Search Results: "Dirk Eddelbuettel"

11 August 2023

Dirk Eddelbuettel: RcppArmadillo 0.12.6.1.0 on CRAN: New Upstream

armadillo image Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language and is widely used by (currently) 1092 other packages on CRAN, downloaded 30.1 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper (preprint / vignette) by Conrad and myself has been cited 545 times according to Google Scholar. This release brings bugfix upstream release 12.6.1. Conrad release 12.6.0 when CRAN went on summer break. I rolled it up ran the full reverse-depenency check against the now more than 1000 packages. And usage from one those revealed a corner-case bug (of not always flattening memory for sparse matrices to zero values) so 12.6.1 followed. This is what was uploaded today. And as I prepared it earlier in the week as CRAN reopened, Conrad released a new 12.6.2. However, its changes are only concerned with settings for Armadillo-internal use of its random number generators (RNGs). And as RcppArmadillo connects Armadillo to the RNGs provided by R, the upgrade does not affect R users at all. However it is available in the github repo, in the Rcpp drap repo and at r-universe. The set of changes for this RcppArmadillo release follows.

Changes in RcppArmadillo version 0.12.6.1.0 (2023-07-26)
  • Upgraded to Armadillo release 12.6.1 (Cortisol Retox)
    • faster multiplication of dense vectors by sparse matrices (and vice versa)
    • faster eigs_sym() and eigs_gen()
    • faster conv() and conv2() when using OpenMP
    • added diags() and spdiags() for generating band matrices from set of vectors

Courtesy of my CRANberries, there is a [diffstat report relative to previous release]. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the Rcpp R-Forge page. If you like this or other open-source work I do, you can sponsor me at GitHub.

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

8 August 2023

Dirk Eddelbuettel: dtts 0.1.1 on CRAN: Enhancements

Leonardo and I are happy to announce the release of a first follow-up release 0.1.1 of our dtts package which got to [CRAN][cran] in its initial upload last year. dtts builds upon our nanotime package as well as the beloved data.table to bring high-performance and high-resolution indexing at the nanosecond level to data frames. dtts aims to bring the time-series indexing versatility of xts (and zoo) to the immense power of data.table while supporting highest nanosecond resolution. This release fixes a bug flagged by valgrind and brings several internal enhancements.

Changes in version 0.1.1 (2023-08-08)
  • A simplifcation was applied to the C++ interface glue code (#9 fixing #8)
  • The package no longer enforces the C++11 compilation standard (#10)
  • An uninitialized memory read has been correct (#11)
  • A new function ops has been added (#12)
  • Function names no longer start with a dot (#13)
  • Arbitrary index columns are now supported (#13)

Courtesy of my CRANberries, there is also a diffstat report for the this release this release. Questions, comments, issue tickets can be brought to the GitHub repo. If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

7 August 2023

Dirk Eddelbuettel: RQuantLib 0.4.19 on CRAN: More Maintenance

A new release 0.4.19 of RQuantLib arrived at CRAN earlier today, and has already been uploaded to Debian too. QuantLib is a rather comprehensice free/open-source library for quantitative finance. RQuantLib connects it to the R environment and language, and has been part of CRAN for more than twenty years (!!) This release of RQuantLib brings a small update to three unit tests as very recent 1.31 release QuantLib brought a subtle change to some fixed income payment schedules and dates. On a sadder note, as CRAN now checks the ratio of user time over elapsed time , excessive threading was inferred for five examples. As we seemingly cannot limit std::thread here, I opted to park these examples behind a \dontrun . Not ideal. Lastly, a few version checks in configure were updated.

Changes in RQuantLib version 0.4.19 (2023-08-07)
  • Three calendaring / schedule tests were adjusted for slightly changed values under QuantLib 1.31
  • Several checks in the configure script have been updated to reflect current versions of packages.
  • Five examples no longer run because, even while extremely short, use of (too many default) threads was seen.

