Thu, 08 Feb 2024

RcppArmadillo 0.12.8.0.0 on CRAN: New Upstream, Interface Polish

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) 1119 other packages on CRAN, downloaded 32.5 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 575 times according to Google Scholar.

This release brings a new (stable) upstream (minor) release Armadillo 12.8.0 prepared by Conrad two days ago. We, as usual, prepared a release candidate which we tested against the over 1100 CRAN packages using RcppArmadillo. This found no issues, which was confirmed by CRAN once we uploaded and so it arrived as a new release today in a fully automated fashion.

We also made a small change that had been prepared by GitHub issue #400: a few internal header files that were cluttering the top-level of the include directory have been moved to internal directories. The standard header is of course unaffected, and the set of ‘full / light / lighter / lightest’ headers (matching we did a while back in Rcpp) also continue to work as one expects. This change was also tested in a full reverse-dependency check in January but had not been released to CRAN yet.

The set of changes since the last CRAN release follows.

Changes in RcppArmadillo version 0.12.8.0.0 (2024-02-06)

  • Upgraded to Armadillo release 12.8.0 (Cortisol Injector)

    • Faster detection of symmetric expressions by pinv() and rank()

    • Expanded shift() to handle sparse matrices

    • Expanded conv_to for more flexible conversions between sparse and dense matrices

    • Added cbrt()

    • More compact representation of integers when saving matrices in CSV format

  • Five non-user facing top-level include files have been removed (#432 closing #400 and building on #395 and #396)

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 Rcpp 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

Tue, 23 Jan 2024

RcppAnnoy 0.0.22 on CRAN: Maintenance

annoy image

A very minor maintenance release, now at version 0.0.22, 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. It had all the buzzwords already a decade ago: it is one of the algorithms behind (drum roll …) vector search as it finds approximate matches very quickly and also allows to persist the data.

This release responds to a CRAN request to clean up empty macros and sections in Rd files.

Details of the release follow based on the NEWS file.

Changes in version 0.0.22 (2024-01-23)

  • Replace empty examples macro to satisfy CRAN request.

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

Fri, 12 Jan 2024

RcppSpdlog 0.0.16 on CRAN: New Upstream

Version 0.0.16 of RcppSpdlog is now on CRAN and will be uploaded to 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. You can learn more at the nice package documention site.

This releases updates the code to the version 1.13 of spdlog which was release this morning.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.16 (2024-01-12)

  • Upgraded to upstream releases spdlog 1.13.0

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

Tue, 09 Jan 2024

Rcpp 1.0.12 on CRAN: New Maintenance / Update Release

rcpp logo

The Rcpp Core Team is once again thrilled to announce a new release 1.0.12 of the Rcpp package. It arrived on CRAN early today, and has since been uploaded to Debian as well. 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 should catch up tomorrow. The release was uploaded yesterday, and run its reverse dependencies overnight. Rcpp always gets flagged nomatter what because the grandfathered .Call(symbol) but … we had not single ‘change to worse’ among over 2700 reverse dependencies!

This release continues with the six-months January-July 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 long established itself as the most popular way of enhancing R with C or C++ code. Right now, 2791 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 254 in BioConductor. On CRAN, 13.8% of all packages depend (directly) on Rcpp, and 59.9% of all compiled packages do. From the cloud mirror of CRAN (which is but a subset of all CRAN downloads), Rcpp has been downloaded 78.1 million times. The two published papers (also included in the package as preprint vignettes) have, respectively, 1766 (JSS, 2011) and 292 (TAS, 2018) citations, while the the book (Springer useR!, 2013) has another 617.

This release is incremental as usual, generally preserving existing capabilities faithfully while smoothing our corners and / or extending slightly, sometimes in response to changing and tightened demands from CRAN or R standards.

The full list below details all changes, their respective PRs and, if applicable, issue tickets. Big thanks from all of us to all contributors!

Changes in Rcpp release version 1.0.12 (2024-01-08)

  • Changes in Rcpp API:

    • Missing header includes as spotted by some recent tools were added in two places (Michael Chirico in #1272 closing #1271).

    • Casts to avoid integer overflow in matrix row/col selections have neem added (Aaron Lun #1281).

    • Three print format correction uncovered by R-devel were applied with thanks to Tomas Kalibera (Dirk in #1285).

    • Correct a print format correction in the RcppExports glue code (Dirk in #1288 fixing #1287).

    • The upcoming OBJSXP addition to R 4.4.0 is supported in the type2name mapper (Dirk and Iñaki in #1293).

  • Changes in Rcpp Attributes:

    • Generated interface code from base R that fails under LTO is now corrected (Iñaki in #1274 fixing a StackOverflow issue).
  • Changes in Rcpp Documentation:

    • The caption for third figure in the introductory vignette has been corrected (Dirk in #1277 fixing #1276).

