Fri, 30 Jul 2021

RcppAnnoy 0.0.19 on CRAN: Maintenance

annoy image

A minor maintenance release, now at version 0.0.19, of RcppAnnoy is now 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 famous Spotify music discovery algorithm.

This release only contains internal packaging changes. Nothing changes upstream, or in package functionality. Detailed changes follow.

Changes in version 0.0.19 (2021-07-30)

  • Minor tweaks to default CI setup and DESCRIPTION file

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.

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Mon, 26 Jul 2021

RcppFarmHash 0.0.1: New CRAN Package

A new package RcppFarmHash is now on CRAN in an inaugural version 0.0.1.

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.

The package was prepared and uploaded yesterday afternoon, and to my surprise already on CRAN this (early) morning when I got up. So here is another #ThankYouCRAN for very smoothing operations.

The very brief NEWS entry follows:

Changes in version 0.0.1 (2021-07-25)

  • Initial version and CRAN upload

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

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

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Sat, 24 Jul 2021

littler 0.3.13: Moar Goodies

max-heap image

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

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

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

A few examples are highlighted at the Github repo, as well as in the examples vignette.

This release brings two new example scripts and command wrappers (compiledDeps.r, silenceTwitterAccount.r), along with extensions, corrections, or polish for a number a of other examples as detailed in the NEWS file entry below.

Changes in littler version 0.3.13 (2021-07-24)

  • Changes in examples

    • New script compiledDeps.r to show which dependencies are compiled

    • New script silenceTwitterAccount.r wrapping rtweet

    • The -c or --code option for installRSPM.r was corrected

    • The kitten.r script now passes options ‘bunny’ and ‘puppy’ on to the pkgKitten::kitten() call; new options to call the Arma and Eigen variants were added

    • The getRStudioDesktop.r and getRStudioServer.r scripts were updated for a change in rvest

    • Two typos in the tt.r help message were correct (Aaron Wolen in #86)

    • The message in cranIncoming.r was corrected.

  • Changes in package

    • Added Continuous Integration runner via run.sh from r-ci.

    • Two vignettes got two extra vignette attributes.

    • The mkdocs-material documentation input was moved.

    • The basic unit tests were slightly refactored and updated.

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

Comments and suggestions are welcome at the GitHub repo.

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

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

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Thu, 22 Jul 2021

RcppSpdlog 0.0.6 on CRAN: New upstream

A new version 0.0.6 of RcppSpdlog is now on CRAN. It contains releases 1.9.0 of spdlog which in turn contains an updated version of fmt.

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. No R package-side changes were needed or made.

The (minimal) NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.6 (2021-07-21)

  • Upgraded to upstream release spdlog 1.9.0

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog 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, 20 Jul 2021

pkgKitten 0.2.2 on CRAN: Small Updates

kitten

A new release 0.2.2 of pkgKitten is now on CRAN, and will be uploaded to Debian. pkgKitten makes it simple to create new R packages via a simple function invocation. A wrapper kitten.r exists in the littler package to make it even easier.

This release simply corrects on minor aspect in the optional roxygen2 use, and updates the DESCRIPTION file.

Changes in version 0.2.2 (2021-07-19)

  • Small update to DESCRIPTION

  • Document hello2() argument

More details about the package are at the pkgKitten webpage, the pkgKitten docs site, and the pkgKitten GitHub repo.

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

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

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

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Sat, 17 Jul 2021

ttdo 0.0.7: Micro-tweak

A new (and genuinely) minor release of our ttdo package arrived on CRAN today. The ttdo package extends the most excellent (and very minimal / zero depends) unit testing package tinytest by Mark van der Loo with the very clever and well-done diffobj package by Brodie Gaslam to give us test results with visual diffs (as shown in the screenshot below) which seemingly is so compelling an idea that it eventually got copied by another package…

ttdo screenshot

This release cleans up one microscopic wart of an R warning when installing and byte-compiling the package due to a sprintf call with an unused argument.

And once again, this release gets a #ThankYouCRAN mark as it was processed in a fully automated and intervention-free manner in a matter of minutes.

As usual, the NEWS entry follows.

Changes in ttdo version 0.0.8 (2021-07-17)

  • Expand sprintf template to suppress R warning

CRANberries provides the usual summary of changes to the previous version. Please use the GitHub repo and its issues for any questions.

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

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

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Fri, 16 Jul 2021

RcppArmadillo 0.10.6.0.0 on CRAN: A New Upstream

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 882 other packages on CRAN.

This new release gets us Armadillo 10.6.0 which was released yesterday. We did the usual reverse dependency checks (which came out spotless and clean), and had also just done even fuller checks for Rcpp 1.0.7.

Since the previous RcppArmadillo 0.10.5.0.0 release we made a few interim releases to the drat repo. In general, Conrad is a little more active than we want to be with (montly or less frequent) CRAN updates so keep and eye on the drat repo (or follow the GitHub repo) for a higher-frequence cadence. To use the drat repo, use install.packages("RcppArmadillo", repos="https://RcppCore.github.io/drat") or update.packages() with a similar repos argument.

The full set of changes follows. We include the last interim release as well.

Changes in RcppArmadillo version 0.10.6.0.0 (2021-07-16)

  • Upgraded to Armadillo release 10.6.0 (Keep Calm)

    • expanded chol() to optionally use pivoted decomposition

    • expanded vector, matrix and cube constructors to allow element initialisation via fill::value(scalar), eg. mat X(4,5,fill::value(123))

    • faster loading of CSV files when using OpenMP

    • added csv_opts::semicolon option to allow saving/loading of CSV files with semicolon (;) instead of comma (,) as the separator

Changes in RcppArmadillo version 0.10.5.3.0 (2021-07-01)

  • Upgraded to Armadillo release 10.5.3 (Antipodean Fortress)

  • GitHub-only release

  • Extended test coverage with several new tests, added a coverage badge.

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

Sat, 10 Jul 2021

drat 0.2.1: Small Tweak

drat user

A new minor release of drat arrived on CRAN overnight. This is a minor update relative to the 0.2.0 release in April. This release will now create an empty file index.html in the top-level (when initRepo() is called), and check for presence of such a file when adding files to a repo (via insertPackage()). This helps to avoid getting ‘404’ results when (perfectly valid) drat repos are checking by accessing the top-level URL, as for example CRAN does when testing if an Additional_repositoiries is reachable. The ‘step-by-step’ vignette had already suggested creating one by hand, this is now done programmatically (and one is present in the repo suggsted to fork from too).

drat stands for drat R Archive Template, and helps with easy-to-create and easy-to-use repositories for R packages. Since its inception in early 2015 it has found reasonably widespread adoption among R users because repositories with marked releases is the better way to distribute code. See below for a few custom reference examples.

Because for once it really is as your mother told you: Friends don’t let friends install random git commit snapshots. Properly rolled-up releases it is. Just how CRAN shows us: a model that has demonstrated for two-plus decades how to do this. And you can too: drat is easy to use, documented by six vignettes and just works.

The NEWS file summarises the release as follows:

Changes in drat version 0.2.1 (2021-07-09)

  • Two internal functions now have a note in their documentation stating them as not exported (Dirk in response to #123)

  • Repositories created by initRepo now have an placeholder index.html to not trigger a curl check at CRAN (Dirk)

  • Adding to a repository now checks for a top-level index.html and displays a message if missing (Dirk)

  • The DratStepByStep.Rmd vignette mentions the added index.html file

Courtesy of my CRANberries, there is a comparison to the previous release. More detailed information is on the drat 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/drat | permanent link

Wed, 07 Jul 2021

Rcpp 1.0.7: More Updates

rcpp logo

The Rcpp team is pleased to announce release 1.0.7 of Rcpp which arrived at CRAN earlier today, and will be uploaded to Debian shortly. Windows and macOS builds should appear at CRAN in the next few days. This release continues with the six-months cycle started with release 1.0.5 last July. As a reminder, interim ‘dev’ or ‘rc’ releases will alwasys be available in the Rcpp drat repo; this cycle there were seven (!!). These rolling release 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. As of today, 2323 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 227 in BioConductor.

This release contains a change which Luke Tierney urged us to make a good year ago in #1081) (and which we had looked at earlier in #382). Implementing the change in a regular update proved a little tricky, and my initial branch lay dormant until Iñaki revived it, and finished the transition (which we then did in two PRs). The change concerns how Rcpp grows internal objects, and the new approach (thanks to the hint by Luke) closer to what R does guaranteeing linear behaviour. It turns out that we overlooked one aspect (of coping with Modules built under earlier Rcpp releases) so the initial upload to CRAN on Saturday revealed that we needed a small adjustment that we made for the final release. This version should now be more performant, and rest on a stable API. Based on the reverse depends checks by both us and CRAN (using the updated version), we expect no issues with existing code. However, it something does act up a fresh compilation of the packages using Rcpp may help.

We also made a few other minor changes in the API such as silencing a silly compiler warning, ensuring global Rcout and Rcerr objects, adding support for a new Rcpp::message() call, completing a switch to uint32_t instead of unsigned int and including the cfloat header (which relates to STRICT_R_HEADERS discussed below). Similarly, the Rcpp Attributes feature was enhanced by coping better with packages with a dot in their name and their for per-package include files, along with support for more quiet compilation if desired.

As some Rcpp users may have seen, we plan to enable STRICT_R_HEADERS by the next release (expected in January 2022). A long issue tick #1158 is laying the ground work. Maintainers of 81 packages which are affected and need a small change (such as for example switching from PI to M_PI); of these 56 have already responded. We plan to be in touch in the fall. Adding the cfloat header is one help in this transition (as the corresponding C header was pulled in when STRICT_R_HEADERS is not defined) as it ensures DBL_EPSILON and alike are defined.

Last but not least this is also the first relase in which we welcome Iñaki as a new member of the Rcpp Core team. Yay!