Courtesy of my CRANberries, there is also a diffstat report for the this release 0.4.19. As always, more detailed information is on the RQuantLib page. Questions, comments etc should go to the rquantlib-devel mailing list. Issue tickets can be filed at the GitHub repo. If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

23 July 2023

Dirk Eddelbuettel: #41: Another r2u Example Really Simple CI

Welcome to the 41th post in the $R^4 series. Just as the previous post illustrated r2u use to empower interactive Google Colab sessions, today we want to look at continuous integration via GitHub Actions. Actions are very powerful, yet also intimidating and complex. How does one know what to run? How does ensure requirements are installed? What does these other actions do? Here we offer a much simpler yet fully automatic solution. It takes advantage of the fact that r2u integrates fully and automatically with the system, here apt, without us having to worry about the setup. One way to make this very easy is the use of the Rocker containers for r2u. They already include the few lines of simple (and scriptable) setup, and have bspm setup so that R commands to install packages dispatch to apt and will bring all required dependencies automatically and easily. With that the required yaml file for an action can be as simple as this: 
name: r2u

on:
  push:
  pull_request:
  release:

jobs:
  ci:
    runs-on: ubuntu-latest
    container:
      image: rocker/r2u:latest
    steps:
      - uses: actions/checkout@v3
      - name: SessionInfo
        run: R -q -e 'sessionInfo()'
      #- name: System Dependencies
      #  # can be used to install e.g. cmake or other build dependencies
      #  run: apt update -qq && apt install --yes --no-install-recommends cmake git
      - name: Package Dependencies
        run: R -q -e 'remotes::install_deps(".", dependencies=TRUE)'
      - name: Build Package
        run: R CMD build --no-build-vignettes --no-manual .
      - name: Check Package
        run: R CMD check --no-vignettes --no-manual $(ls -1tr *.tar.gz   tail -1)
There are only a few key components here. First, we have the on block where for simplicity we select pushes, pull requests and releases. One could reduce this to just pushes by removing or commenting out the next two lines. Many further refinements are possible and documented but not reqired. Second, the jobs section and its sole field ci saythat we are running this CI on Ubuntu in its latest release. Importantly we then also select the rocker container for r2 meaning that we explicitly select running in this container (which happens to be an extension and refinement of ubuntu-latest). The latest tag points to the most recent LTS release, currently jammy aka 22.04. This choice also means that our runs are limited to Ubuntu and exclude macOS and Windows. That is a choice: not every CI task needs to burn extra (and more expensive) cpu cycles on the alternative OS, yet those can always be added via other yaml files possibly conditioned on fewer runs (say: only pull requests) if needed. Third, we have the basic sequence of steps. We check out the repo this file is part of (very standard). After that we ask R show the session info in case we need to troubleshoot. (These two lines could be commented out.) Next we show a commented-out segment we needed in another repo where we needed to add cmake and git as the package in question required local compilation during build. Such a need is fairly rare, but as shown can be be accomodated easily while taking advantage of the rich development infrastructure provided by Ubuntu. But the step should be optional for most R packages so it is commented out here. The next step uses the remotes package to look at the DESCRIPTION file and install all dependencies which, thanks to r2u and bspm, will use all Ubuntu binaries making it both very fast, very easy, and generally failsafe. Finally we do the two standard steps of building the source package and checking it (while omitting vignettes and the (pdf) manual as the container does not bother with a full texlive installation this could be altered if desired in a derived container). And that s it! The startup cost is a few seconds to pull the container, plus a few more seconds for dependencies and let us recall that e.g. the entire tidyverse installs all one hundred plus packages in about twenty seconds as shown in earlier post. After that the next cost is generally just what it takes to build and check your package once all requirements are in. To use such a file for continuous integration, we can install it in the .github/workflows/ directory of a repository. One filename I have used is .github/workflows/r2u.yaml making it clear what this does and how. More information about r2u is at its site, and we answered some question in issues, and at stackoverflow. More questions are always welcome! If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

20 July 2023

Dirk Eddelbuettel: qlcal 0.0.7 on CRAN: QuantLib 1.31 Updates

The seventh release of the still pretty new qlcal package arrivied at CRAN today. qlcal delivers the calendaring parts of QuantLib. It is provided (for the R package) as a set of included files, so the package is self-contained and does not depend on an external QuantLib library (which can be demanding to build). qlcal covers over sixty country / market calendars and can compute holiday lists, its complement (i.e. business day lists) and much more. This release brings updates from the just-released QuantLib 1.31 version.

