Wed, 28 Nov 2018

RcppArmadillo 0.9.200.5.0

armadillo image

A new RcppArmadillo release arrived at CRAN overnight. The version 0.9.200.5.0 is a minor upgrade and based on the new Armadillo bugfix release 9.200.5 from yesterday. I also just uploaded the Debian version.

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) 539 other packages on CRAN.

This release just brings one upstream bug fix, see below for details.

Changes in RcppArmadillo version 0.9.200.5.0 (2018-11-09)

  • Upgraded to Armadillo release 9.200.5 (Carpe Noctem)

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.

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Sat, 24 Nov 2018

RcppEigen 0.3.3.5.0

Another minor release 0.3.3.5.0 of RcppEigen arrived on CRAN today (and just went to Debian too) bringing support for Eigen 3.3.5 to R.

As we now carry our small set of patches to Eigen as diff in our repo, it was fairly straightforward to bring these few changes to the new upstream version. I added one trivial fix of changing a return value to void as this is also already in the upstream repo. Other than that, we were fortunate to get two nice and focussed PRs since the last release. Ralf allowed us to use larger index values by using R_xlen_t, and Michael corrected use of RcppArmadillo in a benchmarking example script.

Next, it bears repeating what we said in February when we release 0.3.3.4.0:

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 uses RcppEigen very noisy so consider adding -Wno-ignored-attributes to the compiler flags added in your ~/.R/Makevars.

It’s still super-noise, but hey, CRAN made us do it …

The complete NEWS file entry follows.

Changes in RcppEigen version 0.3.3.5.0 (2018-11-24)

  • Updated to version 3.3.5 of Eigen (Dirk in #65)

  • Long vectors are now supported via R_xlen_t (Ralf Stubner in #55 fixing #54).

  • The benchmarking example was updated in its use of RcppArmadillo (Michael Weylandt in #56).

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.

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Sun, 18 Nov 2018

RcppMsgPack 0.2.3

Another maintenance release of RcppMsgPack got onto CRAN today. Two new helper functions were added and not unlike the previous 0.2.2 release in, some additional changes are internal and should allow compilation on all CRAN systems.

MessagePack itself is an efficient binary serialization format. It lets you exchange data among multiple languages like JSON. But it is faster and smaller. Small integers are encoded into a single byte, and typical short strings require only one extra byte in addition to the strings themselves. RcppMsgPack brings both the C++ headers of MessagePack as well as clever code (in both R and C++) Travers wrote to access MsgPack-encoded objects directly from R.

Changes in version 0.2.3 (2018-11-18)

  • New functions msgpack_read and msgpack_write for efficient direct access to MessagePackage content from files (#13).

  • Several internal code polishes to smooth compilation (#14 and #15).

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

More information is on the RcppRedis 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.

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Fri, 16 Nov 2018

RcppGetconf 0.0.3

A second and minor update for the RcppGetconf package for reading system configuration — not unlike getconf from the libc library — is now on CRAN.

Changes are minor. We avoid an error on a long-dead operating system cherished in one particular corner of the CRAN world. In doing so some files were updated so that dynamically loaded routines are now registered too.

The short list of changes in this release follows:

Changes in inline version 0.0.3 (2018-11-16)

  • Examples no longer run on Solaris where they appear to fail.

Courtesy of CRANberries, there is a diffstat report. More about the package is at the local RcppGetconf page and 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.

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Thu, 15 Nov 2018

Rcpp now used by 1500 CRAN packages

1500 Rcpp packages

Right now Rcpp stands at 1500 reverse-dependencies on CRAN. The graph is on the left depicts the growth of Rcpp usage (as measured by Depends, Imports and LinkingTo, but excluding Suggests) over time. What an amazing few days this has been as we also just marked the tenth anniversary and the big one dot oh release.

Rcpp cleared 300 packages in November 2014. It passed 400 packages in June 2015 (when I only 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, and 1250 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 kept on this page.

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 this year. We are currently at 11.199 percent or just 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 every growth curve should, eventually. But we leave all that for another time.

1500 Rcpp packages

1500 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 13400 with Rcpp at 11.2% and still growing (albeit slightly more slowly). Amazeballs.

This puts a whole lot of responsibility on us in the Rcpp team as we continue to keep Rcpp as performant and reliable as it has been.