The NEWS file entries follow summarizing the nine key PRs in this release.

Changes in Rcpp release version 1.0.7 (2021-07-06)

  • Changes in Rcpp API:

    • Refactored Rcpp_PreserveObject and Rcpp_ReleaseObject which are now O(1) (Dirk and Iñaki in #1133 and #1135 fixing #382 and #1081).

    • A spuriously assigned variable was removed (Dirk in #1138 fixing #1137).

    • Global Rcout and Rcerr objects are supported via a compiler directive (Iñaki in #1139 fixing #928)

    • Add support for Rcpp::message (Dirk in #1146 fixing #1145).

    • The uint32_t type is used throughout instead of unsigned int (Dirk in #1153 fixing #1152).

    • The cfloat header for floating point limits is now included (Dirk in #1162 fixing #1161).

  • Changes in Rcpp Attributes:

    • Packages with dots in their name can now have per-package include files (Dirk in #1132 fixing #1129).

    • New argument echo to quieten optional evaluation in sourceCpp (Dirk in #1138 fixing #1126).

  • Forthcoming Changes in Rcpp API:

    • Starting with Rcpp 1.0.8 anticipated in January 2022, STRICT_R_HEADERS will be enabled by default, see #1126.

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) 2616 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

Tue, 06 Jul 2021

ttdo 0.0.7: Small tinytest update

A new minor release of our ttdo package arrived on CRAN today. The ttdo package extends the most excellent (and very minimal / zero depends) unit testing package tinytest by Mark van der Loo with the very clever and well-done diffobj package by Brodie Gaslam to give us test results with visual diffs (as shown in the screenshot here) which seemingly is so compelling an idea that another package decided to copied it more recently:

ttdo screenshot

This release is mostly procedural to accomodate changes in tinytest 1.3.1 released today, and brought to us via a pull request by Mark himself. Other than that we also updated the CI runner to use r-ci and accomodated new CRAN check for a superfluous LazyData: field in a package without a data/ directory.

This release also gets another #ThankYouCRAN mark as it was once again fully automated and intervention-free (once the new tinytest release hit CRAN).

As usual, the NEWS entry follows.

Changes in ttdo version 0.0.7 (2021-07-06)

  • The CI setup was updated to use run.sh from r-ci (Dirk).

  • The package was updated for an API extension in tinytest 1.3.1 or later (Mark van der Look in #7)

  • The unused LazyData field was removed from DESCRIPTION (Dirk)

CRANberries provides the usual summary of changes to the previous version. Please use the GitHub repo and its issues for any questions.

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/ttdo | permanent link

Sat, 26 Jun 2021

RcppRedis 0.1.11: Minor Update

A new minor release of RcppRedis arrived on CRAN, the first update since the last release in January of last year.

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 release updates CI to using r-ci, adds a quit() methods, and updates the windows library in builds thanks to a PR by Jeroen which also enables builds under the experimemtal ‘UCRT’ windows flavor.

Changes in version 0.1.11 (2021-06-26)

  • The CI setup was updated to use run.sh from r-ci (Dirk).

  • A new function quit can be used to close a connection (Dirk).

  • The windows build was updated to libhiredis 1.0.0, and UCRT support was added (Jeroen in #42).

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

Wed, 23 Jun 2021

RcppGSL 0.3.9: Polish and More Builds

Release 0.3.9 of the RcppGSL package arrived at CRAN today, pretty much exactly one year since the last upload. The RcppGSL package provides an interface from R to the GNU GSL by relying on the Rcpp package.

This release brings some small documentation and CI polish, and enables builds on the newer (and still experimental) windows ‘UCRT’ flavor (which will bring native utf-8 chars to Windows, see this and this write-up) thanks to a PR by Jeroen.

Changes in version 0.3.9 (2021-06-23)

  • The pdf vignette was extended by a small subsection (Dirk).

  • The CI setup was updated to use run.sh from r-ci (Dirk).

  • The windows was updated to GSL 2.7, and UCRT support was added (Jeroen in #28).

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

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

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

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

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Wed, 09 Jun 2021

#33: Collaborative Editing and Execution in Shared Byoby Sessions

Welcome to the 33th post in the rigorously raconteuring R recommendations series, or R4 for short. This post is also a post in the T4 series of tips, tricks, tools, and toys as it picks up and extends earlier posts on byobu. And it fits nicely in the more recent ESS-Intro series as we show some Emacs. You can find earlier R4 posts here, and the T4 posts here; the ESS-Intro series is here.

The focus of this short video (and slides) is on collaboration using files, but also entire sessions, execution and all aspects of joint exploration, development or debugging. Anything you can do in a terminal you can also do shared in a terminal. The video contains a brief lightning talk, and a shared session jointly with Grant McDermott and Vicent Arel-Bundock. My big big thanks to both of them for prodding and encouragement, as well as fearless participation in the joint section of the video:

The corresponding pdf slides are here.

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

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

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Sat, 05 Jun 2021

td 0.0.4 on CRAN: More Maintenance

The still fairly recent td package for accessing the twelvedata API for financial data has been updated on CRAN this morning, and is now at released version 0.0.4. This corrects something the previous 0.0.3 release from last weekend was meant to address, but didn’t quite do it.

Access to the helper function finding a proper user config file (for .e.g., the API config) is now correctly conditioned on R 4.0.0, and the versioned depends has been removed.

The NEWS entry follows.

Changes in version 0.0.4 (2021-06-05)

  • The version comparison was corrected and the package no longer (formally) depends on R (>= 4.0.0)

  • Very minor README.md edits

Courtesy of my CRANberries, there is a comparison to the previous release. For questions or comments use the issue tracker off the GitHub repo.

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

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

/code/td | permanent link

Mon, 31 May 2021

inline 0.3.19: Another Update

A new release of the inline package got to CRAN today, following and further updating the recent update from earlier in the month. inline facilitates writing code in-line in simple string expressions or short files. The package was used quite extensively by Rcpp in the days before Rcpp Attributes arrived on the scene providing an even better alternative for its use cases. inline is still used by rstan and a number of other packages.

This release builds on and extends the work of the recent 0.3.18 release and tweaks some of the test. We cannot fully test all platforms used by CRAN so some times iterations such as this one are needed. The package was uploaded a few days ago, but it sometimes takes a few days to clarify changes over email to the CRAN maintainers whose work is still greatly appreciated.

The NEWS extract follows and details the changes some more.

Changes in inline version 0.3.19 (2021-05-25)

  • Documentation for moveDLL was updated and extended (Johannes in #22).

  • A few more tests were made conditional the test platform (Dirk in #24).

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

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

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

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Sun, 30 May 2021

td 0.0.3 on CRAN: Maintenance release

The still recent-ish td package for accessing the twelvedata API for financial data has been updated on CRAN yesterday, and is now at released version 0.0.3.

A few URLs were updated to please the lint checker, and a Depends: on R 4.0.0 or later was added. We then realized (as always just after the release …) that the core issue was an incorrect version comparison which we already fixed in the git repo.

The NEWS entry follows.

Changes in version 0.0.3 (2021-05-29)

  • The package now (formally) depends on R (>= 4.0.0) as it uses a recently added R function for the default config file.

  • A few URLs were updated in the README.md file

Courtesy of my CRANberries, there is a comparison to the previous release. For questions or comments use the issue tracker off the GitHub repo.

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

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

/code/td | permanent link

Sun, 23 May 2021

RcppArmadillo 0.10.5.0.0 on CRAN: New Upstream

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 865 other packages on CRAN.

This new release brings Armadillo 10.5.0 which was released early on Friday. We had done one full test in the ‘10.5 rc1’ prerelease one week earlier, and did another test on 10.5.0 and this 0.10.5.0.0 RcppArmadillo release just for added rigour. The package was then uploaded to CRAN late Friday (my timezone). The automated process flagged one NOTE as a false positive (yet another instance of the well-known (yet dreaded) issue of ‘Suggests != Depends’ by one these 865 packages). This lead to a need of an inspection by one of the CRAN maintainers, and the weekend being the weekend it was only processed just now.

Upstream moves at a speed that is a little faster than the cadence CRAN likes. As we had released RcppArmadillo 0.10.4.0.0 on April 13 we did not want to follow-up ‘too soon thereafter’ with 0.10.4.1.0 which was thusly only a GitHub and drat release (which can always be had easily too via install.packages("RcppArmadillo", repos="https://RcppCore.github.io/drat").)

The full set of changes follows. We include the aforementioned interim release as well.

Changes in RcppArmadillo version 0.10.5.0 (2021-05-21)

  • Upgraded to Armadillo release 10.5 (Antipodean Fortress)

    • added .clamp() member function

    • expanded the standalone clamp() function to handle complex values

    • more efficient use of OpenMP

    • vector, matrix and cube constructors now initialise elements to zero by default; use the fill::none specifier, eg. mat X(4,5,fill::none), to disable element initialisation

  • Added codecov.yml to exclude Armadillo from coverage analysis

Changes in RcppArmadillo version 0.10.4.1.0 (2021-04-23)

  • Upgraded to Armadillo release 10.4.1 (Pressure Cooker)

  • GitHub-only release

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, 19 May 2021

RcppDate 0.0.3: New Upstream

RcppDate wraps the featureful date library written by Howard Hinnant for use with R. This header-only modern C++ library has been in pretty wide-spread use for a while now, and adds to C++11/C++14/C++17 what will be (with minor modifications) the ‘date’ library in C++20.

Our previous 0.0.2 release already contained date version 3.0.0 from last year plus some of changes accumulated since then. Now that date 3.0.1 was just released, we are providing a quick sync with this version.

