Sun, 31 May 2020

T^4 #4: Introducing Byobu

The next video (following the announcement, and shells sessions one, two, and three) is up in the T^4 series of video lightning talks with tips, tricks, tools, and toys. This time we introduce the wonderful byobu tool which is called both a ‘text-based window manager’ and a ‘terminal multiplexer’:

The slides are here.

This repo at GitHub support the series: use it to open issues for comments, criticism, suggestions, or feedback.

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/t4 | permanent link

Sat, 30 May 2020

drat 0.1.6: Rewritten macOS binary support

drat user

A new version of drat arrived on CRAN overnight, once again taking advantage of the fully automated process available for such packages with few reverse depends and no open issues. As we remarked at the last release fourteen months ago when we scored the same nice outcome: Being a simple package can have its upsides…

This release is mostly the work of Felix Ernst who took on what became a rewrite of how binary macOS packages are handled. If you need to distribute binary packages for macOS users, this may help. Two more small updates were made, see below for full details.

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.

As your mother told you: Friends don’t let friends install random git commit snapshots. Rolled-up releases it is. drat is easy to use, documented by five vignettes and just works.

The NEWS file summarises the release as follows:

Changes in drat version 0.1.6 (2020-05-29)

  • Changes in drat functionality

    • Support for the various (current) macOS binary formats was rewritten (Felix Ernst in #89 fixing #88).

    • Travis CI use was updated to R 4.0.0 and bionic (Dirk).

    • A drat repo was added to the README (Thomas Fuller in #86)

Courtesy of 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. 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/drat | permanent link

Sun, 24 May 2020

#3 T^4: Customizing The Shell

The third video (following the announcement, the shell colors) one as well as last week’s shell prompt one, is up in the stil new T^4 series of video lightning talks with tips, tricks, tools, and toys. Today we cover customizing the shell some more.

The slides are here.

This repo at GitHub support the series: use it to open issues for comments, criticism, suggestions, or feedback.

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/t4 | permanent link

Sat, 23 May 2020

RcppSimdJson 0.0.5: Updated Upstream

A new RcppSimdJson release with updated upstream simdjson code just arrived on CRAN. RcppSimdJson wraps the fantastic and genuinely impressive simdjson library by Daniel Lemire and collaborators. Via some 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 use per byte parsed; see the video of the recent talk by Daniel Lemire at QCon (which was also voted best talk).

This release brings updated upstream code (thanks to Brendan Knapp) plus a new example and minimal tweaks. The full NEWS entry follows.

Changes in version 0.0.5 (2020-05-23)

  • Add parseExample from earlier upstream announcement (Dirk).

  • Synced with upstream (Brendan in #12) closing #11).

  • Updated example parseExample to API changes (Brendan).

Courtesy of 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

Sun, 17 May 2020

#2 T^4: Customizing The Shell Prompt

The second video (following the announcement and last week’s shell colors) is up in the stil new T^4 series of video lightning talks with tips, tricks, tools, and toys. Today we cover customizing shell prompts.

The slides are available here. Next week we likely continue on shell customization with aliases.

This repo at GitHub support the series: use it to open issues for comments, criticism, suggestions, or feedback.

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/t4 | permanent link

RcppArmadillo 0.9.880.1.0

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) 719 other packages on CRAN.

Conrad released a new upstream version 9.880.1 of Armadillo on Friday which I packaged and tested as usual (result log here in the usual repo). The R package also sports a new OpenMP detection facility once again motivated by macOS which changed its setup yet again.

Changes in the new release are noted below.

Changes in RcppArmadillo version 0.9.880.1.0 (2020-05-15)

  • Upgraded to Armadillo release 9.880.1 (Roasted Mocha Detox)

    • expanded qr() to optionally use pivoted decomposition

    • updated physical constants to NIST 2018 CODATA values

    • added ARMA_DONT_USE_CXX11_MUTEX confguration option to disable use of std::mutex

  • OpenMP capability is tested explicitly (Kevin Ushey and Dirk in #294, #295, and #296 all fixing #290).

Courtesy of 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

Fri, 15 May 2020

Let’s celebrate Anna!

Today is graduation at Washington University, and just like many other places, the ceremonies are a lot more virtual and surreal that in other years. For Anna today marks the graduation from Biomedical Engineering with a BSc. The McKelvey School of Engineering put a Zoom meeting together yesterday which was nice, and there is something more virtual here. Hopefully a real-life commencenment can take place in a year—the May 30, 2021, date has been set. The university also sent out a little commencement site/video which was cute. But at end of the day online-only still falls short of the real deal as we all know too well by now.

During those years, just about the only thing really I ever tweeted about appears to be soccer related. As it should because ball is life, as we all know. Here is one from 1 1/2 years ago when her Club Team three-peated in their NIRSA division:

And that opens what may be the best venue for mocking Anna: this year, which her a senior and co-captain, the team actually managed to loose a league game (a shocking first in these years) and to drop the final. I presume they anticipated that all we would all talk about around now is The Last Dance and three-peats, and left it at that. Probably wise.

Now just this week, and hence days before graduating with her B.Sc., also marks the first time Anna was addressed as Dr Eddelbuettel. A little prematurely I may say, but not too shabby to be in print already!

But on the topic of gratulations and what comes next, this tweet was very sweet:

As was this, which marked another impressive score:

So big thanks from all of us to WashU for being such a superb environment for Anna for those four years, and especially everybody at the Pappu Lab for giving Anna a home and base to start a research career.

And deepest and most sincere congratulations to Anna before the next adventure starts….

/misc | permanent link

Sun, 10 May 2020

#1 T^4: Adding Some Color to the Shell

The first proper video (following last week’s announcement) is up for new T^4 series of video lightning talks with tips, tricks, tools, and toys. Today we just to a little enhancement for the shell enabled color output (if not already on by default).

The slides are available here.

Next week we continue on shell customization by looking at the prompt.

Also of note, a new repo at GitHub to support the series: use it to open issues for comments, criticism, suggestions, or feedback.

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/t4 | permanent link

Sat, 09 May 2020

ttdo 0.0.5: Reflect tinytest update

A maintenance release of our (still small) ttdo package just arrived on CRAN. As introduced last fall, 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:

ttdo screenshot

tinytest has an extension mechanism we use, and as tinytest was just upgraded to version 1.2.0 changing, among other nice extensions, one interface by allowing for a new error class argument, we had to rebuild as well in order to document the new argument.

The release was actually prepared three days ago when tinytest itself was updated, but we waited for the binaries at CRAN to be updated and rebuilt to take advantage of the fully automated submission and test process at CRAN.

The NEWS entry follow.

Changes in ttdo version 0.0.5 (2020-05-06)

  • Rebuilt under tinytest 1.2.0 to add support for class argument in error-code test predicates

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. 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/ttdo | permanent link

Thu, 07 May 2020

Rcpp Virtual Talk on June 5

We had to cancel R/Finance 2020 due to what is happening all around us. But I plan to present the one-hour workshop I often give in the tutorial session preceding the first day—but this time online!

To keep it simple, we will stick with the same day, and possibly the same time: Friday morning at 8:00am! So that makes Friday, June 5, at 08:00h Central time.

This YouTube! link should then provide the stream, I reckon there may also be a recording afterwards.

The talk / demo / presentation will be about an hour long, and material should be similar to the previous ones (of the same length) still available at the talks page (which also has longer talks all the way to the two-day workshops).

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.

/misc | permanent link

Sun, 03 May 2020

#0: Introducing T^4: Tips, Tricks, Tools, and Toys

For way too long now something I had meant to start was a little series about tips, tricks, tools, and toys. I had mentioned the idea a few times to a friend or two, and generally received a thumbs up or a ‘go for it’. But it takes a little to get over the humb and get going. And it turns out that last week’s r^4 talk on upgrading to R 4.0.0 hit some latent demand as we are now at 1400 views on YouTube. Wowser.

So hence without further ado, let’s kick off T^4. Similar in spirit to R^4, but broader in scope and going beyond R. The opening slides explaining what we plan to do are here, and the video link follows below:

With some luck we should have the first actual talk next week. See you then!

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/t4 | permanent link

Mon, 27 Apr 2020

RcppArmadillo 0.9.870.2.0

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) 705 other packages on CRAN.