And with that, and as always, a very big 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.

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Sat, 10 Nov 2018

RcppArmadillo 0.9.200.4.0

armadillo image

A new RcppArmadillo release, now at 0.9.200.4.0, based on the new Armadillo release 9.200.4 from earlier this week, is now on CRAN, and should get to Debian very soon.

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) 532 (or 31 more since just the last release!) other packages on CRAN.

This release once again brings a number of improvements, see below for details.

Changes in RcppArmadillo version 0.9.200.4.0 (2018-11-09)

  • Upgraded to Armadillo release 9.200.4 (Carpe Noctem)

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

    • faster transpose of matrices with size ≥ 512x512

    • faster handling of compound sparse matrix expressions by accu(), diagmat(), trace()

    • faster handling of sparse matrices by join_rows()

    • expanded sign() to handle scalar arguments

    • expanded operators (*, %, +, ) to handle sparse matrices with differing element types (eg. multiplication of complex matrix by real matrix)

    • expanded conv_to() to allow conversion between sparse matrices with differing element types

    • expanded solve() to optionally allow keeping solutions of systems singular to working precision

    • workaround for gcc and clang bug in C++17 mode

  • Commented-out sparse matrix test consistently failing on the fedora-clang machine CRAN, and only there. No fix without access.

  • The 'Unit test' vignette is no longer included.

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.

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Wed, 07 Nov 2018

Rcpp 1.0.0: The Tenth Birthday Release

As mentioned here two days ago, the Rcpp package turned ten on Monday—and we used to opportunity to mark the current version as 1.0.0! Thanks to everybody who liked and retweeted our tweet about this. And of course, once more a really big Thank You! to everybody who helped along this journey: Rcpp Core team, contributors, bug reporters, workshop and tutorial attendees and last but not least all those users – we did well. So let’s enjoy and celebrate this moment.

As indicated in Monday’s blog post, we had also planned to upload this version to CRAN, and this 1.0.0 release arrived on CRAN after the customary inspection and is now available. I will build the Debian package in a moment, it will find its way to Ubuntu and of the CRAN-mirrored backport that Michael looks after so well.

While this release is of course marked as 1.0.0 signifying the feature and release stability we have had for some time, it also marks another regular release at the now-common bi-monthly schedule following nineteen releases since July 2016 in the 0.12.* series as well as another five in the preceding 0.11.* series.

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1493 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with another 150 in the (very recent) BioConductor release 3.8. Per the (partial) logs of CRAN downloads, we were reaching more than 900,000 downloads a month of late.

Once again, we have a number of nice pull requests from the usual gang of contributors in there, see below for details.

Changes in Rcpp version 1.0.0 (2018-11-05)

  • Happy tenth birthday to Rcpp, and hello release 1.0 !

  • Changes in Rcpp API:

    • The empty destructor for the Date class was removed to please g++-9 (prerelease) and -Wdeprecated-copy (Dirk).

    • The constructor for NumericMatrix(not_init(n,k)) was corrected (Romain in #904, Dirk in #905, and also Romain in #908 fixing #907).

    • Rcpp::String no longer silently drops embedded NUL bytes in strings but throws new Rcpp exception embedded_nul_in_string. (Kevin in #917 fixing #916).

  • Changes in Rcpp Deployment:

    • The Dockerfile for Continuous Integration sets the required test flag (for release versions) inside the container (Dirk).

    • Correct the R CMD check call to skip vignettes (Dirk).

  • Changes in Rcpp Attributes:

    • A new [[Rcpp::init]] attribute allows function registration for running on package initialization (JJ in #903).

    • Sort the files scanned for attributes in the C locale for stable output across systems (JJ in #912).

  • Changes in Rcpp Documentation:

    • The 'Rcpp Extending' vignette was corrected and refers to EXPOSED rather than EXPORTED (Ralf Stubner in #910).

    • The 'Unit test' vignette is no longer included (Dirk in #914).

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.

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Mon, 05 Nov 2018

Happy 10th Bday, Rcpp – and welcome release 1.0 !!

Ten years ago today I wrote the NEWS.Rd entry in this screenshot for the very first Rcpp_release:

First Rcpp release
First Rcpp release

So Happy Tenth Birthday, Rcpp !! It has been quite a ride. Nearly 1500 packages on CRAN, or about one in nine (!!), rely on Rcpp to marshall data between R and C++, and to extend R with performant C++ code.