    • A small formatting issue was correct in an Rd file as noticed by R-devel (Dirk in #1282).

    • The Rcpp FAQ vignette has been updated (Dirk in #1284).

    • The Rcpp.bib file has been refreshed to current package versions.

  • Changes in Rcpp Deployment:

    • The RcppExports file for an included test package has been updated (Dirk in #1289).

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).

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

Sat, 09 Dec 2023

RcppInt64 0.0.4 on CRAN: Minor Bugfix

The new-ish package RcppInt64 (announced earlier this fall in this post, with two small updates following) arrived on CRAN minutes ago as relase 0.0.4. RcppInt64 collects some of the previous conversions between 64-bit integer values in R and C++, and regroups them in a single package. It offers two interfaces: both a more standard as<>() converter from R values along with its companions wrap() to return to R, as well as more dedicated functions ‘from’ and ‘to’.

This release addresses an issues Sebastian reported a few hours and which is reported by newer, pickier compilers: We need to include <cstdint> so that int64_t is declared. CRAN was at its usual best processing this efficiently including tests of the by now two reverse dependencies. Twenty two minutes total, all automated:

The brief NEWS entry follows:

Changes in version 0.0.4 (2023-12-09)

  • The cstdint header is now included (closes #1).

Courtesy of my CRANberries, there is a diffstat report relative to previous 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

Mon, 04 Dec 2023

RcppArmadillo 0.12.6.6.1 on CRAN: No More 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) 1126 other packages on CRAN, downloaded 31.7 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 569 times according to Google Scholar.

This release ends the practice on asking Armadillo to suppress deprecation warnings. RcppArmadillo, as noted, has a large user base. Sometimes Conrad sometimes made changes without too much of a heads-up so at times it was opportune to not bring those warnings to dozens (or maybe hundreds) of packages at CRAN. Yet we need to balance this with the demonstrable need to call out older deprecated code use. So sixteen months ago, with GitHub issue #391, we started to alert author of 30+ affected packages and supplied either pull requests or emailed patches to all. Eleven months ago GitHub issues #402 was added for a second deprecation.

And the time of making the switch has come. Release 0.12.6.6.1 no longer defines ARMA_IGNORE_DEPRECATED_MARKER. So among the over 1100 packages using RcppArmadillo at CRAN, around a good dozen or so were flagged in the upload – but CRAN concurred and let the package migrate to CRAN.

If you maintain an affected package, consider applying the patch or pull request now. A simple stop-gap measure also exists by adding -DARMA_IGNORE_DEPRECATED_MARKER to src/Makevars as either PKG_CPPFLAGS or PKG_CXXFLAGS to reactivate it. But a proper code update, which is generally simple, may be better. If you are unsure, do not hesitate to get in touch.

The set of changes since the last CRAN release follows.

Changes in RcppArmadillo version 0.12.6.6.1 (2023-12-03)

  • Following the extendeded transition in #391 and #402, this release no longer sets ARMA_IGNORE_DEPRECATED_MARKER. Maintainers of affected packages have received pull requests or patches and can set -DARMA_IGNORE_DEPRECATED_MARKER as PKG_CPPFLAGS.

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 Rcpp 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

Thu, 30 Nov 2023

RcppClassicExamples 0.1.3 on CRAN: Maintenance

Another upgrade triggered solely by changing CRAN standards (see previous one from five years ago). This time it concerns warnings under r-devel with -Wformat -Wformat-security so we injected a number of "%s" into Rf_error() calls.

No new code or features. Full details below. And as a reminder, don’t use the old RcppClassic – use Rcpp instead.

Changes in version 0.1.3 (2023-11-30)

  • Update Rf_error() call to not tickle -Wformat

  • Minor other packaging and continuous integration tweaks

Thanks to CRANberries, you can also look at a diff to the previous 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

Wed, 29 Nov 2023

RcppSpdlog 0.0.15 on CRAN: Maintenance

Version 0.0.15 of RcppSpdlog is now on CRAN and will be uploaded to 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. You can learn more at the nice package documention site.

This releases updates the code to address warning now shown under R-devel when -Wformat -Wformat-security are enabled. This amounted to re-generating RcppExports.cpp under an updated [Rcpp][rcpp] version. It also updates the package default help page by removing some stubs that were not filled in.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.15 (2023-11-29)

  • Correct default package help page slighly

  • RcppExports.cpp has been regenerated under an updated Rcpp to address a format string warning under R-devel

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

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 releases updates the code to address warning now shown under R-devel when -Wformat -Wformat-security are enabled. This amounted to re-generating RcppExports.cpp under an updated Rcpp version. We also no longer set C++14 explicitly as a compilation standard.

The complete list changes for this release follows.