A new upstream release 9.870.2 of Armadillo was released a few days ago. We had tested two release candidates, and this caught one bug. The release was held up at CRAN for a few days as one package had an overly sensitive test depending on random input data; eventually we all convinced ourselves that there was no (Rcpp)Armadillo issue here. So morale: friends don’t let friends have tests depend on random behavior.

Changes in the new release are noted below.

Changes in RcppArmadillo version 0.9.870.2.0 (2020-04-24)

  • Upgraded to Armadillo release 9.870.2 (Roasted Mocha Retox)

    • faster handling of matrix multiplication expressions by diagvec() and diagmat()

    • added trimatu_ind() and trimatl_ind()

    • more consistent detection of sparse vector expressions

Courtesy of 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

Sun, 26 Apr 2020

#26: Upgrading to R 4.0.0

Welcome to the 26th post in the rationally regularized R revelations series, or R4 for short.

R 4.0.0 was released two days ago, and a casual glance at some social media conversations appears to suggest quite some confusion, almost certainly some misunderstandings, and possibly also a fair amount of fear, uncertainty, and doubt about the process. So I thought I could show how I upgrade my own main workstation, live and in colour without a safety net. (Almost: I did upgrade my laptop yesterday which went swimmingly, if more slowly.) So here is a fresh video about upgrading to R 4.0.0, with some support slides as usual:

The slides used in the video are at this link.

A few quick follow-ups to the ‘live’ nature of this. The pbdZMQ package did in fact install smoothly once the (Ubuntu) -dev packages for Zero MQ were (re-)installed; then IRkernel also followed. BioConductor completed once I realized that GOSemSim needed the annotation package GO.db to be updated, that allowed MNF to install. So the only bug, really, was the circular depdency between pkgload and testthat. Overall, not bad at all for a quick afternoon session!

And as mentioned, if you are interested and have questions concerning use of R on a .deb based system like Debain or Ubuntu (or Mint or …), the r-sig-debian list is a very good and friendly place to ask them.

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/r4 | permanent link

Sun, 19 Apr 2020

prrd 0.0.3: More improvements

Back in early 2018, the prrd package was introduced as release 0.0.1, uploaded to CRAN, and updated once as release 0.0.2. I have used it extensively for every CRAN release of Rcpp, RcppArmadillo, RcppEigen, BH, and possibly others.

The 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 and 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 following (dated) screenshot (running six parallel workers, arranged in split byobu session).

Since the two early releases, I made a few changes to e.g. the analysis of package checks and their summaries (but never pushed these) as well as a few usability enhancements. This release regroups these.

The release is summarised in the NEWS entry:

Changes in prrd version 0.0.3 (2020-04-19)

  • Extended functionality summarise() with optional use of package foghorn (Dirk)

  • New scripts enqueueDepends, dequeueDepends and summmariseJobs (Dirk)

  • Added tweaks and enhancements throughout (Dirk)

  • The default queue location can now be set via options (Dirk)

  • Meta-data on package, version and date is now stored, and shown on dequeue startup (Dirk)

  • The README.md was clarified and improved (Dirk, Avraham Adler in #8, Robert Nuske in #10)

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. 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/prrd | permanent link

Tue, 14 Apr 2020

RcppArmadillo 0.9.860.2.0

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) 706 other packages on CRAN.

A new upstream release 9.860.2 of Armadillo was just released. The theme of “convergence” continues; the previous release increased the minor from 800 to 850, now we are at 860. We first wrapped this up as version 0.9.859.1.0, but it turned out to have been held back by a buglet between R 4.0.0 and Rcpp which the recent patch release fixed (along with other woes on old R or non-CRAN-alike macOS). It then turns out that the new (upstream) version 9.860.1 had a minor bug which I missed as I reverse-depends checked the prior version. Doh. My thanks, as always, to CRAN for spotting this. The fix was added upstream and we have 9.860.2 as RcppArmadillo 0.9.860.2.0.

Changes in the new release are noted below.

Changes in RcppArmadillo version 0.9.860.2.0 (2020-04-13)

  • Upgraded to Armadillo release 9.860.2 (Roasted Mocha Fix)

    • Added powmat()

    • Faster access to columns in sparse submatrix views

    • Faster handling of relational expressions by accu()

    • Faster handling of sympd matrices by expmat(), logmat(), sqrtmat()

    • Workaround for save/load issues with HDF5 v1.12

  • Vignettes are now pre-made and include (#285)

  • Two test files are now skipped on 32-bit Windows

Courtesy of 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

gettz 0.0.4

A minor routine update 0.0.4 of gettz arrived on CRAN overnight.

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

This release adds registration of the compiled routine via R_registerRoutines() and R_useDynamicSymbols(), adds .registration=TRUE to useDynLib() in NAMESPACE, and uses an unquoted symbol in .Call(). Two new badges were added to the README.md as well. And as in the previous release in 2016: No new code, or new features.

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

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

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

Sun, 12 Apr 2020

#25: Test, test, test, … those R 4.0.0 binaries with Ubuntu 20.04 and Rocker

Welcome to the 25nd post in the randomly recurring R recitations series, or R4 for short.

Just yesterday, we posted a short post along with a video and supporting slides. It covered how to test the soon-to-be-released R 4.0.0 on a custom Ubuntu 18.04 Rocker container.

A container for Ubuntu 20.04, which is itself in final beta stages, was being built while the video was made. As it is available now, we created a quick follow-up video showing the use under Ubuntu 20.04:

The updated supporting slides from the video are still at this link.

What we showed in both videos does of course also work directly on Ubuntu (or Debian, using those source repos) installations; the commands shown in the Rocker use case generally apply equally to a normal installation.

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/r4 | permanent link

Sat, 11 Apr 2020

#24: Test, test, test, … those R 4.0.0 binaries with Ubuntu and Rocker

Welcome to the 24nd post in the relentlessly regular R ravings series, or R4 for short.

R 4.0.0 will be released in less than two weeks, and testing is very important. I had uploaded two alpha release builds (at the end of March and a good week ago) as well as a first beta release yesterday, all to the Debian ‘experimental’ distribution (as you can see here) tracking the release schedule set by Peter Dalgaard. Because R 4.0.0 will require reinstallation of all packages, it makes some sense to use a spare machine. Or a Docker container. So to support that latter mode, I have now complemented the binaries created from the r-base source package with all base and recommended packages, providing a starting point for actually running simple tests. Which is what we do in the video, using again the ‘R on Ubuntu (18.04)’ Rocker container:

Slides from the video are at this link.

This container based on 18.04 is described here on the Docker Hub; a new 20.04 container with the pre-release of the next Ubuntu LTS should be there shortly once it leaves the build queue.

What we showed does of course also work on direct Ubuntu (or Debian, using those source repos) installations; the commands shown in the Rocker use case generally apply equally to a normal installation.

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/r4 | permanent link

Thu, 09 Apr 2020

Rcpp 1.0.4.6: Bug fix interim version

rcpp logo

Rcpp 1.0.4 was released on March 17, following the usual sequence of fairly involved reverse-depends check along with a call for community testing issued weeks before the release. In that email I specifically pleaded with folks to pretty-please test non-standard setups:

It would be particularly beneficial if those with “unsual” build dependencies tested it as we would increase overall coverage beyond what I get from testing against 1800+ CRAN packages. BioConductor would also be welcome.

Alas, you can’t always get what you want. Shortly after the release we were made aware that the two (large) pull request at the book ends of the 1.0.3 to 1.0.4 release period created trouble. Of these two, the earliest PR in the 1.0.4 release upset older-than-CRAN-tested installation, i.e. R 3.3.0 or before. (Why you’d want to run R 3.3.* when R 3.6.3 is current is something I will never understand, but so be it.) This got addressed in two new PRs. And the matching last PR had a bit of sloppyness leaving just about everyone alone, but not all those macbook-wearing data scientists when using newer macOS SDKs not used by CRAN. In other words, “unsual” setups. But boy, do those folks have an ability to complain. Again, two quick PRs later that was addressed. Along came a minor PR with two more Rcpp::Shield<> uses (as life is too short to manually count PROTECT and UNPROTECT). And then a real issue between R 4.0.0 and Rcpp first noticed with RcppParallel builds on Windows but then also affecting RcppArmadillo. Another quickly issued fix. So by now the count is up to six, and we arrived at Rcpp 1.0.4.6.

Which is now on CRAN, after having sat there for nearly a full week, and of course with no reason given. Because the powers that be move in mysterious ways. And don’t answer to earthlings like us.

