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.

/code/digest | permanent link

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.

/code/rcpp | permanent link

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.

/code/binb | permanent link

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.

/code/littler | permanent link

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

Mon, 21 Oct 2019

digest 0.6.22: More goodies!

A new version of digest arrived at CRAN earlier today, and I just sent an updated package to Debian too.

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 pretty much exactly one month after the very nice 0.6.21 release but contains five new pull requests. Matthew de Queljoe did a little bit of refactoring of the vectorised digest function he added in 0.6.21. Ion Suruceanu added a CFB cipher for AES. Bill Denney both corrected and extended sha1. And Jim Hester made the windows-side treatment of filenames UTF-8 compliant.

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

Sun, 20 Oct 2019

RcppGSL 0.3.7: Fixes and updates

A new release 0.3.7 of RcppGSL is now on CRAN. The RcppGSL package provides an interface from R to the GNU GSL using the Rcpp package.

Stephen Wade noticed that we were not actually freeing memory from the GSL vectors and matrices as we set out to do. And he is quite right: a dormant bug, present since the 0.3.0 release, has now been squashed. I had one boolean wrong, and this has now been corrected. I also took the opportunity to switch the vignette to prebuilt mode: Now a pre-made pdf is just included in a Sweave document, which makes the build more robust to tooling changes around the vignette processing. Lastly, the package was converted to the excellent tinytest unit test framework. Detailed changes below.

Changes in version 0.3.7 (2019-10-20)

  • A logic error was corrected in the wrapper class, vector and matrix memory is now properly free()'ed (Dirk in #22 fixing #20).

  • The introductory vignettes is now premade (Dirk in #23), and was updated lightly in its bibliography handling.

  • The unit tests are now run by tinytest (Dirk in #24).

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

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

If you like this or other open-source work I do, you can now sponsor me at GitHub. 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, 12 Oct 2019

GitHub Streak: Round Six

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

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

and then showed the first chart of GitHub streaking

github activity october 2013 to october 2014
github activity october 2013 to october 2014

And four year ago a first follow-up appeared in this post:

github activity october 2014 to october 2015
github activity october 2014 to october 2015

And three years ago we had a followup

github activity october 2015 to october 2016
github activity october 2015 to october 2016

And two years ago we had another one

github activity october 2016 to october 2017
github activity october 2016 to october 2017

And last year another one

github activity october 2017 to october 2018
github activity october 2017 to october 2018

As today is October 12, here is the newest one from 2018 to 2019:

github activity october 2018 to october 2019
github activity october 2018 to october 2019

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

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

/computers/misc | permanent link

Wed, 09 Oct 2019

RcppArmadillo 0.9.800.1.0

armadillo image

Another month, another Armadillo upstream release! Hence a new RcppArmadillo release arrived on CRAN earlier today, and was just shipped to Debian as well. It brings a faster solve() method and other goodies. We also switched to the (awesome) tinytest unit test frameowrk, and Min Kim made the configure.ac script more portable for the benefit of NetBSD and other non-bash users; see below for more details. One again we ran two full sets of reverse-depends checks, no issues were found, and the packages was auto-admitted similarly at CRAN after less than two hours despite there being 665 reverse depends. Impressive stuff, so a big Thank You! as always to the CRAN team.

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) 665 other packages on CRAN.

Changes in RcppArmadillo version 0.9.800.1.0 (2019-10-09)

  • Upgraded to Armadillo release 9.800 (Horizon Scraper)

    • faster solve() in default operation; iterative refinement is no longer applied by default; use solve_opts::refine to explicitly enable refinement

    • faster expmat()

    • faster handling of triangular matrices by rcond()

    • added .front() and .back()

    • added .is_trimatu() and .is_trimatl()

    • added .is_diagmat()

  • The package now uses tinytest for unit tests (Dirk in #269).

  • The configure.ac script is now more careful about shell portability (Min Kim in #270).

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.

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, 23 Sep 2019

RcppAnnoy 0.0.13

annoy image

A new release of RcppAnnoy is now on CRAN.

RcppAnnoy is the Rcpp-based R integration of the nifty Annoy library by Erik Bernhardsson. Annoy is a small and lightweight C++ template header library for very fast approximate nearest neighbours—originally developed to drive the famous Spotify music discovery algorithm.