Rcpp would not exist without Dominick Samperi who recognised early just how well C++ template classes could fit the task of seamlessly interchanging data between the two systems, and contributed the first versions to my RQuantLib package. After a few versions he left this and R around 2006. About two years later, as I needed this for what I was working on, I rejuvenated things with the initial “second wave” release whose 10th birthday we celebrate today.

In late 2009 Romain François joined, intially contacted because of the needs of RProtoBuf for some Java tooling. (As an aside, there is a neat story of the very first steps of RProtoBuf here.) And from late 2009 to some time in 2013 or so Romain pushed Rcpp incredibly hard, far and well. We all still benefit from the work he did, and probably will for some time.

These days Rcpp is driven by a small and dedicated core team: JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Doug Bates, John Chambers and myself – plus countless contributors and even more users via GitHub and the mailing list. Thanks to all for making something excellent together!

And because ten is written as one-oh, I felt the time was right to go to the big one oh release and just committed this:

Release 1.0
Release 1.0

I will probably wrap this up as a release in a day or two and sent it to CRAN where it may remain for a few days of testing and checking. If you want it sooner, try the GitHub repo or the Rcpp drat repo where I will push the release once completed.

Again, a very big cheers and heartfelt Thank You! to everybody who helped on this ten year journey of making Rcpp what it is today.

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

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Thu, 01 Nov 2018

RcppAnnoy 0.0.11

A new release of RcppAnnoy is now on CRAN.

RcppAnnoy is the Rcpp-based R integration of the nifty Annoy library by Erik. 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 updates to a new upstream version (including a new distance measure), and includes a spiffy new vignette by Aaron Lun describing how to use who Annoy from C++ as he does in his new BioConductor package BiocNeighbours.

All changes in this version are summarized below:

Changes in version 0.0.11 (2018-10-30)

  • Synchronized with Annoy upstream (#26, #30, #36).

  • Added new Hamming distance measure functionality; should be considered experimental as the functionality depends on integer values.

  • Travis CI use was updated to the R 3.5 PPA (#28)

  • New vignette about Annoy use from C++ via Rcpp (Aaron Lun in #29 addressing #19; also #32, #33)

  • The vignette was rewritten using pinp (#34, #35).

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.

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Wed, 31 Oct 2018

RcppTOML 0.1.5: Small extensions

Coming on the heels of last week’s RcppTOML 0.1.4 release bringing support for TOML v0.5.0, we have a new release 0.1.5 on CRAN with better encoding support as well as support for the time type.

RcppTOML brings TOML to R. TOML is a file format that is most suitable for configurations, as it is meant to be edited by humans but read by computers. It emphasizes strong readability for humans while at the same time supporting strong typing as well as immediate and clear error reports. On small typos you get parse errors, rather than silently corrupted garbage. Much preferable to any and all of XML, JSON or YAML – though sadly these may be too ubiquitous now. TOML has been making inroads with projects such as the Hugo static blog compiler, or the Cargo system of Crates (aka “packages”) for the Rust language.

The list of changes in this incremental version is below.

Changes in version 0.1.5 (2018-10-31)

  • Escape characters treatment now has toggle (Václav Hausenblas in #27 fixing #26)

  • The TOML 0.5.0 'time' type is now supported (somewhat) by returning a formatted string (#29)

  • Encodings are now supported by defaulting to UTF-8 (Václav Hausenblas in #30 fixing #28)

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

More information is on the RcppTOML page 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.

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Sat, 27 Oct 2018

RcppRedis 0.1.9

A new minor release of RcppRedis arrived on CRAN earlier today. RcppRedis is one of several packages to connect 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 adds a few functions for the hash data structure thanks to Whit. I also relented and now embed the small hiredis C library as I got tired of seeing builds fail on macOS where the CRAN maintainer was either unwilling or unable to install an external hiredis library. Some packaging details were also brushed up. Fuller details below.

Changes in version 0.1.9 (2018-10-27)

  • The configure setup is more robust with respect to the C++ setup [CRAN request].

  • The Travis builds was updated to R 3.5 along with all others (#34).

  • A new Redis function hexists was added (Whit Armstrong in #35).

  • The hiredis library source is now included, and built on all systems unwilling or unable to provide it (#36).

