is interest we could borrow a page from upstream and combine them.

The short NEWS entry follows.

Changes in spld version 0.0.3 (2022-12-14)

  • Add filesetup method

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the spdl page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/spdl | permanent link

Tue, 13 Dec 2022

RcppSpdlog 0.0.11 on CRAN: Small Enhancement

Version 0.0.11 of RcppSpdlog is now on CRAN and in Debian. RcppSpdlog bundles spdlog, a wonderful header-only C++ logging library with all the bells and whistles you would want that was written by Gabi Melman, and also includes fmt by Victor Zverovich.

This release adds support for a basic file logger as a alternative to the console logger. This can be helpful with code which suppresses or hides console output – as for example unit test code does. We also expose the formatting helper function for direct use at the C level from other packages, and mention the handy wrapper spdl in the README.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.11 (2022-12-13)

  • Export the formatter at C level

  • Mention package spdl in README.md

  • Support simple file-based logger

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog page, or the package documention site.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Mon, 12 Dec 2022

digest 0.6.31 on CRAN: snprintf Update

Release 0.6.31 of the digest package arrived at CRAN this weekend, and is being uploaded to Debian as well.

digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, spookyhash, and blake3 algorithms) permitting easy comparison of R language objects. It is a mature and widely-used as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation to quickly identify the various objects.

This release contains the tiny change (in maybe a dozen places) triggered recently by macOS and now checked for by r-devel which consists of replacing (v)sprintf calls with (v)snprintf. No more, no less.

My CRANberries provides the usual summary of changes to the previous version. For questions or comments use the issue tracker off the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/digest | permanent link

Thu, 08 Dec 2022

AsioHeaders 1.22.1-2 on CRAN: Small Update

An new minor revision of the AsioHeaders package arrived at CRAN earlier today. Asio provides a cross-platform C++ library for network and low-level I/O programming. It is also included in Boost – but requires linking when used as part of Boost. This standalone version of Asio is a header-only C++ library which can be used without linking (just like our BH package with parts of Boost).

This minor update avoid use of (v)sprintf which CRAN now flags in r-devel (for all R builds), following the decision by Apple to deprecated it for macOS. Winston had notified me about email he had gotten for for his websocket package – also highlighting the issue for both iptools and ipaddress. As the issue ticket dialog shows I was initially a little hamfisted about replicating, falsely thinking I would need an updated compiler. But this really is ‘just’ a change in r-devel once again scanning shared libraries for symbols now warned about. Upstream has newer minor releases but they did not yet cover this; however I found a commit mentioning Xcode and snprint from three days ago which I essentially ported. We needed one more change, and that addressed the issue in websocket. But as it is good to increase the number of random acts of kindness, I also looked into iptools and ipaddress as CRAN has its eyes on them too for this. Turned out they needed simple and limited changes from sprint to snprintf so made those and sent them PRs: iptools PR #42 and ipaddress PR #79.

The short NEWS entry for AsioHeaders follows.

Changes in version 1.22.1-2 (2022-12-07)

  • Switch a handful of upstream (v)sprint uses to (v)snprintf.

Thanks to my CRANberries, there is also a diffstat report relative to the previous release.

Comments and suggestions about AsioHeaders are welcome via the issue tracker at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/asioheaders | permanent link

Thu, 01 Dec 2022

spdl 0.0.2 on CRAN: First Update

A first update to the recently-released package spdl is now om CRAN. The key focus of spdl is a offering the same interface from both R and C++ for logging by relying on spdlog via my RcppSpdlog package.

This release exposes simple helpers fmt() (to format text according to the included fmt library) and cat() which formats and prints.

The very short NEWS entry for this release follows.

Changes in spld version 0.0.2 (2022-12-01)

  • Helper functions fmt() and cat() have been added

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the spdl page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/spdl | permanent link

Tue, 22 Nov 2022

spdl 0.0.1 on CRAN: New Package!

A new package made it to CRAN today: spdl. It provides a very simple interface to spdlog with the key focus being that provides the same interface from both R and C++. I had brought spdlog to R a little while ago via RcppSpdlog, but its use was generally limited to C++ code where we would write something like (taken from one of the examples included in the package)

spdlog::info("Welcome to spdlog!");

I then provided C-level exports from the package accessible in other package but with that the signature only became longer as it also included the package name, here RcppSpdlog. So I experimented a little with that and added another ‘more compactly named’ namespace spdl around it. So then it becomes

spdl::info("Info message with values {} and {}", 42, 1.23);  // C++ code

which now also shows the power of the included fmt library. And I got quite used to that … and now wanted to same from R! But to create a new namespace, we need a new package. So … we made one. Now from R too:

spdl::info("Info message with values {} and {}", 42L, 1.23)  # R code

We layered a very simple wrapper for fmt over this. All R argument are passed to format() and we simply send a vector of strings over the C interface to the RcppSpdlog package where the templated formatter of fmt is invoked – but for character values. You can equally well format the string locally first. Everything works: from paste() to sprintf() to any of the existing string interpolators all of which are nice. But none works just like fmt and I wanted to have the same formatter in both languages, and like how fmt works.

By tradition, the NEWS entry for this release follows.

Changes in spld version 0.0.1 (2022-11-21)

  • Initial release of R and C++ loggers using spdl::* namespace

More detailed information is on the spdl page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/spdl | permanent link

Mon, 21 Nov 2022

RcppClassic 0.9.13 on CRAN: Minor Update

A maintenance release 0.9.14 of the RcppClassic package arrived earlier today on CRAN. This package provides a maintained version of the otherwise deprecated initial Rcpp API which no new projects should use as the normal Rcpp API is so much better.

The changes is. CRAN was reporting (for all four macOS builds, and only there) that an absolute path was embedded, so we updated the (old …) call to install_name_tool use on that (and only that) OS. No other changes were made.

CRANberries also reports the changes relative to the previous release from nearly three years ago.

Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Thu, 17 Nov 2022

RcppSpdlog 0.0.10 on CRAN: New Features

A version 0.0.10 of RcppSpdlog is now on CRAN and in Debian. RcppSpdlog bundles spdlog, a wonderful header-only C++ logging library with all the bells and whistles you would want that was written by Gabi Melman, and also includes fmt by Victor Zverovich.

This release continues on the path started less than two weeks ago with the RcppSpdlog 0.0.9 release. We continue to support both R and C++ access by adding a (simple) variadic template formatter exposing fmt::format() (by focusing on just string arguments). This can be accessed from R via the exact same formatting strings that fmt uses, and which we have come to like for its simplicity. Of course if one prefers a different string interpolation method, or plain sprintf(), or even paste: they all work as all that matters is that a character variable gets passed on. We also added a little bit of new documentation in the vignette.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.10 (2022-11-17)

  • Support variadic templates with fmt::format

  • Add R formatting helper which converts arguments to character taking advantage of variadic template logger: fmt logging from R

  • Expand vignette

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog page, or the package documention site.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Wed, 09 Nov 2022

RcppArmadillo 0.11.4.2.1 on CRAN: Updates

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 1027 packages other packages on CRAN, downloaded 26.9 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper (preprint / vignette) by Conrad and myself has been cited 503 times according to Google Scholar.

This release reflect as new upstream bugfix release 11.4.2 made recently by Conrad. To accomodate CRAN and their preference for at most a release per month, we held it back since the 11.4.0 release early October. As we usually do, we generally update once upstream Armadillo releases are made. When we do not immediately release to CRAN (in order to lower the release cadence), we make those “interim” releases available via GitHub source and the Rcpp drat repo.

This release also brings a rearranged, and as we think, simplified layout of the header files. All existing locations are still supported but we will be starting a (very patient and slow) transition at some point.

The full set of changes (since the last CRAN release 0.11.4.0.1) follows.

Changes in RcppArmadillo version 0.11.4.2.1 (2022-11-08)

  • Upgraded to Armadillo release 11.4.2 (Ship of Theseus)

    • more robust handling of corner cases in multi-threaded contexts
  • Internal header organisation with new sub-directories while providing full compatibility via existing paths (#395 #396)

Changes in RcppArmadillo version 0.11.4.1.0 (2022-10-10) (GitHub Only)

  • Upgraded to Armadillo release 11.4.1 (Ship of Theseus)

    • fix data race in Cube::slice()

    • workarounds for false warnings emitted by GCC 12 when compiling with FORTIFY_SOURCE enabled (already in RcppArmadillo 0.11.4.0.1 too)

Courtesy of my CRANberries, there is a diffstat report relative to previous release. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Sun, 06 Nov 2022

RcppCCTZ 0.2.12 on CRAN: Maintenance

A new release 0.2.12 of RcppCCTZ is now on CRAN.

RcppCCTZ uses Rcpp to bring CCTZ to R. CCTZ is a C++ library for translating between absolute and civil times using the rules of a time zone. In fact, it is two libraries. One for dealing with civil time: human-readable dates and times, and one for converting between between absolute and civil times via time zones. And while CCTZ is made by Google(rs), it is not an official Google product. The RcppCCTZ page has a few usage examples and details. This package was the first CRAN package to use CCTZ; by now several others packages (four the last time we counted) include its sources too. Not ideal, but beyond our control.

This version adds support for NA values when parsing, and updates GitHub Action.

Changes in version 0.2.12 (2022-11-06)

  • Support NA values in numerical or character input

  • GitHub Actions were updated to checkout version 3.

Courtesy of my CRANberries, there is also a diffstat to the previous version. More details are at the RcppCCTZ page; code, issue tickets etc at the GitHub repository.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Sat, 05 Nov 2022

RcppEigen 0.3.3.9.3 on CRAN: Maintenance

A new release 0.3.3.9.3 of RcppEigen arrived on CRAN moments ago (and just went to Debian). Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

This update is again mostly maintenance. To accomodate one small aspect of the Fortran interface, we now require R 3.6.0 or later. Jonah Gabry spotted a really old typo and fixed it. The fastLm support code now uses the unabbreviated df.residual. We accomodated clang-15 in one signature as is common with many recent uploads, and also updated one aspect of GitHub Actions.

And once again as we said for the last four releases:

One additional and recent change was the accomodation of a recent CRAN Policy change to not allow gcc or clang to mess with diagnostic messages. A word of caution: this may make your compilation of packages using RcppEigen very noisy so consider adding -Wno-ignored-attributes to the compiler flags added in your ~/.R/Makevars.

We still find this requirement rather annoying. Eigen is only usable if you set, say,

-Wno-deprecated-declarations -Wno-parentheses -Wno-ignored-attributes -Wno-unused-function

asoptions in~/.R/Makevars`. But CRAN makes the rules. Maybe if a few of us gently and politely nudge them they may relent one day. One can only hope.

The complete NEWS file entry follows.

Changes in RcppEigen version 0.3.3.9.3 (2022-11-04)

  • The dependency on R is now versioned to 3.6.0 or later for support for USE_FC_LEN_T from Fortran.

  • An old example typo was corrected (Jonah Gabry in #114).

  • The fastLm methods now reference df.residual by its full name (Closes #115).

  • A function prototype was updated for clang-15.

  • GitHub Actions were updated to checkout version 3.

Courtesy of CRANberries, there is also a diffstat report for the most recent release.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Fri, 04 Nov 2022

RcppSpdlog 0.0.9 on CRAN: Extended Usability and New Upstream

A brand-new version 0.0.9 of RcppSpdlog got onto CRAN overnight. RcppSpdlog bundles spdlog, a wonderful header-only C++ logging library with all the bells and whistles you would want that was written by Gabi Melman, and also includes fmt by Victor Zverovich.