This release brings several updates. First and foremost, the upstream Annoy C++ code was updated from version 1.12 to 1.16 bringing both speedier code thanks to AVX512 instruction (where available) and new functionality. Which we expose in two new functions of which buildOnDisk() may be of interest for some using the file-back indices. We also corrected a minor wart in which a demo file was saved (via example()) to a user directory; we now use tempfile() as one should, and contributed two small Windows build changes back to Annoy.

Detailed changes follow below.

Changes in version 0.0.13 (2019-09-23)

  • In example(), the saved and loaded filename is now obtained via tempfile() to not touch user directories per CRAN Policy (Dirk).

  • RcppAnnoy was again synchronized with Annoy upstream leading to enhanced performance and more features (Dirk #48).

  • Minor changes made (and send as PRs upstream) to adapt both annoylib.h and mman.h changes (Dirk).

  • A spurious command was removed from one vignette (Peter Hickey in #49).

  • Two new user-facing functions onDiskBuild() and unbuild() were added (Dirk in #50).

  • Minor tweaks were made to two tinytest-using test files (Dirk).

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

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, 20 Sep 2019

digest 0.6.21

A new version of digest is just now arriving at CRAN (following a slight holdup over one likely spurious reverse dependency error), and I will send an updated package to Debian shortly as well.

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 795k downloads) as many tasks may involve caching of objects for which it provides convenient general-purpose hash key generation.

Every now and then open source work really surprises you. Out of nowhere arrived a very fine pull request by Matthew de Queljoe which adds a very clever function getVDigest() supplying a (much faster) vectorized wrapper for digest creation. We illustrate this in a quick demo vectorized.R that is included too. So if you call digest() in bulk, this will most likely be rather helpful to you. Matthew even did further cleanups and refactorings but we are saving that for a subsequent pull request or two.

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

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

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

/code/digest | permanent link

Sun, 15 Sep 2019

pinp 0.0.9: Real Fix and Polish

Another pinp package release! pinp allows for snazzier one or two column Markdown-based pdf vignettes, and is now used by a few packages. A screenshot of the package vignette can be seen below. Additional screenshots are at the pinp page.

pinp vignette

This release comes exactly one week (i.e. the minimal time to not earn a NOTE) after the hot-fix release 0.0.8 which addressed breakage on CRAN tickled by changed in TeX Live. After updating the PNAS style LaTeX macros, and avoiding the issue with an (older) custom copy of titlesec, we now have the real fix, thanks to the eagle-eyed attention of Javier Bezos. The error, as so often, was simple and ours: we had left a stray \makeatother in pinp.cls where it may have been in hiding for a while. A very big Thank You! to Javier for spotting it, to Norbert for all his help and to James for double-checking on PNAS.

The good news in all of this is that the package is now in better shape than ever. The newer PNAS style works really well, and I went over a few of our extensions (such as papersize support for a4 as well as letter), direct on/off off a Draft watermark, a custom subtitle and more—and they all work consistently. So happy vignette or paper writing!

The NEWS entry for this release follows.

Changes in pinp version 0.0.9 (2019-09-15)

  • The processing error first addressed in release 0.0.8 is now fixed by removing one stray command; many thanks to Javier Bezos.

  • The hotfix of also installing titlesec.sty has been reverted.

  • Processing of the 'papersize' and 'watermark' options was updated.

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

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

/code/pinp | permanent link

Fri, 13 Sep 2019

ttdo 0.0.3: New package

A new package of mine arrived on CRAN yesterday, having been uploaded a few days prior on the weekend. It 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. Mark also tweeted about it.

ttdo screenshot

The package was written to address a fairly specific need. In teaching STAT 430 at Illinois, I am relying on the powerful PrairieLearn system (developed there) to provides tests, quizzes or homework. Alton and I have put together an autograder for R (which is work in progress, more on that maybe another day), and that uses this package to provides colorized differences between supplied and expected answers in case of an incorrect answer.

Now, the aspect of providing colorized diffs when tests do not evalute to TRUE is both simple and general enough. As our approach works rather well, I decided to offer the package on CRAN as well. The small screenshot gives a simple idea, the README.md contains a larger screenshoot.

The initial NEWS entries follow below.

Changes in ttdo version 0.0.3 (2019-09-08)

  • Added a simple demo to support initial CRAN upload.

Changes in ttdo version 0.0.2 (2019-08-31)

  • Updated defaults for format and mode to use the same options used by diffobj along with fallbacks.