As may transpire here, I am little tired from all this. I think we can do better, and I think we damn well should, or I may as well throw in the towel and just release to the drat repo where each of the six interim versions was available for all to take as soon as it materialized.

Anyway, here is the state of things. Rcpp has become the most popular way of enhancing R with C or C++ code. As of today, 1897 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 191 in BioConductor. And per the (partial) logs of CRAN downloads, we are running steasy at one millions downloads per month.

The changes for this interim version are summarized below.

Changes in Rcpp patch release version 1.0.4.6 (2020-04-02)

  • Changes in Rcpp API:

    • The exception handler code in #1043 was updated to ensure proper include behavior (Kevin in #1047 fixing #1046).

    • A missing Rcpp_list6 definition was added to support R 3.3.* builds (Davis Vaughan in #1049 fixing #1048).

    • Missing Rcpp_list{2,3,4,5} definition were added to the Rcpp namespace (Dirk in #1054 fixing #1053).

    • A further updated corrected the header include and provided a missing else branch (Mattias Ellert in #1055).

    • Two more assignments are protect with Rcpp::Shield (Dirk in #1059)

  • Changes in Rcpp Attributes:

    • Empty strings are not passed to R CMD SHLIB which was seen with R 4.0.0 on Windows (Kevin in #1062 fixing #1061).
  • Changes in Rcpp Deployment:

    • Travis CI unit tests now run a matrix over the versions of R also tested at CRAN (rel/dev/oldrel/oldoldrel), and coverage runs in parallel for a net speed-up (Dirk in #1056 and #1057).

Thanks to 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) 2356 previous questions.

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

Fri, 03 Apr 2020

RcppSimdJson 0.0.4: Even Faster Upstream!

A new (upstream) simdjson release was announced by Daniel Lemire earlier this week, and my Twitter mentions have been running red-hot ever since as he was kind enough to tag me. Do look at that blog post, there is some impressive work in there. We wrapped up the (still very simple) rcppsimdjson around it last night and shipped it this morning.

RcppSimdJson wraps the fantastic and genuinely impressive simdjson library by Daniel Lemire. Via some 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. For illustration, I highly recommend the video of the recent talk by Daniel Lemire at QCon (which was also voted best talk). 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 use per byte parsed.

This release brings upstream 0.3 (and 0.3.1) plus a minor tweak (also shipped back upstream). Our full NEWS entry follows.

Changes in version 0.0.4 (2020-04-03)

  • Upgraded to new upstream releases 0.3 and 0.3.1 (Dirk in #9 closing #8)

  • Updated example validateJSON to API changes.

But because Daniel is such a fantastic upstream developer to collaborate with, he even filed a full feature-request ‘maybe you can consider upgrading’ as issue #8 at our repo containing the fully detailed list of changes. As it is so impressive I will simple quote the upper half of just the major changes:

Highlights

  • Multi-Document Parsing: Read a bundle of JSON documents (ndjson) 2-4x faster than doing it individually. API docs / Design Details
  • Simplified API: The API has been completely revamped for ease of use, including a new JSON navigation API and fluent support for error code and exception styles of error handling with a single API. Docs
  • Exact Float Parsing: Now simdjson parses floats flawlessly without any performance loss (https://github.com/simdjson/simdjson/pull/558). Blog Post
  • Even Faster: The fastest parser got faster! With a shiny new UTF-8 validator and meticulously refactored SIMD core, simdjson 0.3 is 15% faster than before, running at 2.5 GB/s (where 0.2 ran at 2.2 GB/s).

For questions, suggestions, or issues please use the issue tracker at the GitHub repo.

Courtesy of 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, 02 Apr 2020

RQuantLib 0.4.12: Small QuantLib 1.18 update

A new release 0.4.12 of RQuantLib arrived on CRAN today, and was uploaded to Debian as well.

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

This version does relatively little. When QuantLib 1.18 came out, I immediately did my usual bit of packaging it for Debian as well creating binaries via my Ubuntu PPA so that I could test the package against it. And a few call from RQuantLib are now hitting interface functions marked as ‘deprecated’ leading to compiler nags. So I fixed that in PR #146. And today CRAN sent me email to please fix in the released version—so I rolled this up as 0.4.12. Not other changes.

Changes in RQuantLib version 0.4.12 (2020-04-01)

  • Changes in RQuantLib code:

    • Calls deprecated-in-QuantLib 1.18 were updated (Dirk in #146).

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

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

Sat, 28 Mar 2020

RProtoBuf 0.4.17: Robustified

A new release 0.4.17 of RProtoBuf is now on CRAN. RProtoBuf provides R with bindings for the Google Protocol Buffers (“ProtoBuf”) data encoding and serialization library used and released by Google, and deployed very widely in numerous projects as a language and operating-system agnostic protocol.

This release contains small polishes related to the release 0.4.16 which added JSON support for messages, and switched to ByteSizeLong. This release now makes sure JSON functionality is only tested where available (on version 3 of the Protocol Buffers library), and that ByteSizeLong is only called where available (version 3.6.0 or later). Of course, older versions build as before and remain fully supported.

Changes in RProtoBuf version 0.4.17 (2020-03-xx)

  • Condition use of ByteSizeLong() on building with ProtoBuf 3.6.0 or later (Dirk in #71 fixing #70).

  • The JSON unit tests are skipped if ProtoBuf 2.* is used (Dirk, also #71).

  • The configure script now extracts the version from the DESCRIPTION file ( (Dirk, also #71).

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

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

Tue, 24 Mar 2020

New package RcppDate 0.0.1 now on CRAN!

A new small package with a new C++ header library is now on CRAN. It brings the date library by Howard Hinnant to R. This 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. I had been aware of it for a while, but not needed thanks to CCTZ library out of Google and our RcppCCTZ package. And like CCTZ, it builds upon std::chron adding a whole lot of functionality and useability enhancement. But a some upcoming (and quite exciting!) changes in nanotime required it, I had a reason to set about packaging it as RcppDate. And after a few days of gestation and review it is now available via CRAN.

Two simple example files are included and can be accessed by Rcpp::sourceCpp(). Some brief excerpts follow.

The first example shows three date constructors. Note how the month (and the leading digits) are literals. No quotes for strings anywhere. And no format (just like our anytime package for R).

  constexpr auto x1 = 2015_y/March/22;
  constexpr auto x2 = March/22/2015;
  constexpr auto x3 = 22_d/March/2015;

Note that these are constexpr that resolve at compile-time, and that the resulting year_month_day type is inferred via auto.

A second example constructs the last day of the months similarly:

  constexpr auto x1 = 2015_y/February/last;
  constexpr auto x2 = February/last/2015;
  constexpr auto x3 = last/February/2015;

For more, see the copious date.h documentation.

The (very bland first) NEWS entry (from a since-added NEWS file) for the initial upload follows.

Changes in version 0.0.1 (2020-01-17)

  • Initial CRAN upload of first version

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, 19 Mar 2020

RProtoBuf 0.4.16: Now with JSON

A new release 0.4.16 of RProtoBuf is now on CRAN. RProtoBuf provides R with bindings for the Google Protocol Buffers (“ProtoBuf”) data encoding and serialization library used and released by Google, and deployed very widely in numerous projects as a language and operating-system agnostic protocol.

This release contains a PR contributed by Siddhartha Bagaria which adds JSON support for messages, which had been an open wishlist item. I also appeased a clang deprecation warning that had come up on one of the CRAN test machines.

Changes in RProtoBuf version 0.4.16 (2020-03-19)

  • Added support for parsing and printing JSON (Siddhartha Bagaria in #68 closing wishlist #61).

  • Switched ByteSize() to ByteSizeLong() to appease clang (Dirk).

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

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

Wed, 18 Mar 2020

RcppCCTZ 0.2.7

A new release 0.2.7 of RcppCCTZ is now at CRAN.

RcppCCTZ uses Rcpp to bring CCTZ to R. CCTZ is a C++ library for translating between absolute and civil times using the rules of a time zone. In fact, it is two libraries. One for dealing with civil time: human-readable dates and times, and one for converting between between absolute and civil times via time zones. And while CCTZ is made by Google(rs), it is not an official Google product. The RcppCCTZ page has a few usage examples and details. This package was the first CRAN package to use CCTZ; by now at least three others do—using copies in their packages which remains less than ideal.

This version adds internal extensions, contributed by Leonardo, which support upcoming changes to the nanotime package we are working on.