Changes in version 0.0.7 (2023-07-19)
  • Updates, extensions and corrections to calendars from South Korea, Hong Kong, Singapore, India, Taiwan, South Africa, Denmark and Finland from QuantLib 1.31
  • Added support for UnitedStates/SOFR calendar

As the update comprises a number of small-but-important updates to eight different country calendars as well as a new US calendar (in a slight variation on the government bond calendar) we can also update the little demo highlighting all calendars within the US for the given year: 
> ## see https://github.com/qlcal/qlcal-r/blob/master/demo/allUScalendars.R
> ## see R/calendars.R in qlcal, we prepend 'UnitedStates/' in makeHol()
> cals <- c("LiborImpact", "NYSE", "GovernmentBond", "NERC", "FederalReserve", "SOFR")
> print(Reduce(cbind, Map(makeHol, cals)))
           LiborImpact NYSE GovernmentBond NERC FederalReserve SOFR
2023-01-02        TRUE TRUE           TRUE TRUE           TRUE TRUE
2023-01-16        TRUE TRUE           TRUE   NA           TRUE TRUE
2023-02-20        TRUE TRUE           TRUE   NA           TRUE TRUE
2023-04-07          NA TRUE             NA   NA             NA TRUE
2023-05-29        TRUE TRUE           TRUE TRUE           TRUE TRUE
2023-06-19        TRUE TRUE           TRUE   NA           TRUE TRUE
2023-07-04        TRUE TRUE           TRUE TRUE           TRUE TRUE
2023-09-04        TRUE TRUE           TRUE TRUE           TRUE TRUE
2023-10-09        TRUE   NA           TRUE   NA           TRUE TRUE
2023-11-10        TRUE   NA             NA   NA             NA   NA
2023-11-23        TRUE TRUE           TRUE TRUE           TRUE TRUE
2023-12-25        TRUE TRUE           TRUE TRUE           TRUE TRUE
>
Courtesy of my CRANberries, there is a diffstat report for this release. See the project page and package documentation for more details, and more examples. If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

11 July 2023

Dirk Eddelbuettel: RcppSpdlog 0.0.14 on CRAN: Upstream Update

Version 0.0.14 of RcppSpdlog is now on CRAN and has just been uploaded to Debian. RcppSpdlog bundles spdlog, a wonderful header-only C++ logging library with all the bells and whistles you would want that was written by Gabi Melman, and also includes fmt by Victor Zverovich. You can learn more at the nice package documention site. This release simply brings an update to the just release spdlog 1.12.0 from a few days ago. The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.14 (2023-07-09)
  • Added new badge to README.md
  • Upgraded to upstream releases spdlog 1.12.0

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog page, or the package documention site. If you like this or other open-source work I do, you can sponsor me at GitHub.

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

8 July 2023

Dirk Eddelbuettel: #40: Another r2u Example Making Colab Easier

Welcome to the 40th post in the $R^4 series. This one will just be a very brief illustration of r2u use in what might be an unexpected place: Google Colab. Colab has a strong bent towards Jupyter and Python but has been supporting R compute kernels for some time (by changing what they call the runtime ). And with a little exploration one can identify these are (currently, as of July 2023) running Ubuntu 20.04 aka focal . Which is of course one of two system supported by our lovely r2u project (with the other being the newer 22.04 aka jammy ). And I mostly tweeted / tooted about r2u since the its introduction in #37. And gave basically just a mention in passing in faster feedback post #38 as well as the faster feedback in ci post #39). So a brief recap may be in order. In essence, r2u makes all of CRAN available as full-fledged Ubuntu binaries with complete and full dependencies which are then installed directly and quickly via apt. Which, to top it of, are accessed directly from R via install.packages() so no special knowledge or sauce needed. We often summarize it as fast, easy, reliable: what is not to like . And, as we established in a few minutes of probing, it also works in the focal -based Colab session. The screen shot shows the basic step of fetching the setup script (for plain Ubuntu focal system) from r2u, making it executable and running it. Total time: 34 seconds. And after that we see the pure magic of install.packages("tidyverse") installing all of it in nine seconds. Additionally, we add the brms package in thirty-one seconds cia install.packages("brms"). Both load just fine and echo their current values.
r2u on colab focal r2u on colab focal
The commands that are executed in that R session are just 
download.file("https://github.com/eddelbuettel/r2u/raw/master/inst/scripts/add_cranapt_focal.sh",
              "add_cranapt_focal.sh")
Sys.chmod("add_cranapt_focal.sh", "0755")
system("./add_cranapt_focal.sh")
install.packages("tidyverse")
library(tidyverse)
install.packages("brms")
library(brms)
The timings are the Colab notebook are visible in the left margin. The lack of output makes debugging a little trickier so I still recommend to use r2u for first expploration via a Docker container as e.g. rocker/r2u:jammy. More information about r2u is at its site, and we answered some question in issues, and at stackoverflow. More questions are always welcome! If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