Changes in ttdo version 0.0.1 (2019-08-26)

  • Initial version, with thanks to both Mark and Brodie.

Please use the GitHub repo and its issues for any questions.

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

Sun, 08 Sep 2019

pinp 0.0.8: Bugfix

A new release of our pinp package is now on CRAN. pinp allows for snazzier one or two column Markdown-based pdf vignettes, and is now used by a few packages. A screenshot of the package vignette can be seen below. Additional screenshots are at the pinp page.

pinp vignette

This release was spurned by one of those "CRAN package xyz" emails I received yesterday: processing of pinp-using vignettes was breaking at CRAN under the newest TeX Live release present on Debian testing as well as recent Fedora. The rticles package (which uses the PNAS style directly) apparently has a similar issue with PNAS.

Kurt was a usual extremely helpful in debugging, and we narrowed this down to an interaction with the newer versions of titlesec latex package. So for now we did two things: upgrade our code reusing the PNAS class to their newest verson of the PNAS class (as suggested by Norbert whom I also roped in), but also copying in an older version of titlesec.sty (plus a support file). In the meantime, we are also looking into titlesec directly as Javier offered help—all this was a really decent example of open source firing on all cylinders. It is refreshing.

Because of the move to a newer PNAS version (which seems to clearly help with the occassionally odd formatting of floating blocks near the document end) I may have trampled on earlier extension pull requests. I will reach out to the authors of the PRs to work towards a better process with cleaner diffs, a process I should probably have set up earlier.

The NEWS entry for this release follows.

Changes in pinp version 0.0.8 (2019-09-08)

  • Two erroraneous 'Provides' were removed from the pinp class.

  • The upquote package is now use to use actual (non-fancy) quotes in verbatim mode (Dirk fixing #75)

  • The underlying PNAS style was updated to the most recent v1.44 version of 2018-05-06 to avoid issues with newer TeXLive (Dirk in #79 fixing #77 and #78)

  • The new PNAS code brings some changes eg watermark is longer an option but typesetting paragraphs seems greatly improved. We may have stomped on an existing behavior, if see please file an issue.

  • However, it also conflicts with the current texlive version of titlesec so for now we copy titlesec.sty (and a support file) in using a prior version, just like we do for pinp.cls and jss.bst.

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

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

/code/pinp | permanent link

Mon, 02 Sep 2019

RcppArmadillo 0.9.700.2.0

armadillo image

A new RcppArmadillo release based on a new Armadillo upstream release arrived on CRAN, and will get to Debian shortly. It brings continued improvements for sparse matrices and a few other things; see below for more details. I also appear to have skipped blogging about the preceding 0.9.600.4.0 release (which was actually extra-rigorous with an unprecedented number of reverse-depends runs) so I included its changes (with very nice sparse matrix improvements) as well.

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) 656 other packages on CRAN.

Changes in RcppArmadillo version 0.9.700.2.0 (2019-09-01)

  • Upgraded to Armadillo release 9.700.2 (Gangster Democracy)

    • faster handling of cubes by vectorise()

    • faster faster handling of sparse matrices by nonzeros()

    • faster row-wise index_min() and index_max()

    • expanded join_rows() and join_cols() to handle joining up to 4 matrices

    • expanded .save() and .load() to allow storing sparse matrices in CSV format

    • added randperm() to generate a vector with random permutation of a sequence of integers

  • Expanded the list of known good gcc and clang versions in configure.ac

Changes in RcppArmadillo version 0.9.600.4.0 (2019-07-14)

  • Upgraded to Armadillo release 9.600.4 (Napa Invasion)

    • faster handling of sparse submatrices

    • faster handling of sparse diagonal views

    • faster handling of sparse matrices by symmatu() and symmatl()

    • faster handling of sparse matrices by join_cols()

    • expanded clamp() to handle sparse matrices

    • added .clean() to replace elements below a threshold with zeros

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.

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, 29 Aug 2019

anytime 0.3.6

A fresh and very exciting release of the anytime package is arriving on CRAN right now. This is the seventeenth release, and it comes pretty much exactly one month after the preceding 0.3.5 release.