Changes in version 0.2.7 (2020-03-18)

  • Added functions _RcppCCTZ_convertToCivilSecond that converts a time point to the number of seconds since epoch, and _RcppCCTZ_convertToTimePoint that converts a number of seconds since epoch into a time point; these functions are only callable from C level (Leonardo in #34 and #35).

  • Added function _RcppCCTZ_getOffset that returns the offset at a speficied time-point for a specified timezone; this function is only callable from C level (Leonardo in #32).

We also have a diff to the previous version thanks to CRANberries. More details are at the RcppCCTZ page; code, issue tickets etc at the GitHub repository.

If you like this or other open-source work I do, you can now sponsor me at GitHub. 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, 17 Mar 2020

Rcpp 1.0.4: Lots of goodies

rcpp logo

The fourth maintenance release 1.0.4 of Rcpp, following up on the 10th anniversary and the 1.0.0. release sixteen months ago, arrived on CRAN this morning. This follows a few days of gestation at CRAN. To help during the wait we provided this release via drat last Friday. And it followed a pre-release via drat a week earlier. But now that the release is official, Windows and macOS binaries will be built by CRAN over the next few days. The corresponding Debian package will be uploaded as a source package shortly after which binaries can be built.

As with the previous releases Rcpp 1.0.1, Rcpp 1.0.2 and Rcpp 1.0.3, we have the predictable and expected four month gap between releases which seems appropriate given both the changes still being made (see below) and the relative stability of Rcpp. It still takes work to release this as we run multiple extensive sets of reverse dependency checks so maybe one day we will switch to six month cycle. For now, four months still seem like a good pace.

Rcpp has become the most popular way of enhancing R with C or C++ code. As of today, 1873 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 191 in BioConductor. And per the (partial) logs of CRAN downloads, we are running steasy at one millions downloads per month.

This release features quite a number of different pull requests by seven different contributors as detailed below. One (personal) highlight is the switch to tinytest.

Changes in Rcpp version 1.0.4 (2020-03-13)

  • Changes in Rcpp API:

    • Safer Rcpp_list*, Rcpp_lang* and Function.operator() (Romain in #1014, #1015).

    • A number of #nocov markers were added (Dirk in #1036, #1042 and #1044).

    • Finalizer calls clear external pointer first (Kirill Müller and Dirk in #1038).

    • Scalar operations with a rhs matrix no longer change the matrix value (Qiang in #1040 fixing (again) #365).

    • Rcpp::exception and Rcpp::stop are now more thread-safe (Joshua Pritikin in #1043).

  • Changes in Rcpp Attributes:

    • The cppFunction helper now deals correctly with mulitple depends arguments (TJ McKinley in #1016 fixing #1017).

    • Invisible return objects are now supported via new option (Kun Ren in #1025 fixing #1024).

    • Unavailable packages referred to in LinkingTo are now reported (Dirk in #1027 fixing #1026).

    • The sourceCpp function can now create a debug DLL on Windows (Dirk in #1037 fixing #1035).

  • Changes in Rcpp Documentation:

    • The .github/ directory now has more explicit guidance on contributing, issues, and pull requests (Dirk).

    • The Rcpp Attributes vignette describe the new invisible return object option (Kun Ren in #1025).

    • Vignettes are now included as pre-made pdf files (Dirk in #1029)

    • The Rcpp FAQ has a new entry on the recommended importFrom directive (Dirk in #1031 fixing #1030).

    • The bib file for the vignette was once again updated to current package versions (Dirk).

  • Changes in Rcpp Deployment:

    • Added unit test to check if C++ version remains remains aligned with the package number (Dirk in #1022 fixing #1021).

    • The unit test system was switched to tinytest (Dirk in #1028, #1032, #1033).

Please note that the change to execptions and Rcpp::stop() in pr #1043 has been seen to have a minor side effect on macOS issue #1046 which has already been fixed by Kevin in pr #1047 for which I may prepare a 1.0.4.1 release for the Rcpp drat repo in a day or two.

Thanks to 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) 2356 previous questions.

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, 14 Mar 2020

RcppAPT 0.0.6

A new version of RcppAPT – our interface from R to the C++ library behind the awesome apt, apt-get, apt-cache, … commands and their cache powering Debian, Ubuntu and the like – is now on CRAN.

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.

This new version corrects builds failures under the new and shiny Apt 2.0 release (and the pre-releases like the 1.9.* series in Ubuntu) as some header files moved around. My thanks to Kurt Hornik for the heads-up. I accomodated the change in the (very simple and shell-based) configure script by a) asking pkg-config about the version of pkg-apt and then using that to b) compare to a ‘threshold value’ of ‘1.9.0’ and c) setting another compiler #define if needed so that d) these headers could get included if defined. The neat part is that a) and b) are done in an R one-liner, and the whole script is still in shell. Now, CRAN being CRAN, I now split the script into two: one almost empty one not using bash that passes the ‘omg but bash is not portable’ test, and which calls a second bash script doing the work. Fun and games…

The full set of changes follows.

Changes in version 0.0.6 (2020-03-14)

  • Accomodate Apt 2.0 code changes by including more header files

  • Change is backwards compatible and conditional

  • Added configure call using pkg-config and package version comparison (using R) to determine if the define is needed

  • Softened unit tests as we cannot assume optional source deb information to be present, so demo code runs but zero results tolerated

Courtesy of 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. 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 Mar 2020

RInside 0.2.16

A new release 0.2.16 of RInside arrived on CRAN and in Debian today. This comes almost exactly one year after the previous release 0.2.15. RInside provides a set of convenience classes which facilitate embedding of R inside of C++ applications and programs, using the classes and functions provided by Rcpp.

This release brings one new feature, contributed by Lance Bachmeier (with some additional post-processing by me). It adds the ability to embed and call R from C programs and applications. The interface is more limited as we do not get Rcpp for automagic conversion. But this offers the door to a number of applications supporting plain C interface, and the new examples directory for example shows one for ruby. We may add others.

The short list of changes since the last release were:

Changes in RInside version 0.2.16 (2020-03-12)

  • RInside is now embeddable (with a reduced interface) from C applications thanks to Lance Bachmeier (who is now co-author) plus some polish by Dirk in #43)

  • Added R_SESSION_INIIALIZED to list of excluded variables.

  • Added simple diagnostics function to have a registered function.

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

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

Wed, 11 Mar 2020

AsioHeaders 1.12.2-1

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

This release corresponds to a minor upstream update, and is only the second update ever. It may help overcome one santizer warning which David Hall brought to my attention. We tested this version against all reverse depends (which was easy enough as there are only three).The NEWS entry follows.

Changes in version 1.12.2-1 (2020-03-11)

  • Upgraded to Asio 1.12.2 (Dirk in #4 fixing #3)

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

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

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

/code/asioheaders | permanent link

Sun, 08 Mar 2020

RcppAnnoy 0.0.16

annoy image

A new release 0.0.16 of RcppAnnoy is available via the Github-hosted R Repository (ghrr). Edit a good two hours later: And wonder of wonders, now also on CRAN.

It remains in limbo at CRAN for no apparent reason. No change appears to be imminent either as the CRAN maintainers continue to play a passive-aggressive game of no communication for any reason. Which is a genuine shame as e [E]verbody involved in the package, i.e. Erik (upstream) and myself but also Aaron (downstream) worked pretty hard and well last weekend (while I was traveling / attending the wonderful celebRtion 2020 conference for the 20th anniversary of the R 1.0.0) to iron out all remaining issues. Installation is pretty flawless and silent as all compiler warnings have been takeb care of even under -pedantic on a recent version, and the last remaining UBSAN issue is also fixed.

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.

As I wrote in the announcement for 0.0.15 which fixed many-but-not-all issues:

The other important issue is that there will be another 0.0.16 release real soon to incorporate three more small upstream PRs driven by these discussions which kept going on post-release while I was conferencing (or traveling), and which should fix things for good, or so we hope. This should go out probably by the end of the week to not exceed a weekly upload cadence; if you want to see more, or get earlier access, see the git repo which is in fine shape. If you want to see a pre-release on the ghrr drat drop me a line.

As CRAN is holding the package hostage, all I can do now is to release to the Github-hosted R Repository (ghrr) from where you can install it via a simple install.packages("RcppAnnoy", repos="https://ghrr.github.io/drat") (or any of the other drat supported commands, see the ghrr page for more). Or wait and wait and wait … until CRAN graces us with a manual admission (given that the previous upload left one small UBSAN issue to fix). One day. Hopefully. The package is now on CRAN.