Changes in version 0.0.3 (2021-05-19)

  • Updated to upstream version 3.0.1

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

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

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Tue, 18 May 2021

inline 0.3.18: Routine Update

A new release of the inline package got to CRAN today. inline facilitates writing code in-line in simple string expressions or short files. The package was used quite extensively by Rcpp in the days before Rcpp Attributes arrived on the scene proving an even better alternative for its use cases. inline is still used by rstan and a number of other packages.

Johannes Ranke, who uses and stresses inline via his package mkin, updated the loading/unloading of DLLs which, following updates in R-devel, was failing some tests. As luck will have it, this new version appears to still fail on two of the platforms we do not actually have easy access to so another version may be coming “shortly”.

See below for a detailed list of changes extracted from the NEWS file.

Changes in inline version 0.3.18 (2021-05-17)

  • The moveDLL code and tests were updated for changed in R-devel (Johannes in #22 fixing #21).

Courtesy of my CRANberries, there is a comparison to the previous 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/inline | permanent link

Thu, 22 Apr 2021

drat 0.2.0: Now with ‘docs/’

drat user

A new release of drat arrived on CRAN today. This is the first release in a few months (with the last release in July of last year) and it (finally) makes the leap to supporting docs/ in the main branch as we are all so tired of the gh-pages branch. We also have new vignettes, new (and very shiny) documentation and refreshed vignettes!

drat stands for drat R Archive Template, and helps with easy-to-create and easy-to-use repositories for R packages. Since its inception in early 2015 it has found reasonably widespread adoption among R users because repositories with marked releases is the better way to distribute code. See below for a few custom reference examples.

Because for once it really is as your mother told you: Friends don’t let friends install random git commit snapshots. Or as we may now add: stay away from semi-random universes snapshots too.

Properly rolled-up releases it is. Just how CRAN shows us: a model that has demonstrated for two-plus decades how to do this. And you can too: drat is easy to use, documented by (now) six vignettes and just works.

The NEWS file summarises the release as follows:

Changes in drat version 0.2.0 (2021-04-21)

  • A documentation website for the package was added at https://eddelbuettel.github.io/drat/ (Dirk)

  • The continuous integration was switched to using ‘r-ci’ (Dirk)

  • The docs/ directory of the main repository branch can now be used instead of gh-pages branch (Dirk in #112)

  • A new repository https://github.com/drat-base/drat can now be used to fork an initial drat repository (Dirk)

  • A new vignette “Drat Step-by-Step” was added (Roman Hornung and Dirk in #117 fixing #115 and #113)

  • The test suite was refactored for docs/ use (Felix Ernst in #118)

  • The minimum R version is now ‘R (>= 3.6)’ (Dirk fixing #119)

  • The vignettes were switched to minidown (Dirk fixing #116)

  • A new test file was added to ensure ‘NEWS.Rd’ is always at the current release version.

Courtesy of my CRANberries, there is a comparison to the previous release. More detailed information is on the drat 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/drat | permanent link

Tue, 20 Apr 2021

Rblpapi 0.3.11: Several Updates

A new version 0.3.11 of Rblpapi is now arriving at CRAN. It comes two years after the release of version Rblpapit 0.3.10 and brings a few updates and extensions.

Rblpapi provides a direct interface between R and the Bloomberg Terminal via the C++ API provided by Bloomberg (but note that a valid Bloomberg license and installation is required).

This is the eleventh release since the package first appeared on CRAN in 2016. Changes are detailed below. Special thanks to James, Maxime and Michael for sending us pull requests.

Changes in Rblpapi version 0.3.11 (2021-04-20)

  • Support blpAutoAuthenticate and B-PIPE access, refactor and generalise authentication (James Bell in #285)

  • Deprecate excludeterm (John in #306)

  • Correct example in README.md (Maxime Legrand in #314)

  • Correct bds man page (and code) (Michael Kerber, and John, in #320)

  • Add GitHub Actions continuous integration (Dirk in #323)

  • Remove bashisms detected by R CMD check (Dirk #324)

  • Switch vignette to minidown (Dirk in #331)

  • Switch unit tests framework to tinytest (Dirk in #332)

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

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

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

/code/rblpapi | permanent link

Sat, 17 Apr 2021

RcppAPT 0.0.7: Micro Update

A new version of the RcppAPT package interfacing from R to the C++ library behind the awesome apt, apt-get, apt-cache, … commands and their cache powering Debian, Ubuntu and the like arrived on CRAN yesterday. This comes a good year after the previous maintenance update for release 0.0.6.

RcppAPT allows you to query the (Debian or Ubuntu) package dependency graph at will, with build-dependencies (if you have deb-src entries), reverse dependencies, and all other goodies. See the vignette and examples for illustrations.

The maintenance release responds to call for updates from CRAN desiring that make all implicit dependencies on packages markdown and rmarkdown explicit via a Suggests: entry. Two of the many packages I maintain were part of the (large !!) list in the CRAN email, and this is one of them. While making the update, we refreshed two other packaging details.

Changes in version 0.0.7 (2021-04-16)

  • Add rmarkdown to Suggests: as an implicit conditional dependency

  • Switch vignette to minidown and its water framework, add minidown to Suggests as well

  • Update two URLs in the README.md file

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 as 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

Thu, 15 Apr 2021

Announcing ‘Introductions to Emacs Speaks Statistics’

A new website containing introductory videos and slide decks is now available for your perusal at ess-intro.github.io. It provides a series of introductions to the excellent Emacs Speaks Statistics (ESS) mode for the Emacs editor.

This effort started following my little tips, tricks, tools and toys series of short videos and slide decks “for the command-line and R, broadly-speaking”. Which I had mentioned to friends curious about Emacs, and on the ess-help mailing list. And lo and behold, over the fall and winter sixteen of us came together in one GitHub org and are now proud to present the initial batch of videos about first steps, installing, using with spaceemacs, customizing, and org-mode with ESS. More may hopefully fellow, the group is open and you too can join: see the main repo and its wiki.

This is in fact the initial announcement post, so it is flattering that we have already received over 350 views, four comments and twenty-one likes.

We hope it proves to be a useful starting point for some of you. The Emacs editor is quite uniquely powerful, and coupled with ESS makes for a rather nice environment for programming with data, or analysing, visualising, exploring, … data. But we are not zealots: there are many editors and environments under the sun, and most people are perfectly happy with their choice, which is wonderful. We also like ours, and sometimes someone asks ‘tell me more’ or ‘how do I start’. We hope this series satisifies this initial curiousity and takes it from here.

With that, my thanks to Frédéric, Alex, Tyler and Greg for the initial batch, and for everybody else in the org who chipped in with comments and suggestion. We hope it grows from here, so happy Emacsing with R from us!

/computers/misc | permanent link

Tue, 13 Apr 2021

RcppArmadillo 0.10.4.0.0 on CRAN: New Upstream ‘Plus’

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 852 other packages on CRAN.

This new release brings us the just release Armadillo 10.4.0. Upstream moves at a speed that is a little faster than the cadence CRAN likes. We release RcppArmadillo 0.10.2.2.0 on March 9; and upstream 10.3.0 came out shortly thereafter. We aim to accomodate CRAN with (roughly) monthly (or less frequent) releases) so by the time we were ready 10.4.0 had just come out.

As it turns, the full testing had a benefit. Among the (currently) 852 CRAN packages using RcppArmadillo, two were failing tests. This is due to a subtle, but important point. Early on we realized that it would be beneficial if the standard R control over random-number creation and seeding affected Armadillo too, which Conrad accomodated kindly with an optional RNG interface—which RcppArmadillo supplies. With recent changes he made, the R side saw normally-distributed draws (via the Armadillo interface) changed, which lead to the two changes. All hail unit tests. So I mentioned this to Conrad, and with the usual Chicago-Brisbane time difference late my evening a fix was in my inbox. The CRAN upload was then halted as I had missed that due to other changes he had made random draws from a Gamma would now call std::rand() which CRAN flags. Another email to Brisbane, another late (one-line) fix back and all was good. We still encountered one package with an error but flagged this as internal to that package’s setup, so Uwe let RcppArmadillo onto CRAN, I contacted that package’s maintainer—who was very receptive and a change should be forthcoming. So with all that we have 0.10.4.0.0 on CRAN giving us Armadillo 10.4.0.

The full set of changes follows. As Armadillo 10.3.0 was not uploaded to CRAN, its changes are included too.

Changes in RcppArmadillo version 0.10.4.0.0 (2021-04-12)

  • Upgraded to Armadillo release 10.4.0 (Pressure Cooker)

    • faster handling of triangular matrices by log_det()

    • added log_det_sympd() for log determinant of symmetric positive matrices

    • added ARMA_WARN_LEVEL configuration option, to control the degree of emitted warning messages

    • reduced the default degree of warning messages, so that failed decompositions, failed saving/loading, etc, no longer emit warnings

  • Apply one upstream corrections for arma::randn draws when using alternative (here R) generator, and arma::randg.

Changes in RcppArmadillo version 0.10.3.0.0 (2021-03-10)

  • Upgraded to Armadillo release 10.3 (Sunrise Chaos)

    • faster handling of symmetric positive definite matrices by pinv()

    • expanded .save() / .load() for dense matrices to handle coord_ascii format

    • for out of bounds access, element accessors now throw the more nuanced std::out_of_range exception, instead of only std::logic_error

    • improved quality of random numbers

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, 31 Mar 2021

Rcpp now used by 2250 CRAN packages!

2250 Rcpp packages

As of today, Rcpp stands at 2255 reverse-dependencies on CRAN. The graph on the left depicts the growth of Rcpp usage (as measured by Depends, Imports and LinkingTo, but excluding Suggests) over time. We actually crossed 2250 once a week ago, but “what CRAN giveth, CRAN also taketh” and counts can fluctuate. It had dropped back to 2248 a few days later.