This release contains two changes. First, we extend usability by offering both a set of simple R functions for logging from R, and a matching set of functions at the C++ level that are directly callable (and exported) from this package (so that client packages do not need to compile). Both these changes are described (as sections seven and eight) in the vignette. Second, while we were working on this Gabi released version 1.11.0 upstream so we included this as well.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.9 (2022-11-04)

  • Add both an R and an C++ interface to spdlog

  • Update GitHub Actions to checkout@v3

  • Add a shorter aliased namespace for C++

  • Upgraded to upstream releases spdlog 1.11.0

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog page, or the package documention site.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Thu, 03 Nov 2022

RProtoBuf 0.4.20 on CRAN: Maintenance

A new release 0.4.20 of RProtoBuf arrived on CRAN earlier today. RProtoBuf provides R with bindings for the Google Protocol Buffers (“ProtoBuf”) data encoding and serialization library used and released by Google, and deployed very widely in numerous projects as a language and operating-system agnostic protocol.

This release is somewhat mechanical and in the spirit of many other recent releases. clang-15 is, as more recent compilers do, more stringent on definitions and wants to see some void in argument-less signatures. Happy to oblige. At the same time, GitHub Actions started to nag us about minimum versions of node code so an upgrade to a newer action is warranted, again as with many other affected packages. We also found another http:// URL hiding somewhere so that was cleaned. Lastly, it appears Protocol Buffers themselves moved on and now need / prefer C++17 so were happy to oblige.

The following section from the NEWS.Rd file has full details.

Changes in RProtoBuf version 0.4.20 (2022-11-02)

  • Two function prototype were updated for clang-15.

  • GitHub Actions were updated to checkout version 3.

  • One more http:// URL was updated to https://

  • The package compilation is now donw with C++17 as the Protocol Buffer headers require it (and clang-15 nags otherwise).

Thanks to my CRANberries, there is a diff to the previous release. The RProtoBuf page has copies of the (older) package vignette, the ‘quick’ overview vignette, and the pre-print of our JSS paper. Questions, comments etc should go to the GitHub issue tracker off the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rprotobuf | permanent link

Tue, 01 Nov 2022

tint 0.1.4 on CRAN: Miscellaneous Updates

A new version 0.1.4 of the tint package arrived at CRAN today. tint provides a style ‘not unlike Tufte’ for use in html and pdf documents created from markdown. The github repo shows several examples in its README, more as usual in the package documentation.

This is the first release in over two years and it brings a few incremental changes which are described in detail below. The trigger was an email from CRAN desiring compacted pdf files inside the package sources. Which, coincidentally, was made a default about a year ago in the build.r script from littler I use to make packages. But as we had not updated tint this has not reached CRAN. So there.

The set of changes follows, which includes a helpful contributed PR for which we are always thankful. I also improved table rendering, most other changes are packaging mechanics.

Changes in tint version 0.1.4 (2022-11-01)

  • Added continuous integration at GitHub using run.sh

  • Non-margin reference in html mode now have an improved display (David Selby and Dirk in #47)

  • The LaTeX package array is now installed for improved table support (Dirk addressing #48)

  • Minor updates made the package directory and README.md

  • GitHub Actions were updated to checkout version 3.

  • Several http:// URLs were updated to https://

Courtesy of CRANberries, there is a comparison to the previous release. More information is on the tint page.

For questions or comments use the issue tracker off the GitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/tint | permanent link

RcppXts 0.0.5 on CRAN: Maintenance

A new maintenance release 0.0.6 of RcppXts is now on CRAN. The RcppXts package demonstrates how to access the export C API of xts which we contributed a looong time ago.

This release, like so many these days, was triggered by clang-15 wanting to see a void in an otherwise argument-less signature. We also updated a GitHub Action to avoid another nag from there.

The NEWS entries follow.

Changes in version 0.0.6 (2022-08-05)

  • One function prototype was updated for clang-15.

  • GitHub Actions were updated to checkout version 3.

Courtesy of my CRANberries, there is also a diffstat report for this release. A bit more information about the package is available here as well as at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Mon, 31 Oct 2022

RcppRedis 0.2.2 on CRAN: Maintenance and Enhancement

A new minor release 0.2.2 of our RcppRedis package arrived on CRAN this evening. RcppRedis is one of several packages connecting R to the fabulous Redis in-memory datastructure store (and much more). RcppRedis does not pretend to be feature complete, but it may do some things faster than the other interfaces, and also offers an optional coupling with MessagePack binary (de)serialization via RcppMsgPack. The package has carried production loads for several years now.

This packages now brings a neat enhancement to the real-time data plotter code (and example) I have been using with for a while now. Paul Murrell kindly suggested dev.hold() and dev.flush() when I inquired how to minimize ‘flicker’ from frequent updated. And this is perfect. I can now keep several data displays ‘on’ during market hours without being distracted by ‘flicker’. It just updates, smooth as silk. Also included in the release are the usual two updates so en vogue these days: a (sole) sprinkling of void to appease clang-15, and an update the GitHub Action for checkout. Both silence some nags we would rather not see.

The detailed changes list follows.

Changes in version 0.2.2 (2022-10-31)

  • Thanks to a suggestion by Paul Murrell, the real-time chart demo now uses dev.hold() and.flush() for flicker-free updates.

  • One function prototype was updated for clang-15.

  • GitHub Actions were updated to checkout version 3.

Courtesy of CRANberries, there is also a diffstat report for this release. More information is on the RcppRedis page.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Sun, 30 Oct 2022

RcppGSL 0.3.12 on CRAN: Maintenance

A new release 0.3.12 of RcppGSL is now on CRAN. The RcppGSL package provides an interface from R to the GNU GSL by relying on the Rcpp package.

This release accomodates, just like so many other releases this week, the more stringent views of clang-15 about what a correct function prototype is. While we were at it, an updatet to GitHub Actions was made as well.

The NEWS entry follows:

Changes in version 0.3.12 (2022-10-30)

  • Two function prototypes were updated for clang-15.