Detailed changes follow below.

Changes in version 0.0.16 (2020-03-06)

  • Use int in two interfaces (Dirk in #59 for upstream PR 460 and closing #56).

  • Use inline for two helper functions (Dirk in #59 for upstream PR 461 and closing #57; also Aaron in #58 after earlier discussion).

  • Removed a noisy pragma (Dirk in #60 for upstream PR 462).

  • Add a simple helper function displaying compiler status.

Courtesy of CRANberries, there will also be diffstat report if and when the package ever makes it to CRAN. 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

Wed, 04 Mar 2020

RcppSimdJson 0.0.3: Second Update!

Following up on both the initial RcppSimdJson release and the first update, the second update release 0.0.3 arrived on CRAN yesterday.

RcppSimdJson wraps the fantastic simdjson library by Daniel Lemire which is truly impressive. Via some very clever algorithmic engineering to obtain largely branch-free code, coupled with modern C++ and newer compiler instructions, it results in persing gigabytes of JSON parsed per second which is quite mindboggling. For illustration, I highly recommend the video of the recent talk by Daniel Lemire at QCon (which was also voted best talk). 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 use per byte parsed.

This release once again syncs the simdjson headers with upstream, and strengthens the build setup a little bit more. We only turn C++17 (which is needed) on when R knows it (from its builds), report the architecture status at package load (in a suppressable message), and only attempt to parse in examples and unit tests when know that we are on a sufficient platform. The full NEWS entry follows.

Changes in version 0.0.3 (2020-03-03)

  • Sychronized once more with upstream.

  • Created new C++ function to check for unsupported architecture, and report the status on package load.

  • Only run example and unit tests if supported architecture is found.

  • Created small configure script to see if R was built with C++17 support, and record it in src/Makevars.

For questions, suggestions, or issues please use the issue tracker at the GitHub repo.

Courtesy of 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

Mon, 02 Mar 2020

RcppAnnoy 0.0.15

annoy image

A few days ago, a new release 0.0.15 of RcppAnnoy got onto CRAN while I was traveling / attending the wonderful celebRtion 2020 for the 20th anniversary of the R 1.0.0 release.

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 releases makes great strides towards avoiding long-standing SAN/UBSAN issues. Upstream author Erik has been most helpful, as has been the feedback and input from two downstream users of RcppAnnoy, namely Aaron and James. This 0.0.15 release addresses one key, and longstanding, SAN/UBSAN issue. It is actually rather tricky as the code, for efficiency reason, bounces at the edge of what can be done. But a small rearrangement suppresses one such message which is good. We also got a hint from CRAN (thanks for that as always) to re-read one section of Writing R Extensions to make alloca more portable so that Solaris does not have to cry, and Bill Venables kindly helped with a small correction to the docs.

The other important issue is that there will be another 0.0.16 release real soon to incorporate three more small upstream PRs driven by these discussions which kept going on post-release while I was conferencing (or traveling), and which should fix things for good, or so we hope. This should go out probably by the end of the week to not exceed a weekly upload cadence; if you want to see more, or get earlier access, see the git repo which is in fine shape. If you want to see a pre-release on the ghrr drat drop me a line.

Detailed changes follow below.

Changes in version 0.0.15 (2020-02-25)

  • RcppAnnoy synchronized with upstream PR 455 (Dirk in #55).

  • The help page has a small correction thanks to Bill1 Venables.

  • The alloca() function is now declared portably thanks to a working example in Writing R Extensions.

Courtesy of 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

Sat, 22 Feb 2020

digest 0.6.25: Spookyhash bugfix

And a new version of digest is getting onto CRAN now, and to Debian shortly.

digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, and spookyhash algorithms) permitting easy comparison of R language objects. It is a fairly widely-used package (currently listed at 889k monthly downloads with 255 direct reverse dependencies and 7340 indirect reverse dependencies) as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation.

This release is a one issue fix. Aaron Lun noticed some issues when spookyhash is used in streaming mode. Kendon Bell, who also contributed spookyhash quickly found the issue which is a simple oversight. This was worth addressing in new release, so I pushed 0.6.25.

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

RcppSimdJson 0.0.2: First Update!

Following up on the initial RcppSimdJson release, a first updated arrived on CRAN yesterday.

RcppSimdJson wraps the fantastic simdjson library by Daniel Lemire which truly impressive. Via some very clever algorithmic engineering to obtain largely branch-free code, coupled with modern C++ and newer compiler instructions, it results in persing gigabytes of JSON parsed per second which is quite mindboggling. I highly recommend the video of the recent talk by Daniel Lemire at QCon (which was also voted best talk). 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 use per byte parsed.

This release syncs the simdjson headers with upstream, and polishes the build a little by conditioning on actually having a C++17 compiler rather than just suggesting it. The NEWS entry follows.

Changes in version 0.0.2 (2020-02-21)

  • Sychronized with upstream (Dirk in #4 and #5).

  • The R side of validateJSON now globs the file argument, expanding symbols like ~ appropriately.

  • C++ code in validateJSON now conditional on C++17 allowing (incomplete) compilation on lesser systems.

  • New helper function returning value of __cplusplus macro, used in package startup to warn if insufficient compiler used.

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

Thu, 13 Feb 2020

RcppSimdJson 0.0.1 now on CRAN!

A fun weekend-morning project, namely wrapping the outstanding simdjson library by Daniel Lemire (with contributions by Geoff Langdale, John Keiser and many others) into something callable from R via a new package RcppSimdJson lead to a first tweet on January 20, a reference to the brand new github repo, and CRAN upload a few days later—and then two weeks of nothingness.

Well, a little more than nothing as Daniel is an excellent “upstream” to work with who promptly incorporated two changes that arose from preparing the CRAN upload. So we did that. But CRAN being as busy and swamped as they are we needed to wait. The ten days one is warned about. And then some more. So yesterday I did a cheeky bit of “bartering” as Kurt wanted a favour with an updated digest version so I hinted that some reciprocity would be appreciated. And lo and behold he admitted RcppSimdJson to CRAN. So there it is now!

We have some upstream changes already in git, but I will wait a few days to let a week pass before uploading the now synced upstream code. Anybody who wants it sooner knows where to get it on GitHub.

simdjson is a gem. Via some very clever algorithmic engineering to obtain largely branch-free code, coupled with modern C++ and newer compiler instructions, it results in persing gigabytes of JSON parsed per second which is quite mindboggling. I highly recommend the video of the recent talk by Daniel Lemire at QCon (which was also voted best talk).

The NEWS entry (from a since-added NEWS file) for the initial RcppSimdJson upload follows.

Changes in version 0.0.1 (2020-01-24)

  • Initial CRAN upload of first version

  • Comment-out use of stdout (now updated upstream)

  • Deactivate use computed GOTOs for compiler compliance and CRAN Policy via #define

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, 12 Feb 2020

digest 0.6.24: Some more refinements

Another new version of digest arrived on CRAN (and also on Debian) earlier today.

digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, and spookyhash algorithms) permitting easy comparison of R language objects. It is a fairly widely-used package (currently listed at 889k monthly downloads with 255 direct reverse dependencies and 7340 indirect reverse dependencies) as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation.

This release comes a few month after the previous release. It contains a few contributed fixes, some of which prepare for R 4.0.0 in its current development. This includes a testing change to the matrix/array class, and corrects the registration for the PMurHash routine as pointed out by Tomas Kalibera and Kurt Hornik (who also kindly reminded me to finally upload this as I had made the fix already in December). Moreover, Will Landau sped up one operation affecting his popular drake pipeline toolkit. Lastly, Thierry Onkelinx corrected one more aspect related to sha1.

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.

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Sun, 09 Feb 2020

RcppArmadillo 0.9.850.1.0

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) 685 other packages on CRAN.

A new upstream release 9.850.1 of Armadillo was just released. And as some will undoubtedly notice, Conrad opted for an increment of 50 rather 100. We wrapped this up as version 0.9.850.1.0, having prepared a full (github-only) tarball and the release candidate 9.850.rc1 a few days ago. Both the release candidate and the release got the full reverse depends treatment, and no issues were found.

Changes in the new release below.