7 July 2023

Dirk Eddelbuettel: digest 0.6.33 on CRAN: Bugfix

Release 0.6.33 of the digest package arrived at CRAN today and has been uploaded to Debian already. digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, spookyhash, blake3, and crc32c algorithms) permitting easy comparison of R language objects. It is a mature and widely-used (with 58.6 million downloads just on the partial cloud mirrors of CRAN which keep logs) as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation to quickly identify the various objects. This release corrects a bad bug we accidentally introduced in release 0.6.32 a little under two weeks ago. As described we added crc32c and aimed for the simple portable approach (given that the accelerated version is now availble in our package crc32c) but overlooked one setting which promptly broked compilation on M1/M2/Arm64 (which we do not have access too, sadly). This was actually reported in issue #189 on the very day 0.6.32 was released and even before we got to blog about its announcement so that we could even mention it in the third paragraph there. This fix was a one-liner, and was committed hours later. Now, as it sometimes happens, processing the new upload at CRAN took some time. They appeared to be down the next day not processing anything. Once opened again, they reported changes to worse as can be seen in reverse-dependency checks. Turns out those were false positive ( it happens ) but then the package lingered a little longer and quite a lot of folks chimed in at in issue #189. I have now learned that there were in fact some temporary hardware issues in one of the CRAN locations, so it all had a reason but most importantly it is all better now. My apologies for the temporary breakage, we attempted to address it swiftly but sometimes things beyond our control (and reach) do slow things down. Now new and fixed binaries should appear in the next few days. My CRANberries provides the usual summary of changes to the previous version. For questions or comments use the issue tracker off the GitHub repo. If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

Dirk Eddelbuettel: Rcpp 1.0.11 on CRAN: Updates and Maintenance

rcpp logo The Rcpp Core Team is delighted to announce that the newest release 1.0.11 of the Rcpp package arrived on CRAN and in Debian earlier today. Windows and macOS builds should appear at CRAN in the next few days, as will builds in different Linux distribution and of course at r2u. The release was finalized three days ago, but given the widespread use and extended reverse dependencies at CRAN it usually takes a few days to be processed. This release continues with the six-months January-July cycle started with release 1.0.5 in July 2020. As a reminder, we do of course make interim snapshot dev or rc releases available via the Rcpp drat repo and strongly encourage their use and testing I run my systems with these versions which tend to work just as well, and are also fully tested against all reverse-dependencies. Rcpp has long established itself as the most popular way of enhancing R with C or C++ code. Right now, 2720 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 251 in BioConductor. On CRAN, 13.7% of all packages depend (directly) on Rcpp, and 59.6% of all compiled packages do. From the cloud mirror of CRAN (which is but a subset of all CRAN downloads), Rcpp has been downloaded 72.5 million times. The two published papers (also included in the package as preprint vignettes) have, respectively, 1678 (JSS, 2011) and 259 (TAS, 2018) citations, while the the book (Springer useR!, 2013) has another 588. This release is incremental as usual, generally preserving existing capabilities faithfully while smoothing our corners and / or extending slightly, sometimes in response to changing and tightened demands from CRAN or R standards. The full list below details all changes, their respective PRs and, if applicable, issue tickets. Big thanks from all of us to all contributors!

Changes in Rcpp version 1.0.11 (2023-07-03)
  • Changes in Rcpp API:
    • Rcpp:::CxxFlags() now quotes only non-standard include path on linux (Lukasz in #1243 closing #1242).
    • Two unit tests no longer accidentally bark on stdout (Dirk and I aki in #1245).
    • Compilation under C++20 using clang++ and its standard library is enabled (Dirk in #1248 closing #1244).
    • Use backticks in a generated .Call() statement in RcppExports.R (Dirk #1256 closing #1255).
    • Switch to system2() to capture standard error messages in error cases (I aki in #1259 and #1261 fixing #1257).
  • Changes in Rcpp Documentation:
    • The CITATION file format has been updated (Dirk in #1250 fixing #1249).
  • Changes in Rcpp Deployment:
    • A test for qnorm now uses the more accurate value from R 4.3.0 (Dirk in #1252 and #1260 fixing #1251).
    • Skip tests with path issues on Windows (I aki in #1258).
    • Container deployment in continuous integrations was improved. (I aki and Dirk in #1264, Dirk in #1269).
    • Several files receives minor edits to please R CMD check from r-devel (Dirk in #1267).