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 updates a number of things (see below for details). For users, maybe the most important change is that we now also convert single-digit months, i.e. a not-quite ISO input like “2019-7-5” passes. This required adding %e as a month format; I had overlooked this detail in the (copious) Boost date_time documentation. Another nice change is that we now use standard S3 dispatching rather a manual approach as we probably should have for a long time :-) but better late than never. The code change was actually rather minimal and done in a few minutes. Another change is a further extended use of unit testing via the excellent tinytest package which remains a joy to use. We also expanded the introductory pdf vignette; the benchmark comparisons we included look pretty decent for anytime which still combines ease of use and versability with performance.

Lastly, a somewhat sad “lowlight”. We submitted the package to the Journal of Open Source Software who then told us within days of the unworthyness of anytime for lack of research focus. Needless to see, we disagree. So here is plea: If you use anytime in a research setting, would you mind adding to the this very issue ticket and saying so? This may permit us a somewhat more emphatic data-driven riposte to the editors. Many thanks in advance for considering this.

The full list of changes follows.

Changes in anytime version 0.3.6 (2019-08-29)

  • Added, and then removed, required file for JOSS; added 'unworthy' badge as we earned a desk reject (cf #1605 there).

  • Renamed internal helper function format() to fmt() to avoid clashes with base::format() (Dirk in #104).

  • Use S3 dispatch and generics for key functions (Dirk in #106).

  • Continued to tweak tests as we find some of the rhub platform to behave strangely (Dirk via commits as well as #107).

  • Added %e format for single-digit day parsing by Boost (Dirk addressing at least #24, #70 and #99).

  • Expansed and updated vignette with benchmark comparisons.

  • Updated unit tests using tinytest which remains a pleasure to use; versioned Suggests: is now '>= 1.0.0'.

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.

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

Sat, 24 Aug 2019

RcppExamples 0.1.9

A new version of the RcppExamples package is now on CRAN.

The RcppExamples package provides a handful of short examples detailing by concrete working examples how to set up basic R data structures in C++. It also provides a simple example for packaging with Rcpp.

This releases brings a number of small fixes, including two from contributed pull requests (extra thanks for those!), and updates the package in a few spots. The NEWS extract follows:

Changes in RcppExamples version 0.1.9 (2019-08-24)

  • Extended DateExample to use more new Rcpp features

  • Do not print DataFrame result twice (Xikun Han in #3)

  • Missing parenthesis added in man page (Chris Muir in #5)

  • Rewrote StringVectorExample slightly to not run afould the -Wnoexcept-type warning for C++17-related name mangling changes

  • Updated NAMESPACE and RcppExports.cpp to add registration

  • Removed the no-longer-needed #define for new Datetime vectors

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

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

/code/rcpp | permanent link

Wed, 21 Aug 2019

Rcpp now used by 1750 CRAN packages

1751 Rcpp packages

Since this morning, Rcpp stands at just over 1750 reverse-dependencies on CRAN. The graph on the left depicts the growth of Rcpp usage (as measured by Depends, Imports and LinkingTo, but excluding Suggests) over time.

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

Also displayed in the graph is the relative proportion of CRAN packages using Rcpp. The four per-cent hurdle was cleared just before useR! 2014 where I showed a similar graph (as two distinct graphs) in my invited talk. We passed five percent in December of 2014, six percent July of 2015, seven percent just before Christmas 2015, eight percent last summer, nine percent mid-December 2016, cracked ten percent in the summer of 2017 and eleven percent in 2018. We are currently at 11.83 percent: a little over one in nine packages. There is more detail in the chart: how CRAN seems to be pushing back more and removing more aggressively (which my CRANberries tracks but not in as much detail as it could), how the growth of Rcpp seems to be slowing somewhat outright and even more so as a proportion of CRAN – just like one would expect a growth curve to.

1753 Rcpp packages

1750+ user packages is pretty mind-boggling. We can use the progression of CRAN itself compiled by Henrik in a series of posts and emails to the main development mailing list. Not that long ago CRAN itself did not have 1500 packages, and here we are at almost 14810 with Rcpp at 11.84% and still growing (though maybe more slowly). Amazeballs.

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

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

/code/rcpp | permanent link

Mon, 19 Aug 2019

RcppQuantuccia 0.0.3

A maintenance release of RcppQuantuccia arrived on CRAN earlier today.

RcppQuantuccia brings the Quantuccia header-only subset / variant of QuantLib to R. At the current stage, it mostly offers date and calendaring functions.

This release was triggered by some work CRAN is doing on updating C++ standards for code in the repository. Notably, under C++11 some constructs such ptr_fun, bind1st, bind2nd, … are now deprecated, and CRAN prefers the code base to not issue such warnings (as e.g. now seen under clang++-9). So we updated the corresponding code in a good dozen or so places to the (more current and compliant) code from QuantLib itself.