Changes in RcppArmadillo version 0.9.850.1.0 (2020-02-09)

  • Upgraded to Armadillo release 9.850.1 (Pyrocumulus Wrath)

    • faster handling of compound expressions by diagmat()

    • expanded .save() and .load() to handle CSV files with headers via csv_name(filename,header) specification

    • added log_normpdf()

    • added .is_zero()

    • added quantile()

  • The sparse matrix test using scipy, if available, is now simplified thanks to recently added reticulate conversions.

Courtesy of 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

Sat, 08 Feb 2020

RProtoBuf 0.4.15: One fix, some updates, depcrecation coming

A new release 0.4.15 of RProtoBuf just arrived at CRAN. RProtoBuf provides R with bindings for the Google Protocol Buffers (“ProtoBuf”) data encoding and serialization library used and released by Google, and deployed very widely in numerous projects as a language and operating-system agnostic protocol.

This release contains a small bug fix for repeated messages and groups. While making changes, I used the opportunity to change the unit testing framework to the excellent and lightweight tinytest package permitting, among other things, tests of the installed package, and also simplified the build by using pre-made pdf vignettes. A list of changes follows below.

As one heads-up and deprecation message, we are planning to remove the (entirely unused as best as we can tell, and minimal) remote procedure call feature. Protocol Buffers itself always lacked this, but eventually gRPC arrived to fill that void. All use cases should rely on it. So we prepared a test release 0.14.15.1 corresponding to the feature/retire_minimal_rpc branch. You can install this dev release from the ghrr drat repo via one of the drat-assisted commands, or directly via install.packages("RProtoBuf", repos="https://ghrr.github.io/drat"). Please do so and test if you suspect that the change may affect you. Otherwise the removal is likely to happen in the next release (but we will strive to wait a couple of months before doing so).

Changes in RProtoBuf version 0.4.15 (2020-02-08)

  • Repeated Message and Group objects are now returned correctly (Dirk in #64 fixing #62).

  • The unit tests are now run by tinytest (Dirk in #65).

  • The vignettes are now included pre-made (Dirk in #67).

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

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

Fri, 24 Jan 2020

RcppArmadillo 0.9.800.4.0

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) 680 other packages on CRAN.

A second small Armadillo bugfix upstream update 9.800.4 came out yesterday for the 9.800.* series, following a similar bugfix release 9.800.3 in December. This time just one file was changed (see below).

Changes in RcppArmadillo version 0.9.800.4.0 (2020-20-24)

  • Upgraded to Armadillo release 9.800.4 (Horizon Scraper)

    • fixes for incorrect type promotion in normpdf()

Courtesy of 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

Mon, 20 Jan 2020

anytime 0.3.7

A fresh minor release of the anytime package is arriving on CRAN right now. This is the eighteenth release, and it comes roughly five months after the previous showing the relative feature-stability we have now.

anytime is a very focused package aiming to do just one thing really well: to convert anything in integer, numeric, character, factor, ordered, … format to either POSIXct or Date objects – and to do so without requiring a format string. See the anytime page, or the GitHub README.md for a few examples.

This release brings a clever new option, thanks to Stephen Froehlich. If you know your input has (lots) of duplicates you can now say so and anytime() (and the other entry points for times and dates, UTC or not) will only parse the unique entries leading to potentially rather large speed gains (as in Stephen’s case where he often has more than 95% of the data as duplicates). We also tweaked the test setup some more, but as we are still unable to replicate what is happening with the Fedora test boxen at CRAN due to the non-reproducible setup so this remains a bit of guess work. Lastly, I am making use of a new Rcpp #define to speed up compilation a little bit too.

The full list of changes follows.

Changes in anytime version 0.3.7 (2019-01-20)

  • Test and possibly condition away one more test file.

  • Small enhancement for compilation by setting no-rtti define via Rcpp.

  • New option calcUnique for speed-up by parseing only unique timestamps (Stephen Froehlich in #110 fixing #109).

Courtesy of CRANberries, there is a comparison to the previous release. More information is on the anytime page. The issue tracker tracker off the GitHub repo can be use for questions and comments.

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/anytime | permanent link

Sun, 19 Jan 2020

RPushbullet 0.3.3

RPpushbullet demo

Release 0.3.3 of the RPushbullet package just got to CRAN. RPushbullet offers an interface to 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 further robustifies operations via two contributed PRs. The first by Chan-Yub ensures we set UTF-8 encoding on pushes. The second by Alexandre permits to downgrade from http/2 to http/1.1 which he needed for some operations with a particular backend. I made that PR a bit more general by turning the downgrade into one driven by a new options() toggle. Special thanks also to Jeroen in help debugging this issue. See below for more details.

Changes in version 0.3.3 (2020-01-18)

  • UTF-8 encoding is now used (Chan-Yub Park in #55).

  • Curl can use HTTP/1.1 (Alexandre Shannon in #59 fixing #57, plus Dirk in #60 making it optional).

Courtesy of 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. 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/rpushbullet | permanent link

Thu, 16 Jan 2020

RcppRedis 0.1.10: Switch to tinytest

Another minor release of RcppRedis just arrived on CRAN, following a fairly long break since the last release in October 2018.

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 switches to the fabulous tinytest package, allowing for very flexible testing during development and deployment—three cheers for easily testing installed packages too.

Changes in version 0.1.10 (2020-01-16)

  • The package now uses tinytest for unit tests (Dirk in #41).

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. 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, 15 Jan 2020

RQuantLib 0.4.11: More polish

New year, new RQuantLib! A new release 0.4.11 of RQuantLib arrived overnight on CRAN; and a Debian upload will follow shortly.

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

This version does three new things. First, we fixed an oversight on our end and now allow a null calendar (as the C++ API). Second, the package switched to tinytest as a few of my other packages have done, allowing for very flexible testing during development and deployment—three cheers for easily testing installed packages too. Third, and per a kind nag from Kurt Hornik I updated a few calls which the current QuantLib 1.17 marks as deprecated. That lead to a compile issue with 1.16 so the change is conditional in one part. The complete set of changes is listed below:

Changes in RQuantLib version 0.4.11 (2020-01-15)

  • Changes in RQuantLib code:

    • The 'Null' calendar without weekends or holidays is now recognized.

    • The package now uses tinytest for unit tests (Dirk in #140).

    • Calls deprecated-in-QuantLib 1.17 were updated (Dirk in #144).

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

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

Thu, 09 Jan 2020

rfoaas 2.1.0: New upstream so new access point!

rfoaas greed example

FOAAS, having been resting upstream for some time, released version 2.1.0 of its wonderful service this week! So without too much further ado we went to work and added support for it. And now we are in fact thrilled to announce that release 2.1.0 of rfoaas is now on CRAN as of this afternoon (with a slight delay as yours truly managed to state the package release date as 2019-01-09 which was of course flagged as ‘too old’).

The new 2.1.0 release of FOAAS brings a full eleven new REST access points, namely even(), fewer(), ftfty(), holygrail(), idea(), jinglebells(), legend(), logs(), ratsarse(), rockstar(), and waste(). On our end, documentation and tests were updated.

As usual, CRANberries provides a diff to the previous CRAN release. Questions, comments etc should go to the GitHub issue tracker. More background information is on the project page as well as on 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/rfoaas | permanent link

Wed, 08 Jan 2020

BH 1.72.0-3 on CRAN

Boost

The BH 1.72.0-1 release of BH required one update 1.72.0-2 when I botched a hand-edited path (to comply with the old-school path-length-inside-tar limit).

Turns out another issue needed a fix. This release improved on prior ones by starting from a pristine directory. But as a side effect, Boost Accumulators ended up incomplete with only the dependented-upon-by-others files included (by virtue of the bcp tool). So now we declared Boost Accumulators a full-fledged part of BH ensuring that bcp copies it “whole”. If you encounter issues with another incomplete part, please file an issue ticket at the GitHub repo.

No other changes were made.

Also, this fix was done initially while CRAN took a well-deserved winter break, and I had tweeted on Dec 31 about availability via drat and may use this more often for pre-releases. CRAN is now back, and this (large !!) package is now processed as part of the wave of packages that were in waiting (and Henrik got that right yesterday…).