  • Added hash functions HDEL, HLEN, HKEYS, and HGETALL (Whit Armstrong in #38).

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

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Tue, 23 Oct 2018

RcppTOML 0.1.4: Now with TOML v0.5.0

A new version of our RcppTOML package just arrived on CRAN. It wraps an updated version of the cpptoml parser which, after a correction or two, now brings support for TOML v0.5.0 – which is still rather rare.

RcppTOML brings TOML to R. TOML is a file format that is most suitable for configurations, as it is meant to be edited by humans but read by computers. It emphasizes strong readability for humans while at the same time supporting strong typing as well as immediate and clear error reports. On small typos you get parse errors, rather than silently corrupted garbage. Much preferable to any and all of XML, JSON or YAML – though sadly these may be too ubiquitous now. TOML has been making inroads with projects such as the Hugo static blog compiler, or the Cargo system of Crates (aka “packages”) for the Rust language.

Besides the (exciting !!) support for TOML v0.5.0 and e.g. its dates support, this release also includes a (still somewhat experimental) feature cooked up by Dan Dillon a while back: TOML files can now include other TOML (and in fact, Dan implemented a whole recursing stream processor…). The full list of changes is below.

Changes in version 0.1.4 (2018-10-23)

  • Spelling / grammar fixes to README (Jon Calder in #18)

  • Cast from StretchyList to List ensures lists appear as List objects in R

  • Support optional includize pre-processor for recursive includes by Dan Dillon as a header-only library (#21 and #22)

  • Support includize argument in R and C++ parser interface

  • Added a few more #nocov tags for coverage (#23)

  • Synchronized with new upstream cpptoml version supporting the TOMP v0.5.0 specification (#25)

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

More information is on the RcppTOML page 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.

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Sun, 14 Oct 2018

RcppCCTZ 0.2.5

A new bugfix release 0.2.5 of RcppCCTZ got onto CRAN this morning – just a good week after the previous release.

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—but decided in their infinite wisdom to copy the sources yet again into their packages. Sigh.

This version corrects two bugs. We were not properly accounting for those poor systems that do not natively have nanosecond resolution. And I missed a feature in the Rcpp DatetimeVector class by not setting the timezone on newly created variables; this too has been fixed.

Changes in version 0.2.5 (2018-10-14)

  • Parsing to Datetime was corrected on systems that do not have nanosecond support in C++11 chrono (#28).

  • DatetimeVector objects are now created with their timezone attribute when available.

  • The toTz functions is now vectorized (#29).

  • More unit tests were added, and some conditioning on Solaris (mostly due to missing timezone info) was removed.

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.

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Sat, 13 Oct 2018

RcppNLoptExample 0.0.1: Use NLopt from C/C++

A new package of ours, RcppNLoptExample, arrived on CRAN yesterday after a somewhat longer-than-usual wait for new packages as CRAN seems really busy these days. As always, a big and very grateful Thank You! for all they do to keep this community humming.

So what does it do ?

NLopt is a very comprehensive library for nonlinear optimization. The nloptr package by Jelmer Ypma has long been providing an excellent R interface.

Starting with its 1.2.0 release, the nloptr package now exports several C symbols in a way that makes it accessible to other R packages without linking easing the installation on all operating systems.

The new package RcppNLoptExample illustrates this facility with an example drawn from the NLopt tutorial. See the (currently single) file src/nlopt.cpp.

How / Why ?

R uses C interfaces. These C interfaces can be exported between packages. So when the usual library(nloptr) (or an import via NAMESPACE) happens, we now also get a number of C functions registered.

And those are enough to run optimization from C++ as we simply rely on the C interface provided. Look careful at the example code: the objective function and the constraint functions are C functions, and the body of our example invokes C functions from NLopt. This just works. For either C code, or C++ (where we rely on Rcpp to marshal data back and forth with ease).

On the other hand, if we tried to use the NLopt C++ interface which brings with it someinterface code we would require linking to that code (which R cannot easily export across packages using its C interface). So C it is.

Status

The package is pretty basic but fully workable. Some more examples should get added, and a helper class or two for state would be nice. The (very short) NEWS entry follows:

Changes in version 0.0.1 (2018-10-01)

  • Initial basic package version with one example from NLopt tutorial

Code, issue tickets etc are 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.