Rcpp was first released in November 2008. It probably cleared 50 packages around three years later in December 2011, 100 packages in January 2013, 200 packages in April 2014, and 300 packages in November 2014. It passed 400 packages in June 2015 (when I tweeted about it), 500 packages in late October 2015, 600 packages in March 2016, 700 packages last July 2016, 800 packages last October 2016, 900 packages early January 2017, 1000 packages in April 2017, 1250 packages in November 2017, 1500 packages in November 2018, 1750 packages in August 2019, and then the big 2000 packages (as well as one in eight) in July 2020. The chart extends to the very beginning via manually compiled data from CRANberries and checked with crandb. The next part uses manually saved entries. The core (and by far largest) part of the data set was generated semi-automatically via a short script appending updates to a small file-based backend. A list of packages using Rcpp is available too.

Also displayed in the graph is the relative proportion of CRAN packages using Rcpp. The four per-cent hurdle was cleared just before useR! 2014 where I showed a similar graph (as two distinct graphs) in my invited keynote. We passed five percent in December of 2014, six percent July of 2015, seven percent just before Christmas 2015, eight percent in the summer of 2016, nine percent mid-December 2016, cracked ten percent in the summer of 2017 and eleven percent in 2018. Last year, along with passing 2000 package, we also passed 12.5 percent—so one more than in every eight CRAN packages depends on Rcpp. Stunning. There is more detail in the chart: how CRAN seems to be pushing back more and removing more aggressively (which my CRANberries tracks but not in as much detail as it could), how the growth of Rcpp seems to be slowing somewhat outright and even more so as a proportion of CRAN – as one would expect a growth curve to.

2250 user packages, and the continued growth, is truly mind-boggling. We can use the progression of CRAN itself compiled by Henrik in a series of posts and emails to the main development mailing list. Not that long ago CRAN itself did have only 1000 packages, then 5000, 10000, and here we are at over 17300 with Rcpp now at nearly 13.0% and still growing. Amazeballs.

The Rcpp team, recently grown in strength with the addition of Iñaki, continues to aim for keeping Rcpp as performant and reliable as it has been. A really big shoutout and Thank You! to all users and contributors of Rcpp for help, suggestions, bug reports, documentation or, of course, code.

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, 30 Mar 2021

x13binary 1.1.39-3 on CRAN: (Imperfect) Package Updates

A new release 1.1.39-3 of x13binary, of the X-13ARIMA-SEATS program by the US Census Bureau (with upstream release 1.1.39) is now on CRAN.

The x13binary package takes the pain out of installing X-13ARIMA-SEATS by making it a fully resolved CRAN dependency. For example, when installing the excellent seasonal package by Christoph, then X-13ARIMA-SEATS will get pulled in via the x13binary package and things just work. Just depend on x13binary and on all major OSs supported by R you should have an X-13ARIMA-SEATS binary installed which will be called seamlessly by the higher-level packages such as seasonal or gunsales. With this the full power of the what is likely the world’s most sophisticated deseasonalization and forecasting package is now at your fingertips and the R prompt, just like any other of the 17350+ CRAN packages. You can read more about this (and the seasonal package) in the Journal of Statistical Software paper by Christoph and myself.

This release was needed because the recent M1mac build was reporting leftover ‘detritus’ in the temporary directory, which we addressed with an explicit removal at end. We also addressed another CRAN Policy change since the last release, namely a conversion of the configure script from bash to sh.

Now, sadly, that second aspect blew up on Solaris, and the ‘detritus’ issue appears to be persist. By now Christoph and a colleague have installed R(-devel) on such an M1 machine, but still cannot reproduce. We will reach out to CRAN to learn more. A follow-up release 1.1.39-4 is likely.

The good news is that the standard macOS binary works on M1 as do other binaries thanks to the translation layer. We do however lack a genuine binary for Solaris so if any of the esteemed readers of this post happens to have access to R on Solaris along with a basic Fortran compiler, we would love to hear from you. Building X-13ARIMA-SEATS from source on Solaris should be straightforward, it is on the other OSs.

Courtesy of my CRANberries, there is also a diffstat report for this release showing changes 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/x13binary | permanent link

Sun, 28 Mar 2021

RcppSpdlog 0.0.5 on CRAN: New upstream versions

About three months after the last update, we can announce a new version 0.0.5 of RcppSpdlog. It contains releases 1.8.3, 1.8.4 and 1.8.5 of spdlog which were made in quick succession mid-week (while we were waiting on an update of CRAN’s own machinery) and was processed yesterday and 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.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.5 (2020-12-11)

  • Upgraded to upstream release spdlog 1.8.5 (and 1.8.4 and 1.8.3)

  • Small enhancements to DESCRIPTION files

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog 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, 20 Mar 2021

An Ode to Stable Interfaces: R and R Core Deserve So Much Praise

A few days ago, a friend and I were riffing about the wonderful stability of R and (subsets of) R packages. The rigorous ASAN/UBSAN/Valgrind/… checks, while at times frustrating for us package maintainers when we do not have easily replicable setups [1], really help in ensuring code quality. As do of course all other layers of quality control at CRAN, and for R. In passing, I mentioned there was an older blog post demonstrating a little power-law-alike behaviour between the most frequent R Core committer and everybody else.

So I was intrigued. Could we just pick up a blog post I had written in August of 2007, or almost fourteen years ago, and run it as is? [2]

Yes, we can.

Which is truly, truly awesome.

Back then I must have taken a minor shortcut and analysed just one calendar year of SVN that was pre-extracted (and a few more still exists here if one scrolls down). Maybe then I might not have had the r-devel SVN repo checkout. But these days (and for probably a decade now) I do, and just a few lines of bash get us a full log:

#!/bin/bash

## adjust as needed
svn=${HOME}/svn/r-devel

rev=$(cd ${svn} && svn info --show-item revision)
today=$(date +%Y-%m-%d)

echo -n "Extracting ${rev} revisions at ${today} ... "
(cd ${svn} && svn log --limit ${rev} ) | gzip -9 > svn-log-${today}.txt.gz
echo "done"

So that leads to one code adjustments given the different input source. But otherwise the first paragraph runs as is (and now gives us 49.2% for the amazing Prof Ripley):

logfile <- "svn-log-2021-03-20.txt.gz"

## cf http://dirk.eddelbuettel.com/blog/2007/08/11/
x <- readLines(logfile)
rx <- x[grep("^r",x)]
who <- gsub(" ","",sapply(strsplit(rx,"\\|"),"[",2))
twho <- table(who)
twho["ripley"]/sum(twho)

That is what one gets by trusting stable interfaces: code untouched for fourteen years runs unchanged.

R itself has had well over sixty releases since then, including two major and eighteen minor releases. Yet the code just runs, including the code for two graphs one can reproduce with the exact same code as we show next.

tod <- unlist(sapply(rx,function(x)strsplit(x,split=" ")[[1]][6]))
tod <- tod[who=="ripley"]

tz <- sub(pattern=".*(-[0-9]{4}).*",replacement="\\1",x=rx)
tz <- tz[who=="ripley"]
tz <- as.numeric(tz)/100
offset <- 3600*tz

z <- strptime(tod,format="%H:%M:%S")
hist(z,"hours",main="Ripley Commit Times in SVN TZ")

h <- z - offset
h <- format(h,format="%H")
h <- factor(as.numeric(h), levels=0:23)
## added as.vector() here to suppress a warning
dotchart(as.vector(table(h)), main="Ripley Commit Times, By Hour in GMT",
         labels=paste(0:23,1:24,sep=":"))

The code reproduces the chart from 2008, but this time uses the full twenty plus years of SVN history. I added just one as.vector() to suppress one new warning which appears under current R and which was presumably added in the fourteen years since (at the chart is produces without it too).

The remainder of the code also runs. I just added one library(zoo) my blog post had omitted. No other changes.

## rather extract both  date and time
dat <- unlist(sapply(rx, function(x) {
  txt <- strsplit(x,split=" ")[[1]]
  paste(txt[5], txt[6])
}))
## subset on Prof Ripley
dat <- dat[who == "ripley"]
## and convert to POSIXct, correcting by tz as well
datpt <- as.POSIXct(strptime(dat,format="%Y-%m-%d %H:%M:%S")) - offset

## turn into zoo -- we use a constant series of ones as each
## committ is taken as a timestamped event
library(zoo)
datzoo <- zoo(1, order.by=datpt)
## and use zoo to aggregate into commits per date
daily <- aggregate(datzoo, as.Date(index(datzoo)), sum)

## now plot as grey bars
plot(daily, col='darkgrey', type='h', lwd=2,
     ylab="Nb of SVN commits, three-week median",
     xlab="R release dates 2.5.0 and 2.5.1 shown in orange",
     main="The amazing Prof. Ripley")
## mark the two R releases of 2007
abline(v=c(as.Date("2007-04-24"),as.Date("2007-06-28")),col='orange',lwd=1.5)
## and do a quick centered rolling median
lines(rollmedian(daily, 21, align="center"), lwd=3)

It produces this chart spanning two decades of commits. [3]

The subtitle highlighting the then-most-recent releases is a little quaint now given that R has had eighten major.minor releases, and over sixty total releases, since then.

Stable and rigourously maintained interfaces are a fantastic resource that is dramatically under-appreciated. Efforts such as the ten-year reproduction challenge demonstrate that this really is not a given. Maybe instead of celebrating band aides (“look, I reproduce via code I have frozen in a virtual environment / container / machine / …”) we should celebrate languages, ecosystems, packages, … that allow us to rely on just the code itself.

Because we can.

And we should strengthen and reinforce that ability. And discourage rapid changes just for changes’ sake. Code running for a decade, or even longer, is a huge boon to everybody relying on it.

Three cheers to R Core.

[1] Docker containers would be really good, and a step above the specs in the README. Winston’s nice r-debug “sumo” container comes closest and helps a lot, and is updated regularly (which my earlier r-devel-san container is not).

[2] The post owes some of its code ideas to Ben Bolker and Simon Jackman, but links to now-stale prior affiliations of theirs.