Changes in version 0.1.2 (2023-11-29)

  • RcppExports.cpp has been regenerated under an updated Rcpp to address a format string warning under R-devel

  • The compilation standard is no longer set to C++14

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, 28 Nov 2023

RcppSimdJson 0.1.11 on CRAN: Maintenance

A new maintenance release 0.1.11 of the RcppSimdJson package is now on CRAN.

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 responds to a CRAN request to address issues now identified by -Wformat -Wformat-security. These are frequently pretty simple changes as it was here: all it took was an call to compileAttributes() from an updated Rcpp version which now injects "%s" as a format string when calling Rf_error().

The (very short) NEWS entry for this release follows.

Changes in version 0.1.11 (2023-11-28)

  • RcppExports.cpp has been regenerated under an update Rcpp to address a print format warning (Dirk in #88).

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

Mon, 27 Nov 2023

RcppCNPy 0.2.12 on CRAN: More Maintenance

A new (and again somewhat minor) maintenance release of the RcppCNPy package arrived on CRAN earlier today.

RcppCNPy provides R with read and write access to NumPy files thanks to the cnpy library by Carl Rogers along with Rcpp for the glue to R.

Recent changes in r-devel hone in on issues concerning printf format string inaccuracies the compiler can detect via the -Wformat -Wformat-security flags. Two fairly simplye ones were present here and have been addressed. In the time since the last release about twenty months ago two or three other minor packaging and setup details have also been taken care of, details are below.

Changes in version 0.2.12 (2022-11-27)

  • The continuous integration workflow received a trivial update, twice.

  • The C++ compilation standard is now implicit per CRAN and R preference.

  • The CITATION file format has been updated for the current usage.

  • Two print format string issues reported by current R-devel have been addressed.

CRANberries also provides a diffstat report for the latest release. As always, feedback is welcome and the best place to start a discussion may be the GitHub issue tickets 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

Fri, 03 Nov 2023

RcppEigen 0.3.3.9.4 on CRAN: Maintenance, Matrix Changes

A new release 0.3.3.9.4 of RcppEigen arrived on CRAN yesterday, and went to Debian today. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

This update contains a small amount of the usual maintenance (see below), along with a very nice pull request by Mikael Jagan which simplifies to interface with the Matrix package and inparticular the CHOLMOD library that is part of SuiteSparse. This release is coordinated with lme4 and OpenMx which are also being updated.

The complete NEWS file entry follows.

Changes in RcppEigen version 0.3.3.9.4 (2023-11-01)

  • The CITATION file has been updated for the new bibentry style.

  • The package skeleton generator has been updated and no longer sets an Imports:.

  • Some README.md URLs and badged have been updated.

  • The use of -fopenmp has been documented in Makevars, and a simple thread-count reporting function has been added.

  • The old manual src/init.c has been replaced by an autogenerated version, the RcppExports file have regenerated

  • The interface to package Matrix has been updated and simplified thanks to an excllent patch by Mikael Jagan.

  • The new upload is coordinated with packages lme4 and OpenMx.

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

Tue, 31 Oct 2023

RcppArmadillo 0.12.6.6.0 on CRAN: Bugfix, Thread Throttling

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) 1110 other packages on CRAN, downloaded 31.2 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 563 times according to Google Scholar.

This release brings upstream bugfix releases 12.6.5 (sparse matrix corner case) and 12.6.6 with an ARPACK correction. Conrad released it this this morning, I had been running reverse dependency checks anyway and knew we were in good shape so for once I did not await a full run against the now over 1100 (!!) packages using RcppArmadillo.

This release also contains a change I prepared on Sunday and which helps with much-criticized (and rightly I may add) insistence by CRAN concerning ‘throttling’. The motivation is understandable: CRAN tests many packages at once on beefy servers and can ill afford tests going off and requesting numerous cores. But rather than providing a global setting at their end, CRAN insists that each package (!!) deals with this. The recent traffic on the helpful-as-ever r-pkg-devel mailing clearly shows that this confuses quite a few package developers. Some have admitted to simply turning examples and tests off: a net loss for all of us. Now, Armadillo defaults to using up to eight cores (which is enough to upset CRAN) when running with OpenMP (which is generally only on Linux for “reasons” I rather not get into…). With this release I expose a helper functions (from OpenMP) to limit this. I also set up an example package and repo RcppArmadilloOpenMPEx detailing this, and added a demonstration of how to use the new throttlers to the fastLm example. I hope this proves useful to users of the package.

The set of changes since the last CRAN release follows.