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Sat, 06 Oct 2018

RcppCCTZ 0.2.4

A new release 0.2.4 of RcppCCTZ is now on CRAN.

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

This version updates to the current upstream, makes the internal tests a bit more rigorous (and skips them on the OS we shall not name as it does not seem to have proper zoneinfo available or installed). One function was properly vectorised in a clean PR, and a spurious #include was removed.

Changes in version 0.2.4 (2018-10-06)

  • An unused main() in src/time_tool.cc was #ifdef'ed away to please another compiler/OS combination.

  • The tzDiff function now supports a vector argument (#24).

  • An unnecessary #include was removed (#25).

  • Some tests are not conditioning on Solaris to not fail there (#26).

  • The CCTZ code was updated to the newest upstream version (#27).

  • Unit tests now use the RUnit package replacing a simpler tests script.

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.

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Mon, 01 Oct 2018

Rcpp 0.12.19: And more updates

The next bi-monthly update in the 0.12.* series of Rcpp releases landed on CRAN early this morning. It was actually released on September 20, but I made a first cut (see #887 below) at a deprecation which CRAN and I decided to reverted for now, then CRAN was unusually busy and under an onslaught of false positives of a new checker, and finally we ran into a change in R-devel from the last two days. It is not easy as Rcpp is complex with over 1400 direct reverse dependencies so releases can take a moment. Hence, also releasing to the Rcpp drat repo as I did this time too may become the norm. In any event, and as usual, a big Thank You! to CRAN for all the work they do so well.

So once more, this release follows the 0.12.0 release from July 2016, the 0.12.1 release in September 2016, the 0.12.2 release in November 2016, the 0.12.3 release in January 2017, the 0.12.4 release in March 2016, the 0.12.5 release in May 2016, the 0.12.6 release in July 2016, the 0.12.7 release in September 2016, the 0.12.8 release in November 2016, the 0.12.9 release in January 2017, the 0.12.10.release in March 2017, the 0.12.11.release in May 2017, the 0.12.12 release in July 2017, the 0.12.13.release in late September 2017, the 0.12.14.release in November 2017, the 0.12.15.release in January 2018, the 0.12.16.release in March 2018, the 0.12.17 release in May 2018, and the 0.12.18 release in July 2018 making it the twenty-third release at the steady and predictable bi-montly release frequency (which started with the 0.11.* series).

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1452 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with another 138 in the current BioConductor release 3.7.

A decent number of changes, contributed by a number of Rcpp core team members as well as Rcpp users, went into this. Full details are below.

Changes in Rcpp version 0.12.19 (2018-09-20)

  • Changes in Rcpp API:

    • The no_init() accessor for vectors and matrices is now wrapped in Shield<>() to not trigger rchk warnings (Kirill Mueller in #893 addressing #892).

    • STRICT_R_HEADERS will be defined twelve months from now; until then we protect it via RCPP_NO_STRICT_HEADERS which can then be used to avoid the definition; downstream maintainers are encouraged to update their packages as needed (Dirk in #900 beginning to address #898).

  • Changes in Rcpp Attributes:

    • Added [[Rcpp::init]] attribute for registering C++ functions to run during package initialization (JJ in #903 addressing #902).
  • Changes in Rcpp Modules:

    • Improved exposeClass functionality along with added test (Martin Lysy in #886 fixing #879).
  • Changes in Rcpp Documentation:

    • Two typos were fixed in the Rcpp Sugar vignette (Patrick Miller in #895).

    • Several vignettes now use the collapse argument to show output in the corresponding code block.

  • Changes in Rcpp Deployment:

    • The old LdFlags() build helper was marked as deprecated [but removed for release] (Dirk in #887).

    • Dockerfiles for continuous integration, standard deployment and 'plus sized' deployment are provided along with builds (Dirk in #894).

    • Travis CI now use the rcpp/ci container for tests (Dirk in #896).

This contains one new deprecation for using stricter R headers. I already emailed around sixty maintainers who need to either make (very small) changes, or set a new #define to skip this. Right now you can test by adding #define STRICT_R_HEADERS before including Rcpp.h, we want to make this the default come September 2019. See my email to Rcpp-devel for more.

A second deprecation may get started with the next release. A lot of packages still needlessly call Rcpp:::LdFlags() even though we have not needed linker options for five years now. I will try assess what the damage may be and hopefully activate the .Deprecated() function in a good year.