Thanks to my CRANberries, you can also look at a diff to the previous release. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page. Bugs reports are welcome at the GitHub issue tracker as well (where one can also search among open or closed issues); questions are also welcome under rcpp tag at StackOverflow which also allows searching among the (currently) 2994 previous questions. If you like this or other open-source work I do, you can sponsor me at GitHub.

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

2 July 2023

Dirk Eddelbuettel: RcppAnnoy 0.0.21 on CRAN: Upstream Update

annoy image Another minor maintenance release, now at version 0.0.20, of RcppAnnoy has arrived on CRAN. RcppAnnoy is the Rcpp-based R integration of the nifty Annoy library by Erik Bernhardsson. Annoy is a small and lightweight C++ template header library for very fast approximate nearest neighbours originally developed to drive the Spotify music discovery algorithm. This release mainly updates the included copy of Annoy to version 1.7.3 which now provides a C++ namespace in the header API. So I sent a pair of PRs to uwot to update its (compiled) use, which James promptly merged. With that the CRAN update was once again seamless. Otherwise the package follows current custom by moving away from C++11 as a set compilation standard to be open for more modern C++ idioms. Here, this allows in particular for possible multithreaded indexing for which everything needed is in C++17. However, we did not turn multithreaded indexing on as the RNG use is such that the streams would differ leading to slightly different (if of course equivalent) results. Users can enable this by recompiling with the switch flipped, see src/Makevars.

Changes in version 0.0.21 (2023-07-02)
  • The build setup switched from C++11 to C++17 which offers threading support (which remains off by default to ensure consistent results)
  • Upstream code was update to Annoy 1.17.3, the switch to an explicit C++ namespace has been accomodated (Dirk in #75)

Courtesy of my CRANberries, there is also a diffstat report for this release. If you like this or other open-source work I do, you can sponsor me at GitHub.

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

1 July 2023

Dirk Eddelbuettel: New Achievement Unlocked: Bugfix Patch into Stable Release Update

Last weekend was the bi-annual time to roll the main machine and server to the current Ubuntu release, now at 23.04. It must now have been fifteen or so years that I have used Ubuntu for my desktop / server (for reasons I may write about another time). And of course it all passed swimmingly as usual. [ And a small aside, if I may. Among all these upgrades, one of my favourite piece of tech trivia that may well be too little known remains the dedication of the PostgreSQL maintainers installing the new version, now PostgreSQL 15, seamlessly in parallel with the existing one, in my case PostgreSQL 14, keeping both running (!!) on two neighbouring ports (!!) so that there is no service disruption. So at some point, maybe this weekend, I will run the provided script to dump-and-restore to trigger the database migration at my convenience. Happy PostgreSQL on Debian/Ubuntu user since the late 1990s. It. Just. Works. ] [ Similarly, it is plainly amazeballs how apt orders and runs package updates to service to keep running for a maximum amount of time. This machine acts as e.g. a web server and it was up and running (as were other services) while thousands of package got updated/replaced. It is pretty amazing. Whereas on other platforms people still maintain the do not ever update anything we demonstrably offer the opposite here. Really not too shabby. ] This time, I had one small hickup. Emacs, now at version 28 bringing loads of niceties along, would not load. And the error soon lead to a post on the magit list where its indefatigable author Jonas Bernoulli suggested a rebuild (and hence re-compilation of the elisp files). Which I did, and which allowed a start of VM inside Emacs. So I was happy. But it allowed it only once for each VM package reinstall. Not good, and I remained curious. Some more digging lead to a breakthrough. A post and commit at the Fedora Project indicated that for just VM within Emacs, byte-compilation throws a spanner. Which one can work around by telling Emacs not to compile the files in the VM folder. So I applied that patch to the VM package in a local build et voil we have working VM. The world is clearly better when your email client of 25+ years just works. And feels snappier because everything under Emacs28 feels snappier! So I set this up properly and filed Debian Bug Report #1039105. To which Ian Jackson, the maintainer, replied a few days later nodding that he could reproduce. And that he concurred with the bug report, and was planning to update throughout. And lo and behold this morning s update reveals that this made into an update for the just-released Debian Bookworm. So yay. In all these years of Debian maintainership (somewhere between twentyfive and thirty) this may be my first bug report with patch going straight into a stable release. But of course, true and full credit goes of course to G ran Uddeborg for putting it up first for Fedora. Lovely how Open Source can work together. We really should do more, not less, of that. But I digress Anyway, in sum: If you try to use VM under the lovely Emacs 28, there is a fix, and if you use it with Debian Bookworm the fix should hit your mirrors soons. Ditto, methinks, for the next Ubuntu release. If you use it under Ubuntu now, the package is (elisp) text-only and can be safely installed on a derivative (which we do not enjoy in general but which is fine here). So enjoy! If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