Changes in RcppArmadillo version 0.12.6.6.0 (2023-10-31)

  • Upgraded to Armadillo release 12.6.6 (Cortisol Retox)

    • Fix eigs_sym(), eigs_gen() and svds() to generate deterministic results in ARPACK mode
  • Add helper functions to set and get the number of OpenMP threads

  • Store initial thread count at package load and use in thread-throttling helper (and resetter) suitable for CRAN constraints

Changes in RcppArmadillo version 0.12.6.5.0 (2023-10-14)

  • Upgraded to Armadillo release 12.6.5 (Cortisol Retox)

    • Fix for corner-case bug in handling sparse matrices with no non-zero elements

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 Rcpp 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

Tue, 19 Sep 2023

RcppInt64 0.0.3 on CRAN: Now with nanotime Support

The still new package RcppInt64 (announced two weeks ago in this post, with this followup last week) arrived on CRAN earlier today in its second update and relase 0.0.3. RcppInt64 collects some of the previous conversions between 64-bit integer values in R and C++, and regroups them in a single package by providing a single header. It offers two interfaces: both a more standard as<>() converter from R values along with its companions wrap() to return to R, as well as more dedicated functions ‘from’ and ‘to’.

This release adds support for the corresponding nanotime conversion between R and C++. nanotime is leveraging the same bit64-based reprensentation of 64-bit integers for nanosecond resolution timestamps. A thorough S4 wrapping the offers R based access for convenient and powerful operations at nanosecond resolution. And as tweeted (here and here), tooted (here and here), and skeeted (here and here) in a quick preview last Sunday, it makes for easy and expressive code.

The brief NEWS entry follows:

Changes in version 0.0.3 (2023-09-19)

  • The as<>() and wrap() converters are now declared inline.

  • Conversion to and from nanotime has been added.

Courtesy of my CRANberries, there is a diffstat report relative to previous 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, 12 Sep 2023

RcppInt64 0.0.2 on CRAN: Small Update

The still very new package RcppInt64 (announced a week ago in this post) arrived on CRAN earlier today in its first update, now at 0.0.2. RcppInt64 collects some of the previous conversions between 64-bit integer values in R and C++, and regroups them in a single package by providing a single header. It offers two interfaces: both a more standard as<>() converter from R values along with its companions wrap() to return to R, as well as more dedicated functions ‘from’ and ‘to’.

The package by now has its first user as we rearranged RcppFarmHash to use it. The change today makes bit64 a weak rather than strong dependency as we use it only for tests and illustrations. We also added two missing fields to DESCRIPTION and added badges to README.md.

The brief NEWS entry follows:

Changes in version 0.0.2 (2023-09-12)

  • DESCRIPTION has been extended, badges have been added to README.md

  • Package bit64 is now a Suggests:

Courtesy of my CRANberries, there is a [diffstat report relative to previous release][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

Sun, 10 Sep 2023

RcppArmadillo 0.12.6.4.0 on CRAN: Another Upstream Bugfix

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) 1096 other packages on CRAN, downloaded 30.5 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 552 times according to Google Scholar.

This release brings bugfix upstream release 12.6.4. Conrad prepared this a few days ago; it takes me the usual day or so to run reverse-dependency check against the by-now almost 1100 CRAN packages using RcppArmadillo. And this time, CRAN thought it had found two issues when I submitted and it took two more days til we were all clear about those two being false positives (as can, and does, happen). So today it reached CRAN.

The set of changes follows.

Changes in RcppArmadillo version 0.12.6.4.0 (2023-09-06)

  • Upgraded to Armadillo release 12.6.4 (Cortisol Retox)

    • Workarounds for bugs in Apple accelerate framework

    • Fix incorrect calculation of rcond for band matrices in solve()

    • Remove expensive and seldom used optimisations, leading to faster compilation times

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 Rcpp 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

Sat, 09 Sep 2023

RcppFarmHash 0.0.3 on CRAN: Small Update

A minor maintenance release of the RcppFarmHash package is now on CRAN as version 0.0.3.

RcppFarmHash wraps the Google FarmHash family of hash functions (written by Geoff Pike and contributors) that are used for example by Google BigQuery for the FARM_FINGERPRINT digest.

This releases farms out the conversion to the integer64 add-on type in R to the new package RcppInt64 released a few days ago and adds some minor maintenance on continuous integration and alike.

The brief NEWS entry follows:

Changes in version 0.0.3 (2023-09-09)

  • Rely on new RcppInt64 package and its header for conversion

  • Minor updates to continuous integration and README.md

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, 05 Sep 2023

RcppInt64 0.0.1 on CRAN: New Package!

Happy to share that a new package RcppInt64 arrived on CRAN earlier today after a brief one-day inspection round. RcppInt64 collects some of the previous conversions between 64-bit integer values in R and C++, and regroups them in a single package.

A single header is provided. It actually offers two interfaces: both a more standard as<>() converter from R values along with its companions wrap() to return to R, as well as more dedicated functions ‘from’ and ‘to’. A key difficulty faced when supporting 64 bit integer payloads is that R has no proper type for it so the standard template-based approaches use by Rcpp do not apply. To ‘carry’ 64 bit integers, the clever approach by Jens Oehlschlägel and his bit64 package is used. However, its use of a double to transport the int64 payload means we must take care to not uninentionally interpret the double variables as, well, double. So we use an simple S3 class in R, and check for it. With some care (as provided by these helper functions) this works well.