[3] And the singularly impressive contributions charted remain unparalled, but were already the focus of the previous post. Yet over three times as a long period, they remain even more stunning.

Edit 2021-03-21: Two minor fixes for grammar and typing.

/computers/R | permanent link

Tue, 09 Mar 2021

RcppArmadillo 0.10.2.2.0 on CRAN: New Upstream Patch Release

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 841 other packages on CRAN.

This release brings us a second update within the Armadillo 10.2 series, one month after the initial release. Upstream work has commenced at a 10.3 series with first pre-releases which we are currently testing. If possible, CRAN release will continue to be at least one month apart (such as this time) but we continue to make interim releases available on the Rcpp drat repo repo.

The full set of changes follows.

Changes in RcppArmadillo version 0.10.2.2.0 (2021-03-09)

  • Upgraded to Armadillo release 10.2.2 (Cicada Swarm)

    • faster handling of subcubes

    • added tgamma()

    • added .brief_print() for abridged printing of matrices & cubes

    • expanded forms of trimatu() and trimatl() with diagonal specification to handle sparse matrices

    • expanded eigs_sym() and eigs_gen() with optional shift-invert mode

  • Removed debian/ directory from repository as packaging is on salsa.debian.org.

  • Relaxed tolerance on two cube tests on Windows to accomodate new 'gcc10-UCRT' builder.

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

Mon, 01 Mar 2021

RPushbullet 0.3.4: Small Update, Nicer Docs

RPpushbullet demo

Release 0.3.4 of the RPushbullet package arrived on CRAN today. RPushbullet interfaces the neat Pushbullet service for inter-device messaging, communication, and more. It lets you easily send (programmatic) alerts like the one to the left to your browser, phone, tablet, … – or all at once.

This release contains a contributed PR to better reflect an error code, and adds a mkdocs-material-based documentation site (just like a few other packages of mine). See below for more details.

Changes in version 0.3.4 (2021-03-01)

  • Return code checking using error code content if it exists (Thomas Shafer in #64).

  • Enabled GitHub Actions with encrypted JSON file for API access.

  • Added a package documentation website.

Courtesy of my CRANberries, there is also a diffstat report for this release. More details about the package are at the RPushbullet webpage and the RPushbullet 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/rpushbullet | permanent link

Wed, 24 Feb 2021

RcppSimdJson 0.1.4 on CRAN: Small Bugfix

A quick note to say that we finalized a bugfix release 0.1.5 of RcppSimdJson yesterday which got onto CRAN earlier 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 (also voted best talk).

This version brings a small fix to Windows where temporary filenames constructed from URLs (as for example constructed by our td package) need an extra sanization for a possible ‘?’ character. We will be addressing that properly “in due course” but for now a simple gsub() will do. The NEWS entry follows.

Changes in version 0.1.5 (2021-02-23)

  • Temporary filenames from request URLs need an extra path sanitization on Windows as seen with package td.

  • A few #nocov tags were added to the code.

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, 22 Feb 2021

pkgKitten 0.2.1: Now with roxygen2 support

kitten

A new release 0.2.1 of pkgKitten hit CRAN earlier today, and has been uploaded to Debian as well. pkgKitten makes it simple to create new R packages via a simple function invocation. A wrapper kitten.r exists in the littler package to make it even easier.

This release builds on the support for tinytest we added in release 0.2.0 by adding more optional support, this time for roxygen2. It also corrects a minor documentation snafu, and updates the CI use.

Changes in version 0.2.1 (2021-02-22)

  • A small documentation error was corrected (David Dalpiaz in #15).

  • A new option ‘bunny’ adds support for roxygen2.

  • Continuous integration now use run.sh from r-ci.

More details about the package are at the pkgKitten webpage, the pkgKitten docs site, and the pkgKitten GitHub repo.

Courtesy of my CRANberries site, 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/pkgkitten | permanent link

Thu, 18 Feb 2021

td 0.0.2 on CRAN: Updated and Expanded

The still very recent td package for accessing the twelvedata API for financial data has been updated and is now at version 0.0.2.

The time_series access point is now vectorised: supply a vector of symbols, and you receive list of data.frame (or xts) objects. See this tweet teasing out the earliest support for this new featire, and showing a quick four-securities plot. We also added simpler accessors get_quote() and get_price() rounding out the basic API support.

One first bug report alerting us to the fact that our use of RcppSimdJson requires an additional sanitizing of the temporary filename if used on Windows. We will fix that properly soon in new release 0.1.5 of that package; in the meantime you can get hot-fix binary 0.1.4.1 for Windows via install.packages("RcppSimdJson", repos="https://ghrr.github.io/drat") from the ghrr drat.

The NEWS entry follows.

Changes in version 0.0.2 (2021-02-18)

  • The time_series is now vectorised and can return a list of return objects when given a vector of symbols

  • The use of tools::R_user_dir() is now conditional on having R 4.0.0 or later, older versions can use env.var for api key

  • New helper function store_key to save api key.

  • New simple accessors get_quote and get_price

Courtesy of my CRANberries, there is a comparison to the previous release. For questions or comments use the issue tracker off the GitHub repo.

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

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

/code/td | permanent link

Wed, 17 Feb 2021

dang 0.0.13: New intradayMarketMonitor

sp500 intraday monitor

A new release of the dang package got to CRAN earlier today, a few months since the last relase. The dang package regroups a few functions of mine that had no other home as for example lsos() from a StackOverflow question from 2009 (!!) is one, this overbought/oversold price band plotter from an older blog post is another.

This release adds one function I tweeted about one month ago. It takes a function Josh Ulrich originally tweeted about in November with a reference to this gist. I refactored this into a proper functions and polished a few edges: the data now properly rolls off after a fixed delay (of two days), should work with other symbols (though we both focused on ^GSPC as a free (!!) real-time SP500 index (albeit only during trading hours), properly gaps between trading days and more. You can simply invoke it via

dang::intradayMarketMonitor()

and a chart just like the one here will grow (though there is no “state”: if you stop it, or reboot, or … the plot starts from scratch).

The short NEWS entry follows.

Changes in version 0.0.13 (2021-02-17)

  • New function intradayMarketMonitor based on an earlier gist-posted snippet by Josh Ulrich.

  • The CI setup was generalized as a test for 'r-ci' and is used essentially unchanged with three different providers.

Courtesy of my CRANberries, there is a comparison to the previous release. For questions or comments use the issue tracker off the GitHub repo.

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

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

/code/dang | permanent link

Sat, 13 Feb 2021

RcppFastFloat 0.0.2: New Function

The second release of RcppFastFloat is now on CRAN. The package wraps fastfloat, another nice library by Daniel Lemire who showed in a recent arXiv paper that one can convert character representations of ‘numbers’ into floating point at rates at or exceeding one gigabyte per second.

Thanks to Brendan, this release adds a helper function as.double2() modeled after the base R function but using, of course, the features from fast_float in RcppFastFloat.

Release notes follow.

Changes in version 0.0.2 (2021-02-13)

  • New function as.double2() demonstrating fast_float (Brendan in #1)

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

Fri, 12 Feb 2021

RcppSimdJson 0.1.4 on CRAN: New Improvements

Brendan and I are happy to share that a new RcppSimdJson release 0.1.4 arrived on CRAN earlier 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 (also voted best talk).

This version brings a new option to always return list types, tweaks to setting option in the the request and other small improvements. The NEWS entry follows.

Changes in version 0.1.4 (2021-02-12)

  • Support additional headers in fload (Dirk in #60).

  • Enable continuous integration via GitHub Actions using run.sh from r-ci repo (Dirk in #61, #62).

  • Add option to always return list to fparse()/fload() (Brendan in #65 closing #64).

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

Thu, 11 Feb 2021

td 0.0.1 on CRAN: New Finance Data Package

Thrilled to announce that a new package of mine just made it to CRAN: the td package accesses the twelvedata API for financial data.

Currently only the time_series REST access point is supported, but it is already supported with all meaningful options (we skipped only ‘JSON or CSV’ which makes no sense here) so for example any resolution between 1 minute and 1 month can be requested for any stock, etf or currency symbol for a wide array of exchanges. Historical access is available too via (optional) start and end dates. We return either raw JSON or a data.frame or an xts object making it trivial to call high-end plotting functions on the data–the project and repo pages show several examples.

As just one example, here is GME during the follies. We simply request via

> gme <- time_series("GME", "1min",
+                    start_date="2021-01-25 09:30:00",
+                    end_date="2021-02-04 16:00:00", as="xts")

(where the API key is either in a user-local config file accessed via the new-ish R function tools::R_user_dir("td") pointing at this package’s directory, or via an environment variable; either is accessed at package load or attachment) from which we can then plot via quantmod

> quantmod::chart_Series(gme, name=paste0(attr(gme, "symbol"), "/", attr(gme, "exchange")))

which shows how we also helpfully store metadata returned by twelvedata as extra attributes of the object. The chart is

You will need an API key to have up to 800 daily accesses for free, higher-performance plans (including websocket access) are available for paying customers too. I have only used the free API so far myself.

I plan to add quote and price support this weekend, and generalize the time series access to returning lists of objects as the API does in fact support multi-security access. As always, feedback is welcomed. Please post comments and suggestions 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/td | permanent link

Wed, 10 Feb 2021

RcppSMC 0.2.3 on CRAN: Updated Snapshot

A new release 0.2.3 of the RcppSMC package arrived on CRAN earlier today. Once again it progressed as a very quick pretest-publish within minutes of submission—thanks CRAN!

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.

This release somewhat belatedly merges a branch Leah had been working on and which we all realized “is ready”. We now have a good snapshot to base new work on, as maybe with the Google Summer of Code 2021.

Changes in RcppSMC version 0.2.3 (2021-02-10)

  • Addition of a Github Action CI runner (Dirk)

  • Switching to inheritance for the moveset rather than pointers to functions (Leah in #45).