We also took this opportunity to significantly reduce the footprint of the sources and the installed shared library of RcppQuantuccia. One (unexported) feature was pricing models via Brownian Bridges based on quasi-random Sobol sequences. But the main source file for these sequences comes in at several megabytes in sizes, and allocates a large number of constants. So in this version the file is excluded, making the current build of RcppQuantuccia lighter in size and more suitable for the (simpler, popular and trusted) calendar functions. We also added a new holiday to the US calendar.

The complete list changes follows.

Changes in version 0.0.3 (2019-08-19)

  • Updated Travis CI test file (#8)).

  • Updated US holiday calendar data with G H Bush funeral date (#9).

  • Updated C++ use to not trigger warnings [CRAN request] (#9).

  • Comment-out pragmas to suppress warnings [CRAN Policy] (#9).

  • Change build to exclude Sobol sequence reducing file size for source and shared library, at the cost of excluding market models (#10).

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

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, 07 Aug 2019

RQuantLib 0.4.10: Pure maintenance

A new version 0.4.10 of RQuantLib just got onto CRAN; a Debian upload will follow in due course.

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

This version does two things related to the new upstream QuantLib release 1.16. First, it updates the Windows build script in two ways: it uses binaries for the brand new 1.16 release as prepapred by Jeroen, and it sets win-builder up for the current and “prospective next version”, also set up by Jeroen. I also updated the Dockerfile used for CI to pick QuantLib 1.16 from Debian’s unstable repo as it is too new to have moved to testing (which the r-base container we build on defaults to). The complete set of changes is listed below:

Changes in RQuantLib version 0.4.10 (2019-08-07)

  • Changes in RQuantLib build system:

    • The src/Makevars.win and tools/winlibs.R file get QuantLib 1.16 for either toolchain (Jeroes in #136).

    • The custom Docker container now downloads QuantLib from Debian unstable to get release 1.16 (from yesterday, no less)

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.

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

/code/rquantlib | permanent link

Mon, 05 Aug 2019

#23: Debugging with Docker and Rocker – A Concrete Example helping on macOS

Welcome to the 23nd post in the rationally reasonable R rants series, or R4 for short. Today’s post was motivated by an exchange on the r-devel list earlier in the day, and a few subsequent off-list emails.

Roger Koenker posted a question: how to best debug an issue arising only with gfortran-9 which is difficult to get hold off on his macOS development platform. Some people followed up, and I mentioned that I had good success using Docker, and particularly our Rocker containers—and outlined a quick mini-tutorial (which had one mini-typo lacking the imporant slash in -w /work). Roger and I followed up over a few more off-list emails, and by and large this worked for him.

So what follows below is a jointly written / edited ‘mini HOWTO’ of how to deploy Docker on macOS for debugging under particular toolchains more easily available on Linux. Windows and Linux use should be very similar, albeit differ in the initial install. In fact, I frequently debug or test in Docker sessions when I do not want to install on my Linux host system. Roger sent one version (I had also edited) back to the list. What follows is my final version.

Debugging with Docker: Getting Hold of Particular Compilers

Context: The quantreg package was seen exhibiting errors when compiled with gfortran-9. The following shows how to use gfortran-9 on macOS by virtue of Docker. It is written in Roger Koenker’s voice, but authored by Roger and myself.

With extensive help from Dirk Eddelbuettel I have installed docker on my mac mini from

https://hub.docker.com/editions/community/docker-ce-desktop-mac

which installs from a dmg in quite standard fashion. This has allowed me to simulate running R in a Debian environment with gfortran-9 and begin the process of debugging my ancient rqbr.f code.

Some further details:

Step 0: Install Docker and Test

Install Docker for macOS following this Docker guide. Do some initial testing, e.g.

Step 1: Download r-base and test OS

We use the plainest Rocker container rocker/r-base, in the aliased form of the official Docker container for, i.e. r-base. We first ‘pull’, then test the version and drop into bash as second test.

Step 2: Setup the working directory

We tell Docker to run from the current directory and access the files therein. For the work on quantreg package this is projects/rq for RogerL

This put the contents of projects/rq into the /work directory, and starts the session in /work (as can be seen from the prompt).