  • GitHub Actions were updated to checkout version 3.

Courtesy of CRANberries, a summary of changes in the most recent release is also available.

More information is on the RcppGSL page. Questions, comments etc should go to the issue tickets at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

RcppBDT 0.2.6 on CRAN: Maintenance

A minor maintenance release for the RcppBDT package is now on CRAN.

The RcppBDT package is an early adopter of Rcpp and was one of the first packages utilizing Boost and its Date_Time library. The now more widely-used package anytime is a direct descentant of RcppBDT.

This release accomodates, just like so many other releases this week, the more stringent views of clang-15 about what a correct function prototype is. While we were at it, an updatet to GitHub Actions was made as well.

The NEWS entry follows:

Changes in version 0.2.6 (2022-10-30)

  • A function prototype was updated for clang-15.

  • GitHub Actions were updated to checkout version 3.

Courtesy of my CRANberries, there is also a diffstat report for this release.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

RApiDatetime 0.0.7 on CRAN: Maintenance

A new release of our RApiDatetime package is now on CRAN.

RApiDatetime provides a number of entry points for C-level functions of the R API for Date and Datetime calculations. The functions asPOSIXlt and asPOSIXct convert between long and compact datetime representation, formatPOSIXlt and Rstrptime convert to and from character strings, and POSIXlt2D and D2POSIXlt convert between Date and POSIXlt datetime. Lastly, asDatePOSIXct converts to a date type. All these functions are rather useful, but were not previously exported by R for C-level use by other packages. Which this package aims to change.

This release accomodates, just like so many other releases this week, the more stringent views of clang-15 about what a correct function prototype is. While we were at, updates to GitHub Actions and https URL were made as well.

Changes in RApiDatetime version 0.0.7 (2022-10-30)

  • A function prototype was updated for clang-15.

  • GitHub Actions were updated to checkout version 3.

  • Several remaining http:// URLs were converted to https://.

Courtesy of my CRANberries, there is are comparisons to the previous release. More information is on the rapidatetime page.

For questions or comments please use the issue tracker off the GitHub repo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rapidatetime | permanent link

Sat, 29 Oct 2022

littler 0.3.17 on CRAN: Maintenance

max-heap image

The eighteenth release of littler as a CRAN package just landed, following in the now sixteen year history (!!) as a package started by Jeff in 2006, and joined by me a few weeks later.

littler is the first command-line interface for R as it predates Rscript. It allows for piping as well for shebang scripting via #!, uses command-line arguments more consistently and still starts faster. It also always loaded the methods package which Rscript only started to do in recent years.

littler lives on Linux and Unix, has its difficulties on macOS due to yet-another-braindeadedness there (who ever thought case-insensitive filesystems as a default were a good idea?) and simply does not exist on Windows (yet – the build system could be extended – see RInside for an existence proof, and volunteers are welcome!). See the FAQ vignette on how to add it to your PATH. A few examples are highlighted at the Github repo, as well as in the examples vignette.

This release, coming just a few weeks since the last release in August, heeds to clang-15 a updates one signature to a proper interface. It also contains one kindly contributed patch updating install2.r (and installBioc.r) to cope with a change in R-devel.

The full change description follows.

Changes in littler version 0.3.17 (2022-10-29)

  • Changes in package

    • An internal function prototype was updated for clang-15.
  • Changes in examples

    • The install2.r and installBioc. were updated for an update in R-devel (Tatsuya Shima and Dirk in #104).

My CRANberries service provides a comparison to the previous release. Full details for the littler release are provided as usual at the ChangeLog page, and also on the package docs website. The code is available via the GitHub repo, from tarballs and now of course also from its CRAN page and via install.packages("littler"). Binary packages are available directly in Debian as well as soon via Ubuntu binaries at CRAN thanks to the tireless Michael Rutter.

Comments and suggestions are welcome at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/littler | permanent link

gettz 0.0.5 on CRAN: Maintenance

A minor routine update 0.0.5 of gettz arrived on CRAN overnight.

gettz provides a possible fallback in situations where Sys.timezone() fails to determine the system timezone. That happened when e.g. the file /etc/localtime somehow is not a link into the corresponding file with zoneinfo data in, say, /usr/share/zoneinfo. Since the package was written (in the fall of 2016), R added a similar extended heuristic approach itself.

This release updates a function signature to satisfy the more stringent tests by clang-15, updates the GitHub Action checkout code to suppress a nag, and changes a few remaining http documentation links to https. As with the previous releses: No functional changes, no new code, or new features.

Courtesy of my CRANberries, there is a comparison to the previous release.

More information is on the gettz page. For questions or comments use the issue tracker off the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/gettz | permanent link

Thu, 27 Oct 2022

RcppAnnoy 0.0.20 on CRAN: Maintenance

annoy image

Another minor maintenance release, now at version 0.0.20, of RcppAnnoy has arrived on CRAN. RcppAnnoy is the Rcpp-based R integration of the nifty Annoy library by Erik Bernhardsson. Annoy is a small and lightweight C++ template header library for very fast approximate nearest neighbours—originally developed to drive the Spotify music discovery algorithm.

This release only contains internal changes to please, respectively clang-15 and (macOS) Xcode 14 (one of which PRed upstream too). No changes in package functionality. Detailed changes follow.

Changes in version 0.0.20 (2022-10-27)

  • Minor tweaks to appease clang-15 and Xcode 14

Courtesy of my CRANberries, there is also a diffstat report for this release.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Tue, 25 Oct 2022

RQuantLib 0.4.17 on CRAN: Maintenance

A new release 0.4.17 of RQuantLib arrived at CRAN earlier today, and has been uploaded to Debian as well.

QuantLib is a very comprehensice free/open-source library for quantitative finance; RQuantLib connects it to the R environment and language.