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

Tue, 09 Feb 2021

RcppArmadillo 0.10.2.1.0: New Upstream Release

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 823 other packages on CRAN.

This release brings us Armadillo 10.2 with a few updates as detailed below in the list of changes. Upstream release 10.2 was made a couple of days ago, but we need to balance new upstream updates with a responsible release cadence at CRAN. As we needed a maintenance release in early January, I opted to wait four weeks with this one which hence gets us 10.2.0 and 10.2.1 at once. As tweeted (with a follow-up) it had yet another very smooth passage at CRAN so we again appreciate the excellent work of the CRAN maintainers and say Thank You!.

Anybody who desires more frequent updates show look at the RcppCore drat repo which provides more frequent interim updates. Here for example we also had 0.10.2.0.0 available for your testing pleasure.

Also of note is that here is now a Python variant pyarma for those who might want enjoy Armadillo with Python.

The full set of changes follows.

Changes in RcppArmadillo version 0.10.2.1.0 (2021-02-09)

  • Upgraded to Armadillo release 10.2.1 (Cicada Swarm)

    • faster handling of subcubes

    • added tgamma()

    • added .brief_print() for abridged printing of matrices & cubes

    • expanded forms of trimatu() and trimatl() with diagonal specification to handle sparse matrices

    • expanded eigs_sym() and eigs_gen() with optional shift-invert mode

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

Fri, 05 Feb 2021

RcppFastFloat 0.0.1: New Package, Already on CRAN

A new package, once again based on wonderful library by Daniel Lemire, is now on CRAN in its initial version 0.0.1. Daniel, in a recent arXiv paper shows that one can convert character representations of ‘numbers’ into floating point at rates at or exceeding one gigabyte per second. His tests show a fourfold gain over library functions such as strtod.

We put a simply package together showing use of the example parser, and containing a simple ‘all-in’ comparison benchmark (where we time the function call overhead as well) and get roughly 3x. See the repo for details; we are borring the table and figure here:

> source("comparison.R")
Unit: milliseconds
      expr      min       lq     mean   median       uq      max neval cld
     scanf 218.8936 224.1223 238.5650 227.1901 229.9116 1343.433   100   c
      atof 124.8087 127.3274 129.4104 128.5858 130.9138  146.334   100  b 
    strtod 124.5705 127.2157 129.1238 129.1042 130.7504  137.143   100  b 
      stod 127.1751 129.7343 131.7339 131.4854 133.1425  147.763   100  b 
 fastfloat  40.6219  41.3042  42.5729  42.3209  43.1738   57.788   100 a  
> 

Or in chart form:

Not much to say yet for the initial release:

Changes in version 0.0.1 (2021-01-31)

  • Initial version and CRAN upload

While the package was waiting to be added to CRAN, Brendan already added a potential as.double() replacement which will be in the next version.

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, 30 Jan 2021

RcppDate 0.0.2: Regular Update

RcppDate wraps the date library by Howard Hinnant for use with R. This header-only modern C++ library has been in pretty wide-spread use for a while now, and adds to C++11/C++14/C++17 what will be (with minor modifications) the ‘date’ library in C++20. Since the original 0.0.1 CRAN release I have also added this package along with RcppCCTZ and nanotime (which uses / requires both) to Debian so an apt based install is also possible for some.

Release 0.0.2 arrived on CRAN yesterday. It simply updates the included library to version upstream version 3.0.0, and touches up some packaging internals for continued integration.

Changes in version 0.0.2 (2021-01-29)

  • Added GitHub Actions CI via run.sh from r-ci

  • Updated to upstream version 3.0.0 (plus newer commits)

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, 23 Jan 2021

prrd 0.0.4: More tweaks

prrd facilitates the parallel running [of] reverse dependency [checks] when preparing R packages. It is used extensively for Rcpp, RcppArmadillo, RcppEigen, BH, and possibly others.

prrd screenshot image

The key idea of prrd is simple, and described in some more detail on its webpage and its GitHub repo. Reverse dependency checks are an important part of package development that is easily done in a (serial) loop. But these checks are also generally embarassingly parallel as there is no or little interdependency between them (besides maybe shared build depedencies). See the (dated) screenshot (running six parallel workers, arranged in split byobu session).

This release brings several smaller tweaks and improvements to the summary report that had accumulated in my use since the last realease last April. We also updated the CI runners as one does these days.

The release is summarised in the NEWS entry:

Changes in prrd version 0.0.4 (2021-01-23)

  • Report summary mode is now compact, more robust and reports extended CRAN summaries. (Dirk via several changes)

  • Continuous Integration now uses run.sh from r-ci

My CRANberries provides the usual summary of changes to the previous version. See the aforementioned webpage and its repo for details. For more questions or comments use the issue tracker off the GitHub repo.

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

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

/code/prrd | permanent link

Fri, 15 Jan 2021

Rcpp 1.0.6: Some Updates

rcpp logo

The Rcpp team is proud to announce release 1.0.6 of Rcpp which arrived at CRAN earlier today, and has been uploaded to Debian too. Windows and macOS builds should appear at CRAN in the next few days. This marks the first release on the new six-months cycle announced with release 1.0.5 in July. As reminder, interim ‘dev’ or ‘rc’ releases will often be available in the Rcpp drat repo; this cycle there were four.

Rcpp has become the most popular way of enhancing R with C or C++ code. As of today, 2174 packages on CRAN depend on Rcpp for making analytical code go faster and further (which is an 8.5% increase just since the last release), along with 207 in BioConductor.

This release features six different pull requests from five different contributors, mostly fixing fairly small corner cases, plus some minor polish on documentation and continuous integration. Before releasing we once again made numerous reverse dependency checks none of which revealed any issues. So the passage at CRAN was pretty quick despite the large dependency footprint, and we are once again grateful for all the work the CRAN maintainers do.

Changes in Rcpp patch release version 1.0.6 (2021-01-14)

  • Changes in Rcpp API:

    • Replace remaining few uses of EXTPTR_PTR with R_ExternalPtrAddr (Kevin in #1098 fixing #1097).

    • Add push_back and push_front for DataFrame (Walter Somerville in #1099 fixing #1094).

    • Remove a misleading-to-wrong comment (Mattias Ellert in #1109 cleaning up after #1049).

    • Address a sanitizer report by initializing two private bool variables (Benjamin Christoffersen in #1113).

    • External pointer finalizer toggle default values were corrected to true (Dirk in #1115).

  • Changes in Rcpp Documentation:

    • Several URLs were updated to https and/or new addresses (Dirk).
  • Changes in Rcpp Deployment:

    • Added GitHub Actions CI using the same container-based setup used previously, and also carried code coverage over (Dirk in #1128).
  • Changes in Rcpp support functions:

    • Rcpp.package.skeleton() avoids warning from R. (Dirk)

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) 2616 previous questions.

If you like this or other open-source work I do, you can sponsor me at GitHub. My sincere thanks to my current sponsors for me keeping me caffeinated.

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, 11 Jan 2021

BH 1.75.0-0: New upstream release, added Beast

Boost

Boost is a very large and comprehensive set of (peer-reviewed) libraries for the C++ programming language, containing well over 100 individual libraries. The BH package provides a sizeable subset of header-only libraries for use by R.

Version 1.75.0 of Boost was released in December, right on schedule with their April, August and December releases. I now try to follow these releases at a lower (annual) cadence and prepared BH 1.75.0-0 in mid-December. Extensive reverse-depends checks revealed a need for changes in a handful of packages whose maintainers I contacted then. With one exception, everybody responded in kind and brought updated packages to CRAN which permitted us to upload the package there two days ago. And thanks to this planned and coordinated upload, the package is now available on CRAN a mere two days later. My thanks to the maintainers of these packages for helping it along; this prompt responses really are appreciated. The version on CRAN is the same as the one the drat announced in this tweet asking for testing help. If you installed that version, you are still current as no changes were required since December and CRAN now contains same file.

This release adds one new library: Boost Beast, an http and websocket library built on top of Boost Asio. Other changes are highlighed below.

Changes in version 1.75.0-0 (2020-12-12)

  • Removed file NAMESPACE as the package has neither R code, nor a shared library to load

  • The file LICENSE_1_0.txt is now included (as requested in #73)

  • Added new beast library (as requested in #74)

  • Upgraded to Boost 1.75.0 (#75)

Via CRANberries, there is a diffstat report relative to the previous release. Its final line is quite impressive: 3485 files changed, 100838 insertions(+), 84890 deletions(-). Wow.

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

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

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

/code/bh | permanent link

Sun, 10 Jan 2021

RcppArmadillo 0.10.1.2.2: Minor update

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 802 other packages on CRAN.

This release was needed because we use the Matrix package for some (optional) tests related to sparse matrices, and a small and subtle change and refinement in the recent 1.3.0 release of Matrix required us to make an update for the testing. Nothing has changed in how we set up, or operate on, sparse matrices. My thanks to Binxiang and Martin Maechler for feedback and suggestion on the initial fix both Binxiang and I set up independently. At the same time we upgrade some package internals related to continuous integration (for that, also see my blog post and video from earlier this week). Lastly Conrad sent in a one-line upstream fix for dealing with NaN in sign().

The full set of changes follows.

Changes in RcppArmadillo version 0.10.1.2.2 (2021-01-08)

  • Correct one unit test for Matrix 1.3.0-caused changed (Binxiang in #319 and Dirk in #322).

  • Suppress one further warning from Matrix (Dirk)

  • Apply an upstream NaN correction (Conrad in #321)

  • Added GitHub Actions CI using run.sh from r-ci (Dirk)

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, 07 Jan 2021

#32: Portable Continuous Integration using r-ci

Welcome to the 32th post in the rarely raucous R recommendations series, or R4 for short. This post covers continuous integration, a topic near and dear to many of us who have to recognise its added value.