The RcppInt64 packages contains both an example function, as well as an entire example package to demonstrate how to use these facilities in your package. We hope others will find this useful.

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, 29 Aug 2023

RcppArmadillo 0.12.6.3.0 on CRAN: New Upstream Bugfix

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) 1092 other packages on CRAN, downloaded 30.3 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 549 times according to Google Scholar.

This release brings bugfix upstream release 12.6.3. We skipped 12.6.2 at CRAN (as discussed in the previous release notes) as it only affected Armadillo-internal random-number generation (RNG). As we default to supplying the RNGs from R, this did not affect RcppArmadillo. The bug fixes in 12.6.3 are for csv reading which too will most likely be done by R tools for R users, but given two minor bugfix releases an update was in order. I ran the full reverse-depenency check against the now more than 1000 packages overnight: no issues. armadillo processing CRAN processed the package fully automatically as it has no issues, and nothing popped up in reverse-dependency checking.

The set of changes for the last two RcppArmadillo releases follows.

Changes in RcppArmadillo version 0.12.6.3.0 (2023-08-28)

  • Upgraded to Armadillo release 12.6.3 (Cortisol Retox)

    • Fix for corner-case in loading CSV files with headers

    • For consistent file handling, all .load() functions now open text files in binary mode

Changes in RcppArmadillo version 0.12.6.2.0 (2023-08-08)

  • Upgraded to Armadillo release 12.6.2 (Cortisol Retox)

    • use thread-safe Mersenne Twister as the default RNG on all platforms

    • use unique RNG seed for each thread within multi-threaded execution (such as OpenMP)

    • explicitly document arma_rng::set_seed() and arma_rng::set_seed_random()

  • None of the changes above affect R use as RcppArmadillo connects the RNGs used by R to Armadillo

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 Rcpp 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, 20 Aug 2023

RcppRedis 0.2.4 on CRAN: Maintenance

Another minor release, now at 0.2.4, of our RcppRedis package arrived on CRAN yesterday. 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 on a trading floor for several years. It also supports pub/sub dissemination of streaming market data as per this earlier example.

This update is (just like the previous one) fairly mechanical. CRAN noticed a shortcoming of the default per-package help page in a number of packages, in our case it was matter of adding one line for a missing alias to the Rd file. We also demoted the mention of the suggested (but retired) rredis package to a mere mention in the DESCRIPTION file as a formal Suggests: entry, even with an added Additional_repositories, create a NOTE. Life is simpler without those,

The detailed changes list follows.

Changes in version 0.2.4 (2023-08-19)

  • Add missing alias for ‘RcppRedis-package’ to rhiredis.Rd.

  • Remove Suggests: rredis which triggers a NOTE nag as it is only on an ‘Additional_repositories’.

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

Thu, 10 Aug 2023

RcppArmadillo 0.12.6.1.0 on CRAN: New Upstream

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) 1092 other packages on CRAN, downloaded 30.1 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 545 times according to Google Scholar.

This release brings bugfix upstream release 12.6.1. Conrad release 12.6.0 when CRAN went on summer break. I rolled it up ran the full reverse-depenency check against the now more than 1000 packages. And usage from one those revealed a corner-case bug (of not always ‘flattening’ memory for sparse matrices to zero values) so 12.6.1 followed. This is what was uploaded today. And as I prepared it earlier in the week as CRAN reopened, Conrad released a new 12.6.2. However, its changes are only concerned with settings for Armadillo-internal use of its random number generators (RNGs). And as RcppArmadillo connects Armadillo to the RNGs provided by R, the upgrade does not affect R users at all. However it is available in the github repo, in the Rcpp drap repo and at r-universe.

The set of changes for this RcppArmadillo release follows.

Changes in RcppArmadillo version 0.12.6.1.0 (2023-07-26)

  • Upgraded to Armadillo release 12.6.1 (Cortisol Retox)

    • faster multiplication of dense vectors by sparse matrices (and vice versa)

    • faster eigs_sym() and eigs_gen()

    • faster conv() and conv2() when using OpenMP

    • added diags() and spdiags() for generating band matrices from set of vectors

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 Rcpp 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

Mon, 10 Jul 2023

RcppSpdlog 0.0.14 on CRAN: Upstream Update

Version 0.0.14 of RcppSpdlog is now on CRAN and has just been uploaded to 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. You can learn more at the nice package documention site.