The release of RQuantLib comes five months after the previous maintenance, and brings a somewhat humurous upgrade from a default C++ standard of C++11 to C++14. We waited so long for C++11 to become available for R (which happened “eventually” when g++ 4.9 was no longer the default on Windows) and now it has become a constraint!! QuantLib 1.28, released today actually switched to C++14 as a minimum required. R also supports this as the default, but we still had C++11 hardwired so this quick maintenance release does away with that.

Changes in RQuantLib version 0.4.17 (2022-10-25)

  • Switch compilation to C++14 which is required by QuantLib 1.28 and, while standard with R 4.2.*, may be needed for R 4.1.*

Courtesy of my CRANberries, there is also a diffstat report for the this release. As always, more detailed information is on the RQuantLib page. Questions, comments etc should go to the new rquantlib-devel mailing list. Issue tickets can be filed at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rquantlib | permanent link

Mon, 24 Oct 2022

nanotime 0.3.7 on CRAN: Enhancements

A new version of our nanotime package arrived at CRAN today as version 0.3.7. nanotime relies on the RcppCCTZ package (as well as the RcppDate package for additional C++ operations) and offers efficient high(er) resolution time parsing and formatting up to nanosecond resolution, and the bit64 package for the actual integer64 arithmetic. Initially implemented using the S3 system, it has benefitted greatly from a rigorous refactoring by Leonardo who not only rejigged nanotime internals in S4 but also added new S4 types for periods, intervals and durations.

This release adds a few more operators, plus some other fixes, that were contributed in several PRs by Trevor Davis. The NEWS snippet has the full details.

Changes in version 0.3.7 (2022-10-23)

  • Update mkdocs for material docs generator (Dirk in #102)

  • Use inherits() instead comparing to class() (Trevor Davis in #104)

  • Set default arguments in nanoduration() (Trevor Davis in #105)

  • Add as.nanoduration.difftime() support (Trevor Davis in #106)

  • Add +/- methods for nanotime and difftime objects (Trevor Davis in #110 closing #108, #107)

Thanks to my CRANberries there is also a diff to the previous version. More details and examples are at the nanotime page; code, issue tickets etc at the GitHub repository – and all documentation is provided at the nanotime documentation site.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/nanotime | permanent link

Sun, 23 Oct 2022

RDieHarder 0.2.4 on CRAN: Packaging Updates

An new version 0.2.4 of the random-number generator tester RDieHarder (based on the DieHarder suite developed / maintained by Robert Brown with contributions by David Bauer and myself along with other contributors) is now on CRAN.

This release comes ten months after the previous release 0.2.3. It is once more related to R and requested CRAN changes as clang-15 brings additional warnings concerning -Wstrict-prototyping. This make use of C more solid, but it was a metric ton of work (see pull request #8).

Thanks to CRANberries, you can also look at the most recent diff.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rdieharder | permanent link

Wed, 19 Oct 2022

qlcal 0.0.3 on CRAN: Maintenance and Updates

The third release of the still pretty new qlcal package arrivied at CRAN today.

qlcal is based on the calendaring subset of QuantLib. It is provided (for the R package) as a set of included files, so the package is self-contained and does not depend on an external QuantLib library (which can be demanding to build). qlcal covers over sixty country / market calendars and can compute holiday lists, its complement (i.e. business day lists) and much more.

This release fixes a small bug affecting one function, brings calendar updates from QuantLib 1.27 and 1.28, and applies a little bit of polish to appease clang++-15.

Changes in version 0.0.3 (2022-10-19)

  • Correct the isBusinessDay() functionality (Fixes #2)

  • Update Australia and Saudi Arabia calendars from QuantLib 1.27

  • Update United Kingdom calendar from QuantLib 1.28

  • Convert one source file to utf-8 to appease clang-15

See the project page and package documentation for more details, and more examples.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/qlcal | permanent link

RcppQuantuccia 0.1.1 on CRAN: Maintenance

A minor release of RcppQuantuccia arrived on CRAN today. RcppQuantuccia started from the Quantuccia header-only subset / variant of QuantLib which it brings it to R. This project validated the idea of making the calendaring functionality of QuantLib available in a more compact and standalone project – which we now do with qlcal which can be seen as a successor to this.

This release merely updates a source file to proper encoding as clang++-15 would otherwise warn.

The complete list changes for this release follows.

Changes in version 0.1.1 (2022-10-19)

  • Minor code reorganization splitting off calendars.cpp

  • Convert the Argentinian calendar sources files as utf-8 to appease clang++-15

  • Advertise the qlcal package as an alternative

Courtesy of CRANberries, there is also a diffstat report relative to the previous release. More information is on the RcppQuantuccia page. Issues and bugreports should go to the GitHub issue tracker.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Tue, 18 Oct 2022

RcppSimdJson 0.1.8 on CRAN: Maintenance

The RcppSimdJson package was just updated to release 0.1.8 today.

RcppSimdJson wraps the fantastic and genuinely impressive simdjson library by Daniel Lemire and collaborators. Via very clever algorithmic engineering to obtain largely branch-free code, coupled with modern C++ and newer compiler instructions, it results in parsing gigabytes of JSON parsed per second which is quite mindboggling. The best-case performance is ‘faster than CPU speed’ as use of parallel SIMD instructions and careful branch avoidance can lead to less than one cpu cycle per byte parsed; see the video of the talk by Daniel Lemire at QCon.

This release simply changes one statement to not trigger a warning under clang++-14.

The very short NEWS entry for this release follows.

Changes in version 0.1.8 (2022-10-18)

  • Use the '||' operator instead of '|' on a set of booleans to appease 'clang-14'.

Courtesy of my CRANberries, there is also a diffstat report for this release. For questions, suggestions, or issues please use the issue tracker at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

digest 0.6.30 on CRAN: More Package Maintenance

Release 0.6.30 of the digest package arrived at CRAN earlier today, and was just uploaded to Debian as well.

digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, spookyhash, and blake3 algorithms) permitting easy comparison of R language objects. It is a mature and widely-used as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation to quickly identify the various objects.