The popular and widely-used service at Travis is undergoing changes driven by a hard-to-argue with need for monetization. A fate that, if we’re honest, lies ahead for most “free” services so who know, maybe one day we have to turn away from other currently ubiquitous service. Because one never knows, it can pay off to not get to tied to any one service. Which brings us to today’s post and my r-ci service which allows me to run CI at Travis, at GitHub, at Azure, and on local Docker containers as the video demonstrates. It will likely also work at GitLab and other services, I simply haven’t tried any others.

The slides are here. The r-ci website introduces r-ci at a high-level. This repo at GitHub contains run.sh, and can be used to raise issues, ask questions, or provide feedback.

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/r4 | permanent link

Thu, 17 Dec 2020

RcppEigen 0.3.3.9.1: New upstream

A new release 0.3.3.9.1 of RcppEigen arrived on CRAN today (and just went to Debian too) bringing support for Eigen 3.3.9 to R. Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

The release started with a gentle nudge from the Stan team to package Eigen 3.3.8. And once I got around to it and sat down, Eigen 3.3.9 had just been released the previous day. The freshly prepared release 0.3.3.9.0 was then announced on Twitter (and the rcpp-devel mailing list) along with a request for testing alongside the usual extended reverse dependency checking we do (just like CRAN asks us to). And it turns out that Eigen 3.3.9 required an update to StanHeaders, a CRAN package that is itself quite widely used. This took a couple of days and its round of testing, but Ben Goodrich shipped it to CRAN last night, so we were able to ship RcppEigen in turn today.

So this release once again bring few required changes to Eigen (see this directory for details). As we said for the previous three 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.

I actually find this requirement rather annoying. Eigen is then only usable if you set, say,

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

as g++ options 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 0.3.3.9.1 (2020-12-17)

  • Upgraded to Eigen 3.3.9 (Dirk in #92 fixing #91).

  • Added GitHub Actions CI using run.sh from r-ci (Dirk)

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, 15 Dec 2020

RcppAnnoy 0.0.18: Tweaks

annoy image

A new maintenance release, now at version 0.0.18, of RcppAnnoy is now 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 famous Spotify music discovery algorithm.

This release is follow-up to release 0.0.17 which was made four weeks ago, and which brought the new upstream release 1.17 of Annoy. We now have an updated upstream with a PR by Aaron aiming for improved control of RNG seeding to ensure better reproducibility, along with extended tests and new helpers for RcppAnnoy and Annoy version numbers. The release was once again coordinated with Annoy and James whose BiocNeighbors and uwot packages both consume the Annoy header library shipped here.

Detailed changes follow below.

Changes in version 0.0.18 (2020-12-15)

  • Small tweaks to threading policy header defines (Dirk closing #65)

  • Vignette code is again compiled during testing (Aaron Lum and Dirk in #66 addressing #64)

  • Upstream code (with Aaron's PR) was synchronized once more (Dirk in #67)

  • A new helper function was added to report the Annoy version (Aaron in #68)

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.

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Fri, 11 Dec 2020

RcppSpdlog 0.0.4: New upstream

Not quite two months after the last release, we are happy to announce version 0.0.4 of RcppSpdlog. It contains release 1.8.2 of spdlog made today, along with version 7.1.3 of fmt.

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.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.4 (2020-12-11)

  • Upgraded to upstream release spdlog 1.8.2

  • Added GitHub Actions CI using run.sh from r-ci

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

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

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

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Thu, 03 Dec 2020

#31: Test your R package against bleeding-edge gcc

Welcome to the 31th post in the rapturously rampant R recommendations series, or R4 for short. This post will once again feature Docker for use with R.

Earlier this week, I received a note from CRAN about how my RcppTOML package was no longer building with the (as of right now of course unreleased) version 11 of the GNU C++ compiler, i.e. g++-11. And very kindly even included a hint about the likely fix (which was of course correct). CRAN, and one of its maintainers in particular, is extremely forward-looking in terms of toolchain changes. A year ago we were asked to updated possible use of global variables in C code as gcc-10 tightened the rules. This changes is a C++ one, and a fairly simple one of simply being more explicit with include headers. Previous g++ release had done the same.

The question now was about the least painful way to get g++-11 onto my machine, with the least amount of side-effects. Regular readers of this blog will know where this is headed, but even use of Docker requires binaries. A look at g++-11 within packages.debian.org comes up empty. No Debian means no Ubuntu. But … there is a PPA for Ubuntu with toolchain builds we have used before. And voilà there we have it: within the PPA for Ubuntu Toolchain repository is the volatile packages PPA with both g++-10 and g++-11. Here Ubuntu 20.10 works with g++-10, but g++-11 requires Ubuntu 21.04. Docker containers are there for either. So with the preliminaries sorted out, the key steps are fairly straightforward:

  • start from ubuntu:21.04 to be able to install g++-11 later
  • install the software-properties-common package to be able to add a PPA
  • (plus a few more packages to deal with the repository signing key)
  • run the sudo add-apt-repository ppa:ubuntu-toolchain-r/volatile command to add the volatile packages PPA
  • install g++-11 (along with, for good measure) gcc-11 and gfortran-11
  • use update-alternative (a clever Debian/Ubuntu command) to make version ‘11’ the default
  • install R itself (via r-base-core) which we simply take from the distro as 21.04 is by construction very recent
  • install Rcpp via the r-cran-rcpp binary which covers all dependencies for the package in question

And that is it! RcppTOML is fairly minimal and could be a member of the tinyverse so no other dependencies are needed—if your package has any you could just use the standard steps to install from source, or binary (including using RSPM or bspm). You can see the resulting Dockerfile which contains a minimal amount of extra stuff to deal with some environment variables and related settings. Nothing critical, but it smoothes the experience somewhat.

This container is now built (under label rocker/r-edge with tags latest and gcc-11), and you can download it from Docker Hub. With that the ‘proof’ of the (now fixed and uploaded) package building becomes as easy as

edd@rob:~/git/rcpptoml(master)$ docker run --rm -ti -v $PWD:/mnt -w /mnt rocker/r-edge:gcc-11 g++ --version
g++ (Ubuntu 11-20201128-0ubuntu2) 11.0.0 20201128 (experimental) [master revision fb6b29c85c4:a331ca6194a:e87559d202d90e614315203f38f9aa2f5881d36e]
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

edd@rob:~/git/rcpptoml(master)$ 
edd@rob:~/git/rcpptoml(master)$ docker run --rm -ti -v $PWD:/mnt -w /mnt rocker/r-edge:gcc-11 R CMD INSTALL RcppTOML_0.1.7.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘RcppTOML’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -DCPPTOML_USE_MAP -I'/usr/lib/R/site-library/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Fuvi9C/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -DCPPTOML_USE_MAP -I'/usr/lib/R/site-library/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-Fuvi9C/r-base-4.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c parse.cpp -o parse.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppTOML.so RcppExports.o parse.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-RcppTOML/00new/RcppTOML/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppTOML)
edd@rob:~/git/rcpptoml(master)$ 

I hope both the availability of such a base container with gcc-11 (and g++-11 and gfortran-11) as well as a “recipe” for building similar containers with newer clang version will help other developers.

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/r4 | permanent link

Wed, 02 Dec 2020

RcppTOML 0.1.7: Support for g++-11, Minor Updates

A new RcppTOML release arrived on CRAN earlier today evening. RcppTOML brings TOML to 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 has been making inroads with projects such as the Hugo static blog compiler, or the Cargo system of Crates (aka “packages”) for the Rust language.

CRAN had sent us a note that the package no longer compiled under the [unreleased, of course, never change, BDR ;-) ] g++-11 compiler, but were kind enough to hint that it was only lacking an #include <limits>. These things happen: newer compilers are generally more strict, and that is generally a good things. (Last year this time we prepped code for the more stringent view on global variables under gcc-10. Earlier g++ version had similar demands to clarify include headers.) I set up a simple Docker contain with on Ubuntu 21.04 with g++-11, R, and Rcpp to build the package and make this change (which was of course also PR’ed upstream at cpptoml), plus some other small ones that update the package since the last release roughly 18 months ago. We also switched CI use to the r-ci setup I should blog about a little more, removed a bashism and updated a few URLs. The bulleted list of changes in this version follows.

Changes in version 0.1.7 (2020-12-01)

  • Add #include <limits> to header file, also contributed upstream, to permit compilation under the (unreleased) g++-11.

  • Switch the simple cleanup script to sh.

  • Switch CI use to r-ci for focal and bspm.

  • Update several TOML URLs to https://toml.io/en/.

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

Mon, 30 Nov 2020

inline 0.3.17: Refactored and New Tests

A new release of the inline package arrived on CRAN this evening and has already been shipped to Debian as well. inline facilitates writing code in-line in simple string expressions or short files. The package was used quite extensively by Rcpp in the days before Rcpp Attributes arrived on the scene proving an even better alternative for its use cases. inline is still use by rstan and a number of other packages.

One of those other packages is mkin, and its author Johannes Ranke overhauled the saving and re-loading of C functions part with a really well-done set of contributions. In the process we also added unit testing via the lovely tinytest, and changed to continuous integration setup to r-ci.

See below for a detailed list of changes extracted from the NEWS file.

Changes in inline version 0.3.17 (2020-11-30)

  • Unit testing is now supported via tinytest (Johannes in #15 addressing #14).

  • CI was updated to use focal and run.sh from r-ci on Travis and GitHub Actions (Dirk)

  • The writing and reading of compiled code was refactored and extended (Johannes in #16 fixing #13).

  • Some minor problems related to CRAN checks and tests were corrected (Johannes and Dirk in #17, Johannes in #18, #19, #20).

  • Small stylistic updates have been applied to some R and Rd files (Dirk).