This release simply brings an update to the just release spdlog 1.12.0 from a few days ago.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.14 (2023-07-09)

  • Added new badge to README.md

  • Upgraded to upstream releases spdlog 1.12.0

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, 06 Jul 2023

Rcpp 1.0.11 on CRAN: Updates and Maintenance

rcpp logo

The Rcpp Core Team is delighted to announce that the newest release 1.0.11 of the Rcpp package arrived on CRAN and in Debian earlier today. 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 finalized three days ago, but given the widespread use and extended reverse dependencies at CRAN it usually takes a few days to be processed. This release continues with the six-months January-July 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 long established itself as the most popular way of enhancing R with C or C++ code. Right now, 2720 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 251 in BioConductor. On CRAN, 13.7% of all packages depend (directly) on Rcpp, and 59.6% of all compiled packages do. From the cloud mirror of CRAN (which is but a subset of all CRAN downloads), Rcpp has been downloaded 72.5 million times. The two published papers (also included in the package as preprint vignettes) have, respectively, 1678 (JSS, 2011) and 259 (TAS, 2018) citations, while the the book (Springer useR!, 2013) has another 588.

This release is incremental as usual, generally preserving existing capabilities faithfully while smoothing our corners and / or extending slightly, sometimes in response to changing and tightened demands from CRAN or R standards.

The full list below details all changes, their respective PRs and, if applicable, issue tickets. Big thanks from all of us to all contributors!

Changes in Rcpp version 1.0.11 (2023-07-03)

  • Changes in Rcpp API:

    • Rcpp:::CxxFlags() now quotes only non-standard include path on linux (Lukasz in #1243 closing #1242).

    • Two unit tests no longer accidentally bark on stdout (Dirk and Iñaki in #1245).

    • Compilation under C++20 using clang++ and its standard library is enabled (Dirk in #1248 closing #1244).

    • Use backticks in a generated .Call() statement in RcppExports.R (Dirk #1256 closing #1255).

    • Switch to system2() to capture standard error messages in error cases (Iñaki in #1259 and #1261 fixing #1257).

  • Changes in Rcpp Documentation:

    • The CITATION file format has been updated (Dirk in #1250 fixing #1249).
  • Changes in Rcpp Deployment:

    • A test for qnorm now uses the more accurate value from R 4.3.0 (Dirk in #1252 and #1260 fixing #1251).

    • Skip tests with path issues on Windows (Iñaki in #1258).

    • Container deployment in continuous integrations was improved. (Iñaki and Dirk in #1264, Dirk in #1269).

    • Several files receives minor edits to please R CMD check from r-devel (Dirk in #1267).

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) 2994 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.

/code/rcpp | permanent link

Sun, 02 Jul 2023

RcppAnnoy 0.0.21 on CRAN: Upstream Update

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 mainly updates the included copy of Annoy to version 1.7.3 which now provides a C++ namespace in the header API. So I sent a pair of PRs to uwot to update its (compiled) use, which James promptly merged. With that the CRAN update was once again seamless. Otherwise the package follows current custom by moving away from C++11 as a set compilation standard to be open for more modern C++ idioms. Here, this allows in particular for possible multithreaded indexing for which everything needed is in C++17. However, we did not turn multithreaded indexing on as the RNG use is such that the streams would differ leading to slightly different (if of course equivalent) results. Users can enable this by recompiling with the switch flipped, see src/Makevars.

Changes in version 0.0.21 (2023-07-02)

  • The build setup switched from C++11 to C++17 which offers threading support (which remains off by default to ensure consistent results)

  • Upstream code was update to Annoy 1.17.3, the switch to an explicit C++ namespace has been accomodated (Dirk in #75)

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

Mon, 19 Jun 2023

RcppArmadillo 0.12.4.1.0 on CRAN: New Upstream Bugfix

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) 1079 other packages on CRAN, downloaded 29.6 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 543 times according to Google Scholar.

This release brings bugfix upstream release 12.4.1 made by Conrad at the end of last week. As usual, I prepared the usual release candidate, tested on the over 1000 reverse depends (which sadly takes a long time on old hardware), found no issues and sent it to CRAN. Where it got tested again and was by a stroke of bad luck upheld for two unrelated issue (one package fell over one of its other dependencies changing a data representation, another fell afoul of a tightened test on total test time) so this awaited the usual email handshake with the CRAN maintainers … and the weekend got in the way. The release also contains a PR kindly provided by Mikael Jagan for an upcoming change in package Matrix.

As a bugfix release, the set of changes is fairly small.

Changes in RcppArmadillo version 0.12.4.1.0 (2023-06-17)

  • Upgraded to Armadillo release 12.4.1 (Cortisol Profusion Redux)

    • fix bug in SpMat::shed_cols()

    • functions such as .is_finite() and find_nonfinite() will now emit a runtime warning when compiled in fast math mode; such compilation mode disables detection of non-finite values

  • Accommodate upcoming change in package Matrix (Mikael Jagan in #417 addressing #415)

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 Rcpp 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

Sat, 17 Jun 2023

RcppSpdlog 0.0.13 on CRAN: Small Extensions

Version 0.0.13 of RcppSpdlog is now on CRAN and will be soon be uploaded to Debian too. 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. You can learn more at the package documention site.