27 June 2023

Dirk Eddelbuettel: digest 0.6.32 on CRAN: CRC32C and AES Updates

Release 0.6.32 of the digest package arrived at CRAN this morning, and will be uploaded to Debian as well. digest creates hash digests of arbitrary R objects (using the md5, sha-1, sha-256, sha-512, crc32, xxhash32, xxhash64, murmur32, spookyhash, blake3, and crc32c algorithms) permitting easy comparison of R language objects. It is a mature and widely-used (with 58.3 million downloads just on the partial cloud mirrors of CRAN which keep logs) as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation to quickly identify the various objects. This release brings two changes. First, we added crc32c as a new hashing algorithm. And we did so in a portable minimal fashion while also adding a new CRAN crc32c package with the full hardware-optimised support form x86_64 and Arm64 (M1/M2) chips. Fully integrating the optional added package is still work in progress we may refine. (Now, as it turns out, a first bug report that this is not as portable as we hoped. But it also looks like we already have a fix. So a quick follow-up release is likely.) Second, Dean Attali had looked into AES digests and cyphers using the CBC mode and noticed what we needed padding which he kindly contributed in PR #186. My CRANberries provides the usual summary of changes to the previous version. For questions or comments use the issue tracker off the GitHub repo. If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

19 June 2023

Dirk Eddelbuettel: RcppArmadillo 0.12.4.1.0 on CRAN: New Upstream Bugfix

armadillo image Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language and is widely used by (currently) 1079 other packages on CRAN, downloaded 29.6 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper) (preprint / vignette) by Conrad and myself has been cited 543 times according to Google Scholar. This release brings bugfix upstream release 12.4.1 made by Conrad at the end of last week. As usual, I prepared the usual release candidate, tested on the over 1000 reverse depends (which sadly takes a long time on old hardware), found no issues and sent it to CRAN. Where it got tested again and was by a stroke of bad luck upheld for two unrelated issue (one package fell over one of its other dependencies changing a data representation, another fell afoul of a tightened test on total test time) so this awaited the usual email handshake with the CRAN maintainers and the weekend got in the way. The release also contains a PR kindly provided by Mikael Jagan for an upcoming change in package Matrix. As a bugfix release, the set of changes is fairly small.

Changes in RcppArmadillo version 0.12.4.1.0 (2023-06-17)
  • Upgraded to Armadillo release 12.4.1 (Cortisol Profusion Redux)
    • fix bug in SpMat::shed_cols()
    • functions such as .is_finite() and find_nonfinite() will now emit a runtime warning when compiled in fast math mode; such compilation mode disables detection of non-finite values
  • Accommodate upcoming change in package Matrix (Mikael Jagan in #417 addressing #415)

Courtesy of my CRANberries, there is a diffstat report relative to previous release. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the Rcpp R-Forge page. If you like this or other open-source work I do, you can sponsor me at GitHub.

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

18 June 2023

Dirk Eddelbuettel: spdl 0.0.5 on CRAN: Small Extension

Another quick update to the still somewhat new package spdl is now om CRAN, and will go to Debian soon too. The key focus of spdl is to offer the exact same interface to logging from both R and C++ by relying on spdlog via my RcppSpdlog package. Usage examples are shown on the RcppSpdlog docs page. This release add support for the wrappers init() and log() wrapping the existing setup() function but requiring only the level argument. This requires version 0.0.13 of RcppSpdlog which was released to CRAN yesterday. The short NEWS entry follows.

Changes in spdl version 0.0.5 (2023-06-18)
  • Add simple aliases init() and log() wrapping setup() but requiring only the logging level argument

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the spdl page If you like this or other open-source work I do, you can sponsor me at GitHub.