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

If you like this or other open-source work I do, you can now sponsor me at GitHub. For the first year, GitHub will match your contributions.

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/inline | permanent link

Mon, 16 Nov 2020

RcppArmadillo 0.10.1.2.0

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 779 other packages on CRAN.

This release ties up a few loose ends from the recent 0.10.1.0.0.

Changes in RcppArmadillo version 0.10.1.2.0 (2020-11-15)

  • Upgraded to Armadillo release 10.1.2 (Orchid Ambush)

  • Remove three unused int constants (#313)

  • Include main armadillo header using quotes instead of brackets

  • Rewrite version number use in old-school mode because gcc 4.8.5

  • Skipping parts of sparse conversion on Windows as win-builder fails

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 now sponsor me at GitHub. For the first year, GitHub will match your contributions.

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

RcppAnnoy 0.0.17

annoy image

A new release 0.0.17 of RcppAnnoy is now 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 famous Spotify music discovery algorithm.

This release brings a new upstream version 1.17, released a few weeks ago, which adds multithreaded index building. This changes the API by adding a new ‘threading policy’ parameter requiring code using the main Annoy header to update. For this reason we waited a little for the dust to settle on the BioConductor 3.12 release before bringing the changes to BiocNeighbors via this commit and to uwot via this simple PR. Aaron and James updated their packages accordingly so by the time I uploaded RcppAnnoy it made for very smooth sailing as we all had done our homework with proper conditional builds, and the package had no other issue preventing automated processing at CRAN. Yay. I also added a (somewhat overdue one may argue) header file RcppAnnoy.h regrouping defines and includes which should help going forward.

Detailed changes follow below.

Changes in version 0.0.17 (2020-11-15)

  • Upgrade to Annoy 1.17, but default to serial use.

  • Add new header file to regroup includes and defines.

  • Upgrade CI script to use R with bspm on focal.

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. For the first year, GitHub will match your contributions.

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 Nov 2020

tidyCpp 0.0.2: More documentation and features

A first update of the still fairly new package tidyCpp is now on CRAN. The packages offers a C++ layer on top of the C API for R which aims to make its use a little easier and more consistent.

The vignette has been extended with a new examples, a new section and some general editing. A few new defines have been added mostly from the Rinternals.h header. We also replaced the Shield class with a simpler yet updated version class Protect. The name better represent the core functionality of offering a simpler alternative to the PROTECT and UNPROTECT macro pairing. We also added a short discussion to the vignette of a gotcha one has to be mindful of, and that we fell for ourselves in version 0.0.1. We also added a typedef so that code using Shield can still be used.

The NEWS entry follows.

Changes in tidyCpp version 0.0.2 (2020-11-12)

  • Expanded definitions in internals.h to support new example.

  • The vignette has been extended with an example based on package uchardet.

  • Class Shield has been replaced by an new class Protect; a compatibility typdef has been added.

  • The examples and vignette have been clarified with respect to proper ownership of protected objects; a new vignette section was added.

Thanks to 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. For the first year, GitHub will match your contributions.

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/tidycpp | permanent link

Mon, 02 Nov 2020

RcppSimdJson 0.1.2: New Upstream, New Utilities

A new RcppSimdJson release arrived on CRAN late yesterday bringing along the one recently updated simdjson release 0.6.0.

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 (also voted best talk).

Other than the upstream update, Brendan added some new utilities to check for valid utf-8 or json format, and to minify json plus a small workaround for a clang-9 bug we encountered. We can confirm Daniel’s statement on ridiculously fast utf-8 validattion. It is so cool to work with amazing tools.

The NEWS entry follows.

Changes in version 0.1.3 (2020-11-01)

  • Added URLs to DESCRIPTION (Dirk closing #50).

  • Upgraded to simdjson 0.6.0 (Dirk in #52).

  • New policy option to always convert integers to int64_t (Brendan in #55 closing #54).

  • Added workaround for odd clang-9 bug (Brendan in #57).

  • New utility functions is_valid_utf8(), is_valid_json() and fminify() (Brendan in #58).

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. For the first year, GitHub will match your contributions.

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, 24 Oct 2020

digest 0.6.27: Build fix

Exactly one week after the previous release 0.6.26 of digest, a minor cleanup release 0.6.27 just arrived on CRAN and will go to Debian shortly.

digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, spookyhash, and blake3 algorithms) permitting easy comparison of R language objects. It is a fairly widely-used package (currently listed at one million monthly downloads, 282 direct reverse dependencies and 8068 indirect reverse dependencies, or just under half of CRAN) as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation.

Release 0.6.26 brought support for the (nice, even cryptographic) blake3 hash algorithm. In the interest of broader buildability we had already (with a sad face) disabled a few very hardware-specific implementation aspects using intrinsic ops. But to our chagrin, we left one #error define that raised its head on everybody’s favourite CRAN build platform. Darn. So 0.6.27 cleans that up and also removes the check and #error as … all the actual code was already commented out. If you read this and tears start running down your cheeks, then by all means come and help us bring blake3 to its full (hardware-accelerated) potential. This (probably) only needs a little bit of patient work with the build options and configurations. You know where to find us…

My CRANberries provides the usual summary of changes to the previous version.

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

If you like this or other open-source work I do, you can now sponsor me at GitHub. For the first year, GitHub will match your contributions.

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

/code/digest | permanent link

Fri, 23 Oct 2020

RcppSpdlog 0.0.3: New features and much more docs

A good month after the initial two releases, we are thrilled to announce relase 0.0.3 of RcppSpdlog. This brings us release 1.8.1 of spdlog as well as a few local changes (more below).

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 Zverovic.

This version of RcppSpdlog brings a new top-level function setLogLevel to control what events get logged, updates the main example to show this and to also make the R-aware logger the default logger, and adds both an extended vignette showing several key features and a new (external) package documentation site.

The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.3 (2020-10-23)

  • New function setLogLevel with R accessor in exampleRsink example

  • Updated exampleRsink to use default logger instance

  • Upgraded to upstream release 1.8.1 which contains finalised upstream use to switch to REprintf() if R compilation detected

  • Added new vignette with extensive usage examples, added compile-time logging switch example

  • A package documentation website was added

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

If you like this or other open-source work I do, you can now sponsor me at GitHub. For the first year, GitHub will match your contributions.

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, 21 Oct 2020

RcppZiggurat 0.1.6

ziggurats

A new release, now at version 0.1.6, of RcppZiggurat is now on the CRAN network for R.

The RcppZiggurat package updates the code for the Ziggurat generator by Marsaglia and other which provides very fast draws from a Normal distribution. The package provides a simple C++ wrapper class for the generator improving on the very basic macros, and permits comparison among several existing Ziggurat implementations. This can be seen in the figure where Ziggurat from this package dominates accessing the implementations from the GSL, QuantLib and Gretl—all of which are still way faster than the default Normal generator in R (which is of course of higher code complexity).

This release brings a corrected seed setter and getter which now correctly take care of all four state variables, and not just one. It also corrects a few typos in the vignette. Both were fixed quite a while back, but we somehow managed to not ship this to CRAN for two years.

The NEWS file entry below lists all changes.

Changes in version 0.1.6 (2020-10-18)

  • Several typos were corrected in the vignette (Blagoje Ivanovic in #9).

  • New getters and setters for internal state were added to resume simulations (Dirk in #11 fixing #10).

  • Minor updates to cleanup script and Travis CI setup (Dirk).

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

If you like this or other open-source work I do, you can now sponsor me at GitHub. For the first year, GitHub will match your contributions.

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 Oct 2020

RcppArmadillo 0.10.1.0.0

armadillo image

Armadillo is a powerful and expressive C++ template library for linear algebra aiming towards a good balance between speed and ease of use with a syntax deliberately close to a Matlab. RcppArmadillo integrates this library with the R environment and language–and is widely used by (currently) 786 other packages on CRAN.

A little while ago, Conrad released version 10.1.0 of Armadillo, a a new major release. As before, given his initial heads-up we ran two full reverse-depends checks, and as a consequence contacted four packages authors (two by email, two via PR) about a miniscule required change (as Armadillo now defaults to C++11, an old existing setting of avoiding C++11 lead to an error). Our thanks to those who promptly update their packages—truly appreciated. As it turns out, Conrad also softened the error by the time the release ran around.

But despite our best efforts, the release was delayed considerably by CRAN. We had made several Windows test builds but luck had it that on the uploaded package CRAN got itself a (completely spurious segfault—which can happen on a busy machine building machine things at once). Sadly it took three or four days for CRAN to reply our email. After which it took another number of days for them to ponder the behaviour of a few new ‘deprecated’ messaged tickled by at the most ten or so (out of 786) packages. Oh well. So here we are, eleven days after I emailed the rcpp-devel list about the new package being on CRAN but possibly delayed (due to that seg.fault). But during all that time the package was of course available via the Rcpp drat.

The changes in this release are summarized below as usual and are mostly upstream along with an improved Travis CI setup due to the aforementioned use of the bspm package for binaries at Travis.

Changes in RcppArmadillo version 0.10.1.0.0 (2020-10-09)

  • Upgraded to Armadillo release 10.1.0 (Orchid Ambush)

    • C++11 is now the minimum required C++ standard

    • faster handling of compound expressions by trimatu() and trimatl()

    • faster sparse matrix addition, subtraction and element-wise multiplication

    • expanded sparse submatrix views to handle the non-contiguous form of X.cols(vector_of_column_indices)

    • expanded eigs_sym() and eigs_gen() with optional fine-grained parameters (subspace dimension, number of iterations, eigenvalues closest to specified value)

    • deprecated form of reshape() removed from Cube and SpMat classes

    • ignore and warn on use of the ARMA_DONT_USE_CXX11 macro

  • Switch Travis CI testing to focal and BSPM

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 now sponsor me at GitHub. For the first year, GitHub will match your contributions.

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