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

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

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

Tue, 17 Dec 2019

BH 1.72.0-2 on CRAN

Boost

Yesterday’s release of BH 1.72.0-1 was so much fun we decided to do it again :)

More seriously, and as mentioned, we have to do some minor adjustments as required by CRAN. One is to ensure all filenames fit with their full paths into a shorter limit imposed by an ancient tar standard. So I always rename inst/include/boost/numeric/odeint/stepper/generation/karp54_classic.hpp by shortening it to .../karp54_cl.hpp and adjust the one file that includes this internal file. Not a big deal, and done for years.

But this time, and inadvertendly, I also renamed a similarly-named file one directory higher. And it gets included by some other files, which then fail and bark. My thanks to Alexey Shiklomanov for noticing this, letting me know, and testing a fixed package. I now wish his ODE-solving package was already on CRAN so that I’d known sooner ;-) as seemingly of the current 192 reverse dependencies, none are doing ODE maths.

No other changes, and sorry for the double download of both 1.72.0-1 and 1.72.0-2 (if you were fast enough to catch the -1 file).

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

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

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

Mon, 16 Dec 2019

BH 1.72.0-1 on CRAN

Boost

The BH package provides a sizeable portion of the Boost C++ libraries as a set of template headers for use by R. It is quite popular, and frequently used together with Rcpp. The BH CRAN page shows e.g. that it is used by rstan, dplyr as well as a few other packages. The current count of reverse dependencies is at 193.

Boost releases every four months. The last release we packaged was 1.69 from last December, prepared just before CRAN’s winter break. As it needed corresponding changes in three packages using it, it arrived on CRAN early January of this year. The process was much smoother this time. Yesterday I updated the package to the Boost 1.72 release made last Wednesday, and we are on CRAN now as there are no apparent issues. Of course, this BH release was also preceded by a complete reverse-depends check on my end, as well as on CRAN.

As you may know, CRAN tightened policies some more. Pragmas suppressing compiler warnings are verboten so I had to disable a few (see this patch file). Expect compilations of packages using Boost, and BH, to be potentially very noisy. Consider adding flags to your local ~/.R/Makeconf and we should add them to the src/Makevars as much as we can. Collecting a few of these on a BH wiki page may not be a bad idea. Contributions welcome!

One change we now made is to actually start fresh, rather than from the previous release. That way we reflect upstream removals better than before. So even though the upstream source release grew, our release tarball is a little smaller than before. Yay. That is likely a one-off, though, and the file is still Yuge.

As far as regularly scheduled changes go, we responded to three issue tickets and added two more (small) libraries, and also attempted to clean up one (which does not fully disappear due to interdependencies).

A detailed list of our local changes from the NEWS file follows. Two diffs to upstream Boost (for diagnostics, plus another small one for path length and other minor issues) are in the repo as well.

Changes in version 1.72.0-1 (2019-12-15)

  • Upgraded to Boost 1.72.0 (plus the few local tweaks) (#65)

  • Applied the standard minimal patch with required changes, as well as the newer changeset for diagnostics pragma suppression.

  • No longer install filesystem _explicitly_ though some files are carried in (#55)

  • Added mp11 (as requested in #62)

  • Added polygon (as requested in #63)

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

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

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

Mon, 09 Dec 2019

RcppClassic 0.9.12

A maintenance release 0.9.12 of the RcppClassic package arrived earlier today on CRAN. This package provides a maintained version of the otherwise deprecated initial Rcpp API which no new projects should use as the normal Rcpp API is so much better.

Changes are all internal. Testing is now done via tinytest, vignettes are now pre-built and at the request of CRAN we no longer strip the resulting library. No other changes were made.

CRANberries also reports the changes relative to the previous release from July of last year.

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

Sat, 07 Dec 2019

RcppArmadillo 0.9.800.3.0

armadillo image

A small Armadillo bugfix upstream update 9.800.3 came out a few days ago. The changes, summarised by Conrad in email to me (and for once not yet on the arma site are fixes for matrix row iterators, better detection of non-hermitian matrices by eig_sym(), inv_sympd(), chol(), expmat_sym() and miscellaneous minor fixes. It also contains a bug fix by Christian Gunning to his sample() implementation.

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) 679 other packages on CRAN.

Changes in RcppArmadillo version 0.9.800.3.0 (2019-12-04)

  • Upgraded to Armadillo release 9.800.3 (Horizon Scraper)

  • The sample function passes the prob vector as const allowing subsequent calls (Christian Gunning in #276 fixing #275)

Courtesy of 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

RDieHarder 0.2.1

A new version, now at 0.2.1, of the random-number generator tester RDieHarder (based on the DieHarder suite developed / maintained by Robert Brown with contributions by David Bauer and myself) is now on CRAN.

This version has only internal changes. Brian Ripley, tireless as always, is testing the impact of gcc 10 on CRAN code and found that the ‘to-be-default’ option -fno-common throws off a few (older) C code bases, this one (which is indeed old) included. So in a nutshell, we declared all global variables extern and defined them once and only once in new file globals.c. Needless to say, this affects the buildability options. In the past we used to rely on an external library libdieharder (which e.g. I had put together for Debian) but we now just build everything internally in the package.

Which builds on the changes in RDieHarder 0.2.0 which I apparently had not blogged about when it came out on December 21 last year. I had refactored the package to use either the until-then-required-but-now-optional external library, or the included library code. Doing so meant more builds on more systems including Windows.

This (very old) package has no NEWS.Rd file to take a summary from, but the ChangeLog file has all the details.

Thanks to CRANberries, you can also look at a diff from 0.2.1 to 0.2.0. or the older diff from 0.2.0 to 0.1.4.

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/rdieharder | permanent link

Sat, 23 Nov 2019

digest 0.6.23: More sha1 refinements

Another new version of digest got onto CRAN earlier today, and was also uploaded to Debian.

digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, and spookyhash algorithms) permitting easy comparison of R language objects. It is a fairly widely-used package (currently listed at 868k monthly downloads) as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation.

This release comes again one month after the previous release and contains further refinements for sha1 digests, thanks once more to Bill Denney and Thierry Onkelinx who added more support for formulae and better support for object attributes. I added some refinement for the encoding / utf8 filename tests from the previous to round things off.

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

Mon, 18 Nov 2019

ttdo 0.0.4: Extension

A first update release to the still very new (and still very small) ttdo package arrived on CRAN today. Introduced about two months ago in September, 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.

ttdo screenshot

Just how the package creation was motivated by our needs in teaching STAT 430 at Illinois, so does the extension code in this release which generalized how we extend the tinytest test predicates with additional arguments which help in the use of the PrairieLearn system (developed at Illinois) to provide tests, quizzes or homework. This release is mostly the work of Alton who is now also a coauthor.

The NEWS entries follow.

Changes in ttdo version 0.0.4 (2019-11-18)

  • Generalize tinytest extensions with additional arguments for test predicates (Alton in #2).

  • Use Travis CI for continuous integration off GitHub (Dirk).

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. 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/ttdo | permanent link

Sat, 16 Nov 2019

RcppEigen 0.3.3.7.0

A new minor release 0.3.3.7.0 of RcppEigen arrived on CRAN today (and just went to Debian too) bringing support for Eigen 3.3.7 to R.

This release comes almost a year after the previous minor release 0.3.3.5.0. Besides the upgrade to the new upstream version, it brings a few accumulated polishes to the some helper and setup functions, and switches to the very nice tinytest package for unit tests; see below for the full list. As before, we carry a few required changes to Eigen in a diff. And as we said before at the previous two 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.

The complete NEWS file entry follows.

Changes in RcppEigen version 0.3.3.7.0 (2019-11-16)

  • Fixed skeleton package creation listing RcppEigen under Imports (James Balamuta in #68 addressing #16).

  • Small RNG use update to first example in skeleton package used by package creation helper (Dirk addressing #69).

  • Update vignette example to use RcppEigen:::eigen_version() (Dirk addressing #71).

  • Correct one RcppEigen.package.skeleton() corner case (Dirk in #77 fixing #75).

  • Correct one usage case with pkgKitten (Dirk in #78).

  • The package now uses tinytest for unit tests (Dirk in #81).

  • Upgraded to Eigen 3.3.7 (Dirk in #82 fixing #80).

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 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, 12 Nov 2019

RcppAnnoy 0.0.14

annoy image

A new minor release of RcppAnnoy is now on CRAN, following the previous 0.0.13 release in September.

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 once again allows compilation on older compilers. The 0.0.13 release in September brought very efficient 512-bit AVX instruction to accelerate computations. However, this could not be compiled on older machines so we caught up once more with upstream to update to conditional code which will fall back to either 128-bit AVX or no AVX, ensuring buildability “everywhere”.