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

Dirk Eddelbuettel: RcppSpdlog 0.0.13 on CRAN: Small Extensions

Version 0.0.13 of RcppSpdlog is now on CRAN and will be soon be uploaded to Debian too. RcppSpdlog bundles spdlog, a wonderful header-only C++ logging library with all the bells and whistles you would want that was written by Gabi Melman, and also includes fmt by Victor Zverovich. You can learn more at the package documention site. This release adds a small (but handy) accessor generalisation: Instead of calling setup() with two arguments for a label and the logging level we now only require the desired level. We also cleaned up one implementation detail for the stopwatch feature added in January, and simplified the default C++ compilation standard setting. The NEWS entry for this release follows.

Changes in RcppSpdlog version 0.0.13 (2023-06-17)
  • Minor tweak to stopwatch setup avoids pulling in fmt
  • No longer set a C++ compilation standard as the default choices by R are sufficient for the package
  • Add convenience wrapper log_init omitting first argument to log_setup while preserving the interface from the latter
  • Add convenience setup wrappers init and log to API header file spdl.h

Courtesy of my CRANberries, there is also a diffstat report. More detailed information is on the RcppSpdlog page, or the package documention site. If you like this or other open-source work I do, you can sponsor me at GitHub.

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

11 June 2023

Dirk Eddelbuettel: sanitizers 0.1.1 on CRAN: Updated and Expanded

bleach The second release of the sanitizers package is now on CRAN. sanitizers provides true positives for programming errors detected by Address Sanitizers and friends. This permits validation of the setup when chasing such bug reports: it allows us to ascertain that the compiler (and instrumented R version) are correctly set up and the errors we expect to be reported are in fact reported. Almost nine years (!!) since the first release, this update brings an added integer overflow sanitizer contributed by Greg Jeffries so long ago that I had thought it was part of the CRAN releases my bad for delaying this. It also updates programming practices by switching to symbol registration for the compiled functions. And of course several R packaging best practices have improved since the initial release so we updated a few small things throughout. A very good resources for all things sanitizers is the Google repo at GitHub and especially its wiki. The brief NEWS entry follows.

Changes in version 0.1.1 (2023-06-11)
  • Added integer overflow example kindly contributed by Greg Jeffries
  • Added continuous integration and badges
  • Updated package to use symbol registration for compiled code
  • Updated and edited DESCRIPTION, README and help pages for current packaging standards
  • Expanded README with usage example via r-devel-san Rocker container

Courtesy of my CRANberries, there is a diffstat report for this release. See the project page, the github repo, and the package documentation for more details. If you like the open-source work I do, you can sponsor me at GitHub.

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

27 May 2023

Dirk Eddelbuettel: RcppArmadillo 0.12.4.0.0 on CRAN: New Upstream Minor

armadillo image Armadillo is a powerful and expressive C++ template library for linear algebra and scientific computing. It aims towards a good balance between speed and ease of use, has a syntax deliberately close to Matlab, and is useful for algorithm development directly in C++, or quick conversion of research code into production environments. RcppArmadillo integrates this library with the R environment and language and is widely used by (currently) 1074 other packages on CRAN, downloaded 29.3 million times (per the partial logs from the cloud mirrors of CRAN), and the CSDA paper (preprint / vignette) by Conrad and myself has been cited 535 times according to Google Scholar. This release brings a new upstream release 12.4.0 made by Conrad a day or so ago. I prepared the usual release candidate, tested on the over 1000 reverse depends (which sadly takes almost a day on old hardware), found no issues and sent it to CRAN. Where it got tested again and was once again auto-processed smoothly by CRAN within a few hours on a Friday night which is just marvelous. So this time I tweeted about it too. The releases actually has a relatively small set of changes as a second follow-up release in the 12.* series.

Changes in RcppArmadillo version 0.12.4.0.0 (2023-05-26)
  • Upgraded to Armadillo release 12.4.0 (Cortisol Profusion Redux)
    • Added norm2est() for finding fast estimates of matrix 2-norm (spectral norm)
    • Added vecnorm() for obtaining the vector norm of each row or column of a matrix

Courtesy of my CRANberries, there is a diffstat report relative to previous release. More detailed information is on the RcppArmadillo page. Questions, comments etc should go to the rcpp-devel mailing list off the R-Forge page. If you like my open-source work, you may consider sponsoring me at GitHub.

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

25 May 2023

Dirk Eddelbuettel: qlcal 0.0.6 on CRAN: More updates from QuantLib

The sixth release of the still new-ish qlcal package arrivied at CRAN today. qlcal delivers the calendaring parts of QuantLib. It is provided (for the R package) as a set of included files, so the package is self-contained and does not depend on an external QuantLib library (which can be demanding to build). qlcal covers over sixty country / market calendars and can compute holiday lists, its complement (i.e. business day lists) and much more. This release brings updates to a few calendars which happened since the QuantLib 1.30 release, and also updates a several of the (few) non-calendaring functions.