This release contains two tiny changes on old standard C code to appease the new / upcoming clang-15 release now used by CRAN in their forward-looking checks.

My CRANberries provides the usual summary of changes to the previous version. For questions or comments use the issue tracker off the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/digest | permanent link

Wed, 12 Oct 2022

GitHub Streak: Round Nine

Eight years ago I referenced the Seinfeld Streak used in an earlier post of regular updates to to the Rcpp Gallery:

This is sometimes called Jerry Seinfeld’s secret to productivity: Just keep at it. Don’t break the streak.

and then showed the first chart of GitHub streaking 366 days:

github activity october 2013 to october 2014

And seven years ago a first follow-up appeared in this post about 731 days:

github activity october 2014 to october 2015

And six years ago we had a followup at 1096 days

github activity october 2015 to october 2016

And five years ago we had another one marking 1461 days

github activity october 2016 to october 2017

And four years ago another one for 1826 days

github activity october 2017 to october 2018

And three years ago another one bringing it to 2191 days

github activity october 2018 to october 2019

And two years ago another one bringing it to 2557 days

github activity october 2019 to october 2020

And last year another one bringing it to 2922 days

github activity october 2020 to october 2021

And as today is October 12 here is the newest one from 2021 to 2022 one bringing it 3287 days:

github activity october 2021 to october 2022

As always, special thanks go to Alessandro Pezzè for the Chrome add-on GithubOriginalStreak.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/computers/misc | permanent link

Thu, 06 Oct 2022

Rblpapi 0.3.14: Updates and Extensions

bloomberg terminal

Version 0.3.14 of the Rblpapi package arrived on CRAN earlier today. Rblpapi provides a direct interface between R and the Bloomberg Terminal via the C++ API provided by Bloomberg (but note that a valid Bloomberg license and installation is required).

This is the fourteenth release since the package first appeared on CRAN in 2016. It comprises a nice PR from Robert Harlow extending support to B-PIPE authentication (for those who have it) along with a few fixes made since the last release in January. The last one provided from a kind assist by Tomas Kalibera who pointed out how to overcome an absolute ‘rpath’ dynamic linker instruction (and as I noticed noticed something I already did in another package – ah well) so that we no longer require StagedInstall: yes.

The detailed list of changes follow below.

Changes in Rblpapi version 0.3.14 (2022-10-05)

  • Build configuration was generalized to consider local copies of library and headers (Dirk in #362)

  • A ticker symbol was corrected (Dirk in #368 addressing an issue #366 and #367)

  • Support for B-PIPE was added (Robert Harlow in #369 closing #342)

  • The package no longer requires staged installation thanks to an assist from Tomas Kalibera (Dirk in #373)

  • The retired package fts is no longer suggested (Dirk in #374 closing #372)

Courtesy of my CRANberries, there is also a diffstat report for the this release. As always, more detailed information is on the Rblpapi page. Questions, comments etc should go to the issue tickets system at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rblpapi | permanent link

Wed, 05 Oct 2022

RVowpalWabbit 0.0.17: Maintenance

Almost to the week one year since the last maintenance release, we can announce another maintenance release, now at version 0.0.17, of the RVowpalWabbit package. The CRAN maintainers kindly and politly pointed out that I was (cough, cough) apparently the last maintainer who had packages that set StagedInstall: no. Guilty as charged.

RVowpalWabbit is one the two packages; the other one will hopefully follow ‘shortly’. And while I long suspected linking aspects to drive this (this is an old package, newer R packaging of the awesome VowpalWabbit is in rvw, I was plain wrong here. The cause was an absolute path to an included dataset, computed in an example, which then gets serialized. As Tomas Kalibera suggested, we can replace the constant with a function and all is well. So here is 0.0.17.

As noted before, there is a newer package rvw based on the excellent GSoC 2018 and beyond work by Ivan Pavlov (mentored by James and myself) so if you are into VowpalWabbit from R go check it out.

CRANberries provides a summary of changes to the previous version. More information is on the RVowpalWabbit page. Issues and bugreports should go to the GitHub issue tracker.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rvowpalwabbit | permanent link

Sun, 02 Oct 2022

RcppArmadillo 0.11.4.0.1 on CRAN: Updates

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 1023 packages other packages on CRAN, downloaded 26.4 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper (preprint / vignette) by Conrad and myself has been cited 497 times according to Google Scholar.

This release reflect as new upstream release 11.4.0 Conrad made recently. It turns out that it triggered warnings under g++-12 for about five packages in the fortify mode default for Debian builds. Conrad then kindly addressed this with a few fixes.

The full set of changes (since the last CRAN release 0.11.2.4.0) follows.

Changes in RcppArmadillo version 0.11.4.0.1 (2022-10-01

  • Upgraded to Armadillo release 11.4.0 (Ship of Theseus)

    • faster handling of compound expressions by sum()

    • extended pow() with various forms of element-wise power operations

    • added find_nan() to find indices of NaN elements

  • Also applied fixes to avoid g++-12 warnings affecting just a handful of CRAN packages.

Courtesy of my CRANberries, there is a diffstat report relative to previous release. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Sun, 11 Sep 2022

RcppArmadillo 0.11.2.4.0 on CRAN: Bugfix and Deprecation

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 1016 packages other packages on CRAN, downloaded 26.2 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper (preprint / vignette) by Conrad and myself has been cited 493 times according to Google Scholar.

This new release (made yesterday) brings three changes. First, it updates the release to the upstream 11.2.4 bugfix release made days ago by Conrad. Second, it contains support for the deprecation transition we are managing in issue #391. In short, the (convenient but non-standard) initialization via use of << has been deprecated upstream. Until all packages are updated, we override this in the RcppArmadillo but aim to become ‘compliant’. Out of the over 1000 packages, a mere 25 need small adjustments. I reached out email and PRs, and the response has been great. Eight packages are already updated on CRAN, and several others have already in integrated or merged the change. Lastly, Conrad pointed out that the fastLm() example and application can be written more concisely by using arma::dot().