Detailed changes follow below.

Changes in version 0.0.14 (2019-11-11)

  • RcppAnnoy again synchronized with upstream to ensure builds with older compilers without AVX512 instructions (Dirk #53).

  • The cleanup script only uses /bin/sh.

Courtesy of 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

Sat, 09 Nov 2019

Rcpp 1.0.3: More Spit and Polish

rcpp logo

The third maintenance release 1.0.3 of Rcpp, following up on the 10th anniversary and the 1.0.0. release both pretty much exactly one year ago, arrived on CRAN yesterday. This deserves a special shoutout to Uwe Ligges who was even more proactive and helpful than usual. Rcpp is a somewhat complex package with many reverse dependencies, and both the initial check tickles one (grandfathered) NOTE, and the reverse dependencies typically invoke a few false positives too. And in both cases did he move the process along before I even got around to replying to the auto-generated emails. So just a few hours passed between my upload, and the Thanks, on its way to CRAN email—truly excellent work of the CRAN team. Windows and macOS binaries are presumably being built now. The corresponding Debian package was also uploaded as a source package, and binaries have since been built.

Just like for Rcpp 1.0.1 and Rcpp 1.0.2, we have a four month gap between releases which seems appropriate given both the changes still being made (see below) and the relative stability of Rcpp. It still takes work to release this as we run multiple extensive sets of reverse dependency checks so maybe one day we will switch to six month cycle. For now, four months seem like a good pace.

Rcpp has become the most popular way of enhancing R with C or C++ code. As of today, 1832 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 190 in BioConductor. And per the (partial) logs of CRAN downloads, we are currently running at 1.1 millions downloads per month.

This release features a number of different pull requests by five different contributors as detailed below.

Changes in Rcpp version 1.0.3 (2019-11-08)

  • Changes in Rcpp API:

    • Compilation can be sped up by skipping Modules headers via a toggle RCPP_NO_MODULES (Kevin in #995 for #993).

    • Compilation can be sped up by toggling RCPP_NO_RTTI which implies RCPP_NO_MODULES (Dirk in #998 fixing #997).

    • XPtr tags are now preserved in as<> (Stephen Wade in #1003 fixing #986, plus Dirk in #1012).

    • A few more temporary allocations are now protected from garbage collection (Romain Francois in #1010, and Dirk in #1011).

  • Changes in Rcpp Modules:

    • Improved initialization via explicit Rcpp:: prefix (Riccardo Porreca in #980).
  • Changes in Rcpp Deployment:

    • A unit test for Rcpp Class exposure was updated to not fail under r-devel (Dirk in #1008 fixing #1006).
  • Changes in Rcpp Documentation:

    • The Rcpp-modules vignette received a major review and edit (Riccardo Porreca in #982).

    • Minor whitespace alignments and edits were made in three vignettes following the new pinp release (Dirk).

    • New badges for DOI and CRAN and BioConductor reverse dependencies have been added to README.md (Dirk).

    • Vignettes are now included pre-made (Dirk in #1005 addressing #1004)).

    • The Rcpp FAQ has two new entries on 'no modules / no rtti' and exceptions across shared libraries (Dirk in #1009).

Thanks to 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) 2255 previous questions.

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.

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Sat, 02 Nov 2019

binb 0.0.5: More improvements

The fifth release of the binb package just arrived on CRAN. binb regroups four rather nice themes for writing LaTeX Beamer presentations much more easily in (R)Markdown. As a teaser, a quick demo combining all four themes follows; documentation and examples are in the package.

This release contains some nice extensions to the Monash theme by Rob Hyndman](https://robjhyndman.com/). You can see the a longer demo in this pdf and the extended options (i.e. for titlepage) in this pdf. David Selby also correct a minor internal wart in Presento.

Changes in binb version 0.0.5 (2019-11-02)

  • The Monash theme was updated with new titlepage and font handling and an expanded demo (Rob in #20).

  • The presento theme is now correctly labeled as exported (David Selby in #22).

  • The two Monash demos are now referenced from README.md (Dirk).

CRANberries provides a summary of changes to the previous version. For questions or comments, please use the issue tracker at GitHub.

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.

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Sun, 27 Oct 2019

littler 0.3.9: More nice new features

max-heap image

The tenth release of littler as a CRAN package is now available, following in the thirteen-ish 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 more recently.

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 where 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 adds several new helper scripts / examples such as a Solaris-checker for rhub, a Sweave runner, and bibtex-record printer for packages. It also extends several existing scripts: render.r can now compact pdf files, build.r does this for package builds, tt.r covers parallel tinytest use, rcc.r reports the exit code from rcmdcheck, update.r corrects which package library directories it looks at, kitten.r can add puppies for tinytest, and thanks to Stefan the dratInsert.r (and render.r) script use call. correctly in stop().

The NEWS file entry is below.

Changes in littler version 0.3.9 (2019-10-27)

  • Changes in examples

    • The use of call. in stop() was corrected (Stefan Widgren in #72).

    • New script cos.r to check (at rhub) on Solaris.

    • New script compactpdf.r to compact pdf files.

    • The build.r script now compacts vignettes and resaves data.

    • The tt.r script now supports parallel tests and side effects.

    • The rcc.r script can now report error codes.

    • The '–libloc' option to update.r was updated.

    • The render.r script can optionally compact pdfs.

    • New script sweave.r to render (and compact) pdfs.

    • New script pkg2bibtex.r to show bibtex entries.

    • The kitten.r script has a new option --puppy to add tinytest support in purring packages.

CRANberries provides a comparison to the previous release. Full details for the littler release are provided as usual at the ChangeLog page. The code is available via the GitHub repo, from tarballs and now of course all 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. 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.

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Thu, 24 Oct 2019

dang 0.0.11: Small improvements

A new release of what may be my most minor package, dang, is now on CRAN. 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. More recently added were helpers for data.table to xts conversion and a git repo root finder.

Some of these functions (like lsos()) where hanging in my .Rprofile, other just lived in scripts so some years ago I started to collect them in a package, and as of February this is now on CRAN too for reasons that are truly too bizarre to go about. It’s a weak and feeble variant of the old Torvalds line about backups and ftp sites …

As I didn’t blog about the 0.0.10 release, the NEWS entry for both follows:

Changes in version 0.0.11 (2019-10-24)

  • New functions getGitRoot, inGit and isConnected.

  • Improved function as.data.table.xts.

Changes in version 0.0.10 (2019-02-10)

  • Initial CRAN release. See ChangeLog for earlier changes.

Courtesy of 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. 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/dang | permanent link

Wed, 23 Oct 2019

linl 0.0.4: Now with footer

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

This version now supports a (pdf, png, …) footer along with the already-supported header, thanks to an intiial PR by Michal Bojanowski to which Aaron added nice customization for scale and placement (as supported by LaTeX package wallpaper). I also added support for continued integration testing at Travis CI via a custom Docker RMarkdown container—which is something I should actually say more about at another point.

Here is screenshot of the vignette showing the simple input for some moderately fancy output (now with a footer):

The NEWS entry follows:

Changes in linl version 0.0.4 (2019-10-23)

  • Continuous integration tests at Travis are now running via custom Docker container (Dirk in #21).

  • A footer for the letter can now be specified (Michal Bojanowski in #23 fixing #10).

  • The header and footer options be customized more extensively, and are documented (Aaron in #25 and #26).

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

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

Tue, 22 Oct 2019

pkgKitten 0.1.5: Creating R Packages that purr

kitten

Another minor release 0.1.5 of pkgKitten just hit on CRAN today, after a break of almost three years.

This release provides a few small changes. The default per-package manual page now benefits from a second refinement (building on what was introduced in the 0.1.4 release) in using the Rd macros referring to the DESCRIPTION file rather than duplicating information. Several pull requests fixes sloppy typing in the README.md, NEWS.Rd or manual page—thanks to all contributors for fixing these. Details below.

Changes in version 0.1.5 (2019-10-22)

  • More extensive use of newer R macros in package-default manual page.

  • Install .Rbuildignore and .gitignore files.

  • Use the updated Travis run script.

  • Use more Rd macros in default 'stub' manual page (#8).

  • Several typos were fixed in README.md, NEWS.Rd and the manual page (#9, #10)

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

Courtesy of 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/pkgkitten | permanent link