Changes in version 0.0.6 (2023-05-24)
  • Several calendars (India, Singapore, South Africa, South Korea) updated with post-QuantLib 1.3.0 changes (Sebastian Schmidt in #6)
  • Three now-used scheduled files were removed (Dirk in #7))
  • A number of non-calendaring files used were synchronised with the current QuantLib repo (Dirk in #8)

Last release, we also added a quick little demo using xts to column-bind calendars produced from each of the different US sub-calendars. This is a slightly updated version of the sketch we tooted a few days ago. The output now is 
> print(Reduce(cbind, Map(makeHol, cals)))
           LiborImpact NYSE GovernmentBond NERC FederalReserve
2023-01-02        TRUE TRUE           TRUE TRUE           TRUE
2023-01-16        TRUE TRUE           TRUE   NA           TRUE
2023-02-20        TRUE TRUE           TRUE   NA           TRUE
2023-04-07          NA TRUE             NA   NA             NA
2023-05-29        TRUE TRUE           TRUE TRUE           TRUE
2023-06-19        TRUE TRUE           TRUE   NA           TRUE
2023-07-04        TRUE TRUE           TRUE TRUE           TRUE
2023-09-04        TRUE TRUE           TRUE TRUE           TRUE
2023-10-09        TRUE   NA           TRUE   NA           TRUE
2023-11-10        TRUE   NA             NA   NA             NA
2023-11-23        TRUE TRUE           TRUE TRUE           TRUE
2023-12-25        TRUE TRUE           TRUE TRUE           TRUE
>
Courtesy of my CRANberries, there is a diffstat report for this release. See the project page and package documentation for more details, and more examples. If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

15 May 2023

Dirk Eddelbuettel: RcppSimdJson 0.1.10 on CRAN: New Upstream

We are happy to share that the RcppSimdJson package has been updated to release 0.1.10. RcppSimdJson wraps the fantastic and genuinely impressive simdjson library by Daniel Lemire and collaborators. Via very clever algorithmic engineering to obtain largely branch-free code, coupled with modern C++ and newer compiler instructions, it results in parsing gigabytes of JSON parsed per second which is quite mindboggling. The best-case performance is faster than CPU speed as use of parallel SIMD instructions and careful branch avoidance can lead to less than one cpu cycle per byte parsed; see the video of the talk by Daniel Lemire at QCon. This release updates the underlying simdjson library to version 3.1.8 (also made today). Otherwise we only made a minor edit to the README and adjusted one tweek for code coverage. The (very short) NEWS entry for this release follows.

Changes in version 0.1.10 (2023-05-14)
  • simdjson was upgraded to version 3.1.8 (Dirk in #85).

Courtesy of my CRANberries, there is also a diffstat report for this release. For questions, suggestions, or issues please use the issue tracker at the GitHub repo. If you like this or other open-source work I do, you can now sponsor me at GitHub.

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

12 May 2023

Dirk Eddelbuettel: crc32c 0.0.2 on CRAN: Build Fixes

A first follow-up to the initial announcement just days ago of the new crc32c package. The package offers cyclical checksum with parity in hardware-accelerated form on (recent enough) intel cpus as well as on arm64. This follow-up was needed because I missed, when switching to a default static library build, that newest compilers would complain if -fPIC was not set. gcc-12 on my box was happy, gcc-13 on recent Fedora as used at CRAN was not. A second error was assuming that saying SystemRequirements: cmake would suffice. But hold on whippersnapper: macOS always has a surprise for you! As described at the end of the appropriate section in Writing R Extensions, on that OS you have to go the basement, open four cupboards, rearrange three shelves and then you get to use it. And then in doing so (from an added configure script) I failed to realize Windows needed a fallback. Gee. The NEWS entry for this (as well the initial release) follows.

Changes in version 0.0.2 (2023-05-11)
  • Explicitly set cmake property for position-independent code
  • Help macOS find its cmake binary as detailed also in WRE
  • Help Windows with a non-conditional Makevars.win pointing at cmake
  • Add more badges to README.md

Changes in version 0.0.1 (2023-05-07)
  • Initial release version and CRAN upload

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

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

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