Next, we update the package information inside the container:

Step 3: Install gcc-9 and gfortran-9

root@90521904fa86:/work# apt-get install gcc-9 gfortran-9
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
cpp-9 gcc-9-base libasan5 libatomic1 libcc1-0 libgcc-9-dev libgcc1 libgfortran-9-dev
libgfortran5 libgomp1 libitm1 liblsan0 libquadmath0 libstdc++6 libtsan0 libubsan1
Suggested packages:
gcc-9-locales gcc-9-multilib gcc-9-doc libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan5-dbg liblsan0-dbg libtsan0-dbg libubsan1-dbg libquadmath0-dbg gfortran-9-multilib
gfortran-9-doc libgfortran5-dbg libcoarrays-dev
The following NEW packages will be installed:
cpp-9 gcc-9 gfortran-9 libgcc-9-dev libgfortran-9-dev
The following packages will be upgraded:
gcc-9-base libasan5 libatomic1 libcc1-0 libgcc1 libgfortran5 libgomp1 libitm1 liblsan0
libquadmath0 libstdc++6 libtsan0 libubsan1
13 upgraded, 5 newly installed, 0 to remove and 71 not upgraded.
Need to get 35.6 MB of archives.
After this operation, 107 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libasan5 amd64 9.1.0-10 [390 kB]
Get:2 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libubsan1 amd64 9.1.0-10 [128 kB]
Get:3 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libtsan0 amd64 9.1.0-10 [295 kB]
Get:4 http://cdn-fastly.deb.debian.org/debian testing/main amd64 gcc-9-base amd64 9.1.0-10 [190 kB]
Get:5 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libstdc++6 amd64 9.1.0-10 [500 kB]
Get:6 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libquadmath0 amd64 9.1.0-10 [145 kB]
Get:7 http://cdn-fastly.deb.debian.org/debian testing/main amd64 liblsan0 amd64 9.1.0-10 [137 kB]
Get:8 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libitm1 amd64 9.1.0-10 [27.6 kB]
Get:9 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libgomp1 amd64 9.1.0-10 [88.1 kB]
Get:10 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libgfortran5 amd64 9.1.0-10 [633 kB]
Get:11 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libcc1-0 amd64 9.1.0-10 [47.7 kB]
Get:12 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libatomic1 amd64 9.1.0-10 [9,012 B]
Get:13 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libgcc1 amd64 1:9.1.0-10 [40.5 kB]
Get:14 http://cdn-fastly.deb.debian.org/debian testing/main amd64 cpp-9 amd64 9.1.0-10 [9,667 kB]
Get:15 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libgcc-9-dev amd64 9.1.0-10 [2,346 kB]
Get:16 http://cdn-fastly.deb.debian.org/debian testing/main amd64 gcc-9 amd64 9.1.0-10 [9,945 kB]
Get:17 http://cdn-fastly.deb.debian.org/debian testing/main amd64 libgfortran-9-dev amd64 9.1.0-10 [676 kB]
Get:18 http://cdn-fastly.deb.debian.org/debian testing/main amd64 gfortran-9 amd64 9.1.0-10 [10.4 MB]
Fetched 35.6 MB in 6s (6,216 kB/s)      
debconf: delaying package configuration, since apt-utils is not installed
(Reading database ... 17787 files and directories currently installed.)
Preparing to unpack .../libasan5_9.1.0-10_amd64.deb ...
Unpacking libasan5:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../libubsan1_9.1.0-10_amd64.deb ...
Unpacking libubsan1:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../libtsan0_9.1.0-10_amd64.deb ...
Unpacking libtsan0:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../gcc-9-base_9.1.0-10_amd64.deb ...
Unpacking gcc-9-base:amd64 (9.1.0-10) over (9.1.0-8) ...
Setting up gcc-9-base:amd64 (9.1.0-10) ...
(Reading database ... 17787 files and directories currently installed.)
Preparing to unpack .../libstdc++6_9.1.0-10_amd64.deb ...
Unpacking libstdc++6:amd64 (9.1.0-10) over (9.1.0-8) ...
Setting up libstdc++6:amd64 (9.1.0-10) ...
(Reading database ... 17787 files and directories currently installed.)
Preparing to unpack .../0-libquadmath0_9.1.0-10_amd64.deb ...
Unpacking libquadmath0:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../1-liblsan0_9.1.0-10_amd64.deb ...
Unpacking liblsan0:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../2-libitm1_9.1.0-10_amd64.deb ...
Unpacking libitm1:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../3-libgomp1_9.1.0-10_amd64.deb ...
Unpacking libgomp1:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../4-libgfortran5_9.1.0-10_amd64.deb ...
Unpacking libgfortran5:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../5-libcc1-0_9.1.0-10_amd64.deb ...
Unpacking libcc1-0:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../6-libatomic1_9.1.0-10_amd64.deb ...
Unpacking libatomic1:amd64 (9.1.0-10) over (9.1.0-8) ...
Preparing to unpack .../7-libgcc1_1%3a9.1.0-10_amd64.deb ...
Unpacking libgcc1:amd64 (1:9.1.0-10) over (1:9.1.0-8) ...
Setting up libgcc1:amd64 (1:9.1.0-10) ...
Selecting previously unselected package cpp-9.
(Reading database ... 17787 files and directories currently installed.)
Preparing to unpack .../cpp-9_9.1.0-10_amd64.deb ...
Unpacking cpp-9 (9.1.0-10) ...
Selecting previously unselected package libgcc-9-dev:amd64.
Preparing to unpack .../libgcc-9-dev_9.1.0-10_amd64.deb ...
Unpacking libgcc-9-dev:amd64 (9.1.0-10) ...
Selecting previously unselected package gcc-9.
Preparing to unpack .../gcc-9_9.1.0-10_amd64.deb ...
Unpacking gcc-9 (9.1.0-10) ...
Selecting previously unselected package libgfortran-9-dev:amd64.
Preparing to unpack .../libgfortran-9-dev_9.1.0-10_amd64.deb ...
Unpacking libgfortran-9-dev:amd64 (9.1.0-10) ...
Selecting previously unselected package gfortran-9.
Preparing to unpack .../gfortran-9_9.1.0-10_amd64.deb ...
Unpacking gfortran-9 (9.1.0-10) ...
Setting up libgomp1:amd64 (9.1.0-10) ...
Setting up libasan5:amd64 (9.1.0-10) ...
Setting up libquadmath0:amd64 (9.1.0-10) ...
Setting up libatomic1:amd64 (9.1.0-10) ...
Setting up libgfortran5:amd64 (9.1.0-10) ...
Setting up libubsan1:amd64 (9.1.0-10) ...
Setting up cpp-9 (9.1.0-10) ...
Setting up libcc1-0:amd64 (9.1.0-10) ...
Setting up liblsan0:amd64 (9.1.0-10) ...
Setting up libitm1:amd64 (9.1.0-10) ...
Setting up libtsan0:amd64 (9.1.0-10) ...
Setting up libgcc-9-dev:amd64 (9.1.0-10) ...
Setting up gcc-9 (9.1.0-10) ...
Setting up libgfortran-9-dev:amd64 (9.1.0-10) ...
Setting up gfortran-9 (9.1.0-10) ...
Processing triggers for libc-bin (2.28-10) ...
root@90521904fa86:/work# pwd