This release adds a small (but handy) accessor generalisation: Instead of calling setup() with two arguments for a label and the logging level we now only require the desired level. We also cleaned up one implementation detail for the stopwatch feature added in January, and simplified the default C++ compilation standard setting.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.13 (2023-06-17)

  • Minor tweak to stopwatch setup avoids pulling in fmt

  • No longer set a C++ compilation standard as the default choices by R are sufficient for the package

  • Add convenience wrapper log_init omitting first argument to log_setup while preserving the interface from the latter

  • Add convenience setup wrappers init and log to API header file spdl.h

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

Sat, 27 May 2023

RcppArmadillo 0.12.4.0.0 on CRAN: New Upstream Minor

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) 1074 other packages on CRAN, downloaded 29.3 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 535 times according to Google Scholar.

This release brings a new upstream release 12.4.0 made by Conrad a day or so ago. I prepared the usual release candidate, tested on the over 1000 reverse depends (which sadly takes almost a day on old hardware), found no issues and sent it to CRAN. Where it got tested again and was once again auto-processed smoothly by CRAN within a few hours on a Friday night which is just marvelous. So this time I tweeted about it too.

The releases actually has a relatively small set of changes as a second follow-up release in the 12.* series.

Changes in RcppArmadillo version 0.12.4.0.0 (2023-05-26)

  • Upgraded to Armadillo release 12.4.0 (Cortisol Profusion Redux)

    • Added norm2est() for finding fast estimates of matrix 2-norm (spectral norm)

    • Added vecnorm() for obtaining the vector norm of each row or column of a matrix

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 my open-source work, you may consider sponsoring 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, 14 May 2023

RcppSimdJson 0.1.10 on CRAN: New Upstream

We are happy to share that the RcppSimdJson package has been updated to release 0.1.10.

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 3.1.8 (also made today). Otherwise we only made a minor edit to the README and adjusted one tweek for code coverage.

The (very short) NEWS entry for this release follows.

Changes in version 0.1.10 (2023-05-14)

  • simdjson was upgraded to version 3.1.8 (Dirk in #85).

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

Wed, 05 Apr 2023

RcppArmadillo 0.12.2.0.0 on CRAN: New Upstream Minor

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) 1052 other packages on CRAN, downloaded 28.6 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 522 times according to Google Scholar.

This release brings a new upstream release 12.2.0 made by Conrad a day or so ago. We prepared the usual release candidate, tested on the over 1000 reverse depends, found no issues and sent it to CRAN. Where it got tested again and was auto-processed smoothly by CRAN.

The releases actually has a relatively small set of changes as a first follow-up release in the 12.2.* series.

Changes in RcppArmadillo version 0.12.2.0.0 (2023-04-04)

  • Upgraded to Armadillo release 12.2.0 (Cortisol Profusion Deluxe)

    • more efficient use of FFTW3 by fft() and ifft()

    • faster in-place element-wise multiplication of sparse matrices by dense matrices

    • added spsolve_factoriser class to allow reuse of sparse matrix factorisation for solving systems of linear equations

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

Wed, 22 Mar 2023

RcppSMC 0.2.7 on CRAN: Extensions and Update

A new release 0.2.7 of our RcppSMC package arrived at CRAN earlier today. It contains several extensions added by team member (and former GSoC student) Ilya Zarubin since the last release. We were a little slow to release those—but “one of those CRAN emails” forced our hand for a release now. The updated ‘uninitialized variable’ messages in clang++-16 have found a fan in Brian Ripley, and so he sent us a note. And as the issue was trivially reproducible with clang++-15 here too I had it fixed in no time. And both changes taken together form the incremental 0.2.7 release.

RcppSMC provides Rcpp-based bindings to R for the Sequential Monte Carlo Template Classes (SMCTC) by Adam Johansen described in his JSS article. Sequential Monte Carlo is also referred to as Particle Filter in some contexts. The package now also features the Google Summer of Code work by Leah South in 2017, and by Ilya Zarubin in 2021.

The release is summarized below.

Changes in RcppSMC version 0.2.7 (2023-03-22)

  • Extensive extensions for conditional SMC and resample, updated hello_world example, added skeleton function for easier package creation (Ilya in #67,#72)

  • Small package updates (Dirk in #75 fixing #74)

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

More information is on the RcppSMC 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

Wed, 08 Mar 2023

RcppRedis 0.2.3 on CRAN: Maintenance

A new minor release 0.2.3 of our RcppRedis package arrived on CRAN today. 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 on a trading floor for several years.