The full set of changes (since the last CRAN release 0.11.2.3.1) follows.

Changes in RcppArmadillo version 0.11.2.4.0 (2022-09-09)

  • Upgraded to Armadillo release 11.2.4 (Classic Roast)

    • fix handling of std::move() involving matrices constructed with auxiliary memory
  • In the fastLm() examples, use arma::dot() to compute to the inner product (as proposed by Conrad), plus small edits

  • Support optional #define named RCPPARMADILLO_FORCE_DEPRECATE to suppress use of ARMA_IGNORE_DEPRECATED_MARKER permitting use and development under deprecation

Courtesy of my CRANberries, there is a diffstat report relative to previous release. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rcpp | permanent link

Sun, 28 Aug 2022

littler 0.3.16 on CRAN: Package Updates

max-heap image

The seventeenth release of littler as a CRAN package just landed, following in the now sixteen year history (!!) as a package started by Jeff in 2006, and joined by me a few weeks later.

littler is the first command-line interface for R as it predates Rscript. It allows for piping as well for shebang scripting via #!, uses command-line arguments more consistently and still starts faster. It also always loaded the methods package which Rscript only started to do in recent years.

littler lives on Linux and Unix, has its difficulties on macOS due to yet-another-braindeadedness there (who ever thought case-insensitive filesystems as a default were a good idea?) and simply does not exist on Windows (yet – the build system could be extended – see RInside for an existence proof, and volunteers are welcome!). See the FAQ vignette on how to add it to your PATH. A few examples are highlighted at the Github repo, as well as in the examples vignette.

This release, the first since last December, further extends install2.r accept multiple repos options thanks to Tatsuya Shima, overhauls and substantially extends installBioc.r thanks to Pieter Moris, and includes a number of (generally smaller) changes I added (see below).

The full change description follows.

Changes in littler version 0.3.16 (2022-08-28)

  • Changes in package

    • The configure code checks for two more headers

    • The RNG seeding matches the current version in R (Dirk)

  • Changes in examples

    • A cowu.r 'check Window UCRT' helper was added (Dirk)

    • A getPandoc.r downloader has been added (Dirk)

    • The -r option tp install2.r has been generalzed (Tatsuya Shima in #95)

    • The rcc.r code / package checker now has valgrind option (Dirk)

    • install2.r now installs to first element in .libPaths() by default (Dirk)

    • A very simple r2u.r help has been added (Dirk)

    • The installBioc.r has been generalized and extended similar to install2.r (Pieter Moris in #103)

My CRANberries service provides a comparison to the previous release. Full details for the littler release are provided as usual at the ChangeLog page, and also on the package docs website. The code is available via the GitHub repo, from tarballs and now of course also from its CRAN page and via install.packages("littler"). Binary packages are available directly in Debian as well as soon via Ubuntu binaries at CRAN thanks to the tireless Michael Rutter.

Comments and suggestions are welcome at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/littler | permanent link

Thu, 25 Aug 2022

RApiSerialize 0.1.2 on CRAN: Small Bugfix

A new bug fix release 0.1.2 of RApiSerialize got onto CRAN earlier. It follows on the 0.1.1 release from earlier this month, and addresses a minor build issue where an error message, only in the case of missing long vector support, tried to use an i18n macro that is not supplied by the build.

The RApiSerialize package is used by both my RcppRedis as well as by Travers excellent qs package. Neither one of us has a need to switch to format 3 yet so format 2 remains the default. But along with other standard updates to package internals, it was straightforward to offer the newer format so that is what we did.

Changes in version 0.1.2 (2022-08-25)

  • Correct an error() call (when missing long vector support) to not use i18n macro

Courtesy of my CRANberries, there is also a diffstat to the previous version. More details are at the RApiSerialize page; code, issue tickets etc at the GitHub repository.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

/code/rapiserialize | permanent link

Thu, 18 Aug 2022

RcppArmadillo 0.11.2.3.1 on CRAN: Double Update

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 1005 packages other packages on CRAN (as celebrated in this blog post on passing 1000 packages from just four days ago), downloaded nearly 26 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper (preprint / vignette) by Conrad and myself has been cited 488 times according to Google Scholar.

This release brings together two distinct changes. First, it updates the relese from upstream 11.2.0 (and CRAN 0.11.2.0.0 released a few weeks ago) to the now current 11.2.3 release by Conrard (given that more than four weeks have passed so that we do not surpass CRAN’s desired cadence of ‘releases no more than once a month’). The changeset includes a few small refinements (see below), it also includedes a deprecation for initialization for which I will need to reach out to a few packages for whom this triggers a deprecation warning. And speaking of deprecation, the other reason for this release is the desire by the Matrix package to phase out a few older conversions (or casts in C/C++ lingo) which we accomodated.

The full set of changes (since the last CRAN release 0.11.2.0.0) follows.

Changes in RcppArmadillo version 0.11.2.3.1 (2022-08-16)

  • Accomodate upcoming Matrix 1.4-2 deprecation for conversion (Dirk in #387)

  • CRAN release with small upstream changes in Armadillo 11.2.1,2,3 made since the last CRAN release 0.11.2.0.0 (Dirk in #383, #384 and #386)

  • Undefine arma_deprecated warning as it affects a number of CRAN packages which will likely need a small transition

Changes in RcppArmadillo version 0.11.2.3.0 (2022-07-12) (GitHub Only)

  • Upgraded to Armadillo release 11.2.3 (Classic Roast)

    • fix Cube::insert_slices() to accept Cube::slice() as input

Changes in RcppArmadillo version 0.11.2.2.0 (2022-07-04) (GitHub Only)

  • Upgraded to Armadillo release 11.2.2 (Classic Roast)

    • fix incorrect and/or slow convergence in single-threaded versions of kmeans(), gmm_diag::learn(), gmm_full::learn()

Changes in RcppArmadillo version 0.11.2.1.0 (2022-06-28) (GitHub Only)

  • Upgraded to Armadillo release 11.2.1 (Classic Roast)

    • old style matrix initialisation via the << operator will now emit a compile-time deprecation warning

    • use of the old and inactive ARMA_DONT_PRINT_ERRORS option will now emit a compile-time deprecation warning

    • the option ARMA_WARN_LEVEL can be used instead

Courtesy of my CRANberries, there is a diffstat report relative to previous release. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page.