Here filenames and versions reflect the Debian repositories as of today, August 5, 2019. While minor details may change at a future point in time, the key fact is that we get the components we desire via a single call as the Debian system has a well-honed package system

Step 4: Prepare Package

At this point Roger removed some dependencies from the package quantreg that he knew were not relevant to the debugging problem at hand.

Step 5: Set Compiler Flags

Next, set compiler flags as follows:

adding the values

CC=gcc-9
FC=gfortran-9
F77=gfortran-9

to the file. Alternatively, one can find the settings of CC, FC, CXX, … in /etc/R/Makeconf (which for the Debian package is a softlink to R’s actual Makeconf) and alter them there.

Step 6: Install the Source Package

Now run

which uses the gfortran-9 compiler, and this version did reproduce the error initially reported by the CRAN maintainers.

Step 7: Debug!

With the tools in place, and the bug reproduces, it is (just!) a matter of finding the bug and fixing it.

And that concludes the tutorial.

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, 03 Aug 2019

RcppCCTZ 0.2.6

A shiny new release 0.2.6 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 updates to CCTZ release 2.3 from April, plus changes accrued since then. It also switches to tinytest which, among other benefits, permits continued testing of the installed package.

Changes in version 0.2.6 (2019-08-03)

  • Synchronized with upstream CCTZ release 2.3 plus commits accrued since then (Dirk in #30).

  • The package now uses tinytest for unit tests (Dirk in #31).