This update is fairly mechanical. CRAN wants everybody off the C++11 train which is fair game given that it 2023 and most sane and lucky people are facing sane and modern compilers so this makes sense. (And I raise a toast to all those poor souls facing RHEL 7 / CentOS 7 with a compiler from many moons ago: I hear it is a vibrant job market out there so maybe time to make a switch…). As with a few of my other packages, this release simply does away with the imposition of C++11 as the package will compile just fine under C++14 or C++17 (as governed by your version of R).

The detailed changes list follows.

Changes in version 0.2.3 (2023-03-08)

  • No longer set a C++ compilation standard as the default choices by R are sufficient for the package

  • Switch include to Rcpp/Rcpp which signals use of all Rcpp features including Modules

Courtesy of my 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

Mon, 06 Mar 2023

RcppFastAD 0.0.1 and 0.0.2: New Package on CRAN!

James Yang and I are thrilled to announce the new CRAN package RcppFastAD which arrived at CRAN last Monday as version 0.0.1, and is as of today at version 0.0.2 with a first set of small updates.

It is based on the FastAD header-only C++ library by James which provides a C++ implementation of both forward and reverse mode of automatic differentiation in an easy-to-use header library (which we wrapped here) that is both lightweight and performant. With a little of bit of Rcpp glue, it is also easy to use from R in simple C++ applications. Included in the package are three example: a simple quadratic expression evaluating x' S x for given x and S return the expression value with a gradient, a linear regression example generalising this and using the gradient to derive to arrive at the least-squares minimizing solution, as well as the well-known Black-Scholes options pricer and its important partial derivatives delta, rho, theta and vega derived via automatic differentiation.

The NEWS file for these two initial releases follows.

Changes in version 0.0.2 (2023-03-05)

  • One C++ operation is protected from operating on a nullptr

  • Additional tests have been added, tests now cover all three demo / example functions

  • Return values and code for the examples linear_regression and quadratic_expression have been adjusted

Changes in version 0.0.1 (2023-02-24)

  • Initial release version and CRAN upload

Courtesy of my CRANberries, there is also a diffstat report for the most recent release. More information is available at the repository or the package 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

Wed, 22 Feb 2023

RcppArmadillo 0.12.0.1.0 on CRAN: New Upstream, New Features

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) 1042 other packages on CRAN, downloaded 28.1 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 513 times according to Google Scholar.

This release brings a new upstream release 12.0.1. We found a small regression with the 12.0.0 release when we tested prior to a CRAN upload. Conrad very promptly fixed this with a literal one liner and made it 12.0.1 which we wrapped up as 0.12.0.1.0. Subsequent testing revealed no issues for us, and CRAN autoprocessed it as I tweeted earlier. This is actually quite impressive given the over 1000 CRAN packages using it all of which got tested again by CRAN. All this is testament to the rigour, as well as the well-oiled process at the repository. Our thanks go to the tireless maintainers!

The releases actually has a rather nice set of changes (detailed below) to which we added one robustification thanks to Kevin.

The full set of changes follows. We include the previous changeset as we may have skipped the usual blog post here.

Changes in RcppArmadillo version 0.12.0.1.0 (2023-02-20)

  • Upgraded to Armadillo release 12.0.1 (Cortisol Profusion)

    • faster fft() and ifft() via optional use of FFTW3

    • faster min() and max()

    • faster index_min() and index_max()

    • added .col_as_mat() and .row_as_mat() which return matrix representation of cube column and cube row

    • added csv_opts::strict option to loading CSV files to interpret missing values as NaN

    • added check_for_zeros option to form 4 of sparse matrix batch constructors

    • inv() and inv_sympd() with options inv_opts::no_ugly or inv_opts::allow_approx now use a scaled threshold similar to pinv()

    • set_cout_stream() and set_cerr_stream() are now no-ops; instead use the options ARMA_WARN_LEVEL, or ARMA_COUT_STREAM, or ARMA_CERR_STREAM

    • fix regression (mis-compilation) in shift() function (reported by us in #409)

  • The include directory order is now more robust (Kevin Ushey in #407 addressing #406)

Changes in RcppArmadillo version 0.11.4.4.0 (2023-02-09)

  • Upgraded to Armadillo release 11.4.4 (Ship of Theseus)

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

    • added find_nan() to find indices of NaN elements

    • faster handling of compound expressions by sum()

  • The package no longer sets a compilation standard, or progagates on in the generated packages as R ensures C++11 on all non-ancient versions

  • The CITATION file was updated to the current format

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, 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.

/code/rcpp | permanent link

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.

/code/rcpp | permanent link

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.

/code/rcpp | permanent link

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.

/code/rcpp | permanent link

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.

/code/rcpp | permanent link

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.

/code/rcpp | permanent link

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.

/code/rcpp | permanent link

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.

/code/rcpp | 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

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, 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

Tue, 01 Nov 2022

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

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

Wed, 19 Oct 2022

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

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

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.

/code/rcpp | permanent link