If you like this or other open-source work I do, you can sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sun, 14 Aug 2022

RcppArmadillo used by 1001 CRAN Packages

It is with a mix of pride and joy, but also some genuine astonishment and amazement, that we can share that the counter of reverse dependencies at CRAN for our RcppArmadillo package for R just crossed 1000 packages [1]:

Conrad actually posted this a few weeks ago, by my count we were then still a few packages shy. In any event, having crossed this marker this summer, either then or now, and after more than a dozen years of working on the package is a really nice moment. Google Scholar counts nearly 500 citations for our CSDA paper (also this vignette), and that ratio of nearly a citation for every two packages used is certainly impressive. We have had the pleasure of working with so many other researchers and scientists using RcppArmadillo. Its combination of performance (C++, after all, and heavily tuned) and ease-of-use (inspired by ‘another popular flavour for matrix computing’ that is however mostly interpreted) makes for a powerful package, and we are delighted to see it used so widely.

Working on this with Conrad has been excellent. The (upstream) package (now at this GitLab repo) has received numerous releases at a rate that is in fact so high that we now ‘slow it down’ to not exceed a monthly cadence of uploads to CRAN. But the package should always be in release condition at its GitHub repo, and is frequently also installable in ‘rc’ versions via the Rcpp drat repo.

So with that, a big Thank You! to Conrad, to Romain for all the early work laying the package foundations, and to all the users of (Rcpp)Armadillo for helping us along with testing, suggestions, extensions, and bug reports. Keep’em coming!

If you like this or other open-source work I do, you can now sponsor me at GitHub.

[1] The code snippet shows that we remove some possible duplicates in the count (mostly for the total of packages). This is a correction we use across packages for consistency. It does not have an effect for RcppArmadillo.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sun, 07 Aug 2022

RApiSerialize 0.1.1 on CRAN: Updates

A new release 0.1.1 of RApiSerialize is now on CRAN. While this is the first release in seven years (!!), it brings mostly minor internal updates along with the option of using serialization format 3.

The package is used by both my RcppRedis as well as by Travers excellent qs package. Neither one of us has a need to switch to format 3 yet so format 2 remains the default. But along with other standard updates to package internals, it was straightforward to offer the newer format so that is what we did.

Changes in version 0.1.1 (2022-08-07)

  • Updated CI use to r-ci

  • Expanded and updated both DESCRIPTION and README.md

  • Updated package internals to register compiled functions

  • Add support for serialization format 3, default remains 2

  • Minor synchronization with upstream

Courtesy of my CRANberries, there is also a diffstat to the previous version. More details are at the RApiSerialize page; code, issue tickets etc at the GitHub repository.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Sat, 06 Aug 2022

RcppCCTZ 0.2.11 on CRAN: Updates

A new release 0.2.11 of RcppCCTZ is now on CRAN.

RcppCCTZ uses Rcpp to bring CCTZ to R. CCTZ is a C++ library for translating between absolute and civil times using the rules of a time zone. In fact, it is two libraries. One for dealing with civil time: human-readable dates and times, and one for converting between between absolute and civil times via time zones. And while CCTZ is made by Google(rs), it is not an official Google product. The RcppCCTZ page has a few usage examples and details. This package was the first CRAN package to use CCTZ; by now four others packages include its sources too. Not ideal, but beyond our control.

This version updates the include headers used in the interface API header thanks to a PR by Jing Lu, updates to upstream changes, and switched r-ci CI to r2u.

Changes in version 0.2.11 (2022-08-06)

  • More specific includes in RcppCCTZ_API.h (Jing Lu in #42 closing #41).

  • Synchronized with upstream CCTZ (Dirk in #43).

  • Switched r-ci to r2u use.

Courtesy of my CRANberries, there is also a diffstat to the previous version. More details are at the RcppCCTZ page; code, issue tickets etc at the GitHub repository.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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Fri, 05 Aug 2022

RcppXts 0.0.5 on CRAN: Routine Refreshment

A full eight and half years (!!) since its 0.0.4 release, version 0.0.5 of RcppXts is now on CRAN. The RcppXts package demonstrates how to access the export C API of xts which we contributed a looong time ago.

This release contains an accumulated small set of updates made as the CRAN Policies evolved. We now register and use the shared library routines (updates in both src/init.c and NAMESPACE), turned on continuous integration, switched it from the now disgraces service to another, adopted our portable r-ci along with r2, added badges to the README.md, updated to https URLs, and made sure the methods package (from base R) was actually imported (something Rcpp has a need for at startup). That latter part now triggered a recent email from the CRAN maintainers which prompted this release.

The NEWS entries follow.

Changes in version 0.0.5 (2022-08-05)

  • Depends on xts 0.9-6 now on CRAN

  • Exports (and documents) a number of additional functions

  • Switch CI use to r-ci and r2u

  • README.md, DESCRIPTION and NEWS.Rd were updated and expanded

  • NAMESPACE import of the shared library uses registration

Courtesy of my CRANberries, there is also a diffstat report for this release. A bit more information about the package is available here as well as at the GitHub repo.

If you like this or other open-source work I do, you can now sponsor me at GitHub.

This post by Dirk Eddelbuettel originated on his Thinking inside the box blog. Please report excessive re-aggregation in third-party for-profit settings.

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