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.

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

/code/rcpp | permanent link

Sun, 28 Jul 2019

anytime 0.3.5

A new release of the anytime package is arriving on CRAN. This is the sixteenth release, and comes a good month after the 0.3.4 release.

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 reworked fallback mechanism enabled via the useR=TRUE option. Because Windows remains a challenging platform which, among other more important ailments, also does not provide timezone information, we no longer rely on the RApiDatetime package which exposes parts of the R API. This works everywhere where timezone information is available, but less so on Windows. Instead, we now use Rcpp::Function to call directly back into R. This received a considerable amount of testing, and the package should now work even better when either a timezone is set, or the Windows fallback is used, or both. My thanks to Christoph Sax for patiently testing and helping to debug this, as well as for his two pull requests contributing to this release (even if one of these is now redundant as we no longer use RApiDatetime).

The full list of changes follows.

Changes in anytime version 0.3.5 (2019-07-28)

  • Fix use of Rcpp::Function-accessed Sys.setenv(), name all arguments in call to C++ (Christoph Sax in #95).

  • Relax constraint on Windows testing in several test files (Christoph Sax in #97).

  • Fix an issue related to TZ environment variable setting (Dirk in #101).

  • Change useR=TRUE behaviour by directly calling R via Rcpp (Dirk in #103 fixing #96).

  • Several updates to unit testing files aiming for more robust behaviour across platforms.

  • Updated documentation in manual pages, README and vignette.

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.

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

Thu, 25 Jul 2019

Rcpp 1.0.2: Small Polish

The second maintenance release of Rcpp, following up on the 10th anniversary and the 1.0.0. release, was prepared last Saturday and released to both the Rcpp drat repo and CRAN. Following all the manual inspection (including a false positive result from reverse dependencies), it has finally arrived on CRAN earlier today. The corresponding Debian package was also uploaded, and binaries have since been built.

Just like for Rcpp 1.0.1, 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.

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1713 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with 176 in BioConductor. Per the (partial) logs of CRAN downloads, we have had over one million downloads a month following the previous release.

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

Changes in Rcpp version 1.0.2 (2019-07-20)

  • Changes in Rcpp API:

    • Files in src/ are now consistentely lowercase (Dirk in #956).

    • The Rcpp 'API Version' is now accessible via getRcppVersion() (Dirk in #963).

  • Changes in Rcpp Attributes:

    • The second END wrapper macro also gets UNPROTECT and a variable reference suppressing compiler warnings (Dirk in #953 fixing #951).

    • Default function arguments are parsed correctly (Pierrick Roger in #977 fixing #975)

  • Changes in Rcpp Sugar:

    • Added decreasing parameter to sort_unique() (James Balamuta in #958 addressing #950).
  • Changes in Rcpp Deployment:

    • Travis CI unit tests are now always running irrespective of the package version (Dirk in #954).
  • Changes in Rcpp Documentation:

    • The Rcpp-modules vignette now covers the RCPP_EXPOSED_* macros, and the Rcpp-extending vignette references it (Ralf Stubner in #959 fixing #952)

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.

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, 21 Jul 2019

RPushbullet 0.3.2

RPpushbullet demo

A new release 0.3.2 of the RPushbullet package is now on CRAN. RPushbullet is interfacing the neat Pushbullet service for inter-device messaging, communication, and more. It lets you easily send alerts like the one to the left to your browser, phone, tablet, … – or all at once.

This is the first new release in almost 2 1/2 years, and it once again benefits greatly from contributed pull requests by Colin (twice !) and Chan-Yub – see below for details.

Changes in version 0.3.2 (2019-07-21)

  • The Travis setup was robustified with respect to the token needed to run tests (Dirk in #48)

  • The configuration file is now readable only by the user (Colin Gillespie in #50)

  • At startup initialization is now more consistent (Colin Gillespie in #53 fixing #52)

  • A new function to fetch prior posts was added (Chanyub Park in #54). `

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.

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, 04 Jul 2019

digest 0.6.20

This morning, digest version 0.6.20 went to CRAN, and I will send a package to Debian shortly as well.

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.

This version contains only internal changes with a switch to the (excellent) tinytest package. This now allows you, dear user of the package, to run tinytest::test_package("digest") at any point post-installation to reassure yourself that all standard assertions and tests are still met in your installation. No other changes were made.

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

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

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

/code/digest | permanent link