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.

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Sat, 29 Sep 2018

RcppAPT 0.0.5

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.

This version is a bit of experiment. I had asked on the r-package-devel and r-devel list how I could suppress builds on macOS. As it does not have the required libapt-pkg-dev library to support the apt, builds always failed. CRAN managed to not try on Solaris or Fedora, but somewhat macOS would fail. Each. And. Every. Time. Sadly, nobody proposed a working solution.

So I got tired of this. Now we detect where we build, and if we can infer that it is not a Debian or Ubuntu (or derived system) and no libapt-pkg-dev is found, we no longer fail. Rather, we just set a #define and at compile-time switch to essentially empty code. Et voilà: no more build errors.

And as before, if you want to use the package to query the system packaging information, build it on system using apt and with its libapt-pkg-dev installed.

A few other cleanups were made too.

Changes in version 0.0.5 (2017-09-29)

  • NAMESPACE now sets symbol registration

  • configure checks for suitable system, no longer errors if none found, but sets good/bad define for the build

  • Existing C++ code is now conditional on having a 'good' build system, or else alternate code is used (which succeeds everywhere)

  • Added suitable() returning a boolean with configure result

  • Tests are conditional on suitable() to test good builds

  • The Travis setup was updated

  • The vignette was updated and expanded

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.

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

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Fri, 17 Aug 2018

RcppArmadillo 0.9.100.5.0

armadillo image

A new RcppArmadillo release 0.9.100.5.0, based on the new Armadillo release 9.100.5 from earlier today, is now on CRAN and in Debian.

It once again follows our (and Conrad's) bi-monthly release schedule. Conrad started with a new 9.100.* series a few days ago. I ran reverse-depends checks and found an issue which he promptly addressed; CRAN found another which he also very promptly addressed. It remains a true pleasure to work with such experienced professionals as Conrad (with whom I finally had a beer around the recent useR! in his home town) and of course the CRAN team whose superb package repository truly is the bedrock of the R community.

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) 479 other packages on CRAN.

This release once again brings a number of improvements to the sparse matrix functionality. We also fixed one use case of the OpemMP compiler and linker flags which will likely hit a number of the by now 501 (!!) CRAN packages using RcppArmadillo.

Changes in RcppArmadillo version 0.9.100.5.0 (2018-08-16)

  • Upgraded to Armadillo release 9.100.4 (Armatus Ad Infinitum)

    • faster handling of symmetric/hermitian positive definite matrices by solve()

    • faster handling of inv_sympd() in compound expressions

    • added .is_symmetric()

    • added .is_hermitian()

    • expanded spsolve() to optionally allow keeping solutions of systems singular to working precision

    • new configuration options ARMA_OPTIMISE_SOLVE_BAND and ARMA_OPTIMISE_SOLVE_SYMPD smarter use of the element cache in sparse matrices

    • smarter use of the element cache in sparse matrices

  • Aligned OpenMP flags in the RcppArmadillo.package.skeleton used Makevars,.win to not use one C and C++ flag.

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.

Edited on 2018-08-17 to correct one sentence (thanks, Barry!) and adjust the RcppArmadillo to 501 (!!) as we crossed the threshold of 500 packages overnight.

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

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Sun, 29 Jul 2018

RcppCNPy 0.2.10

Another small maintenance release of the RcppCNPy package arrived on CRAN a few minutes ago.

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

I updated and refreshed the vignettes, and also mention the reticulate-based alternative, and its still new-ish vignette, in the README.md.

Changes in version 0.2.10 (2018-07-29)

  • The vignettes have been updated using ‘collapse’ mode and edited.

  • The README.md now refers to reticulate as an alternative and points to the “Using reticulate” vignette.

  • The file src/RcppExports.cpp is used for package registration instead of src/init.c.

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

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

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Mon, 23 Jul 2018

Rcpp 0.12.18: Another batch of updates

Another bi-monthly update in the 0.12.* series of Rcpp landed on CRAN early this morning following less than two weekend in the incoming/ directory of CRAN. As always, thanks to CRAN for all the work they do so well.

So once more, this release follows the 0.12.0 release from July 2016, the 0.12.1 release in September 2016, the 0.12.2 release in November 2016, the 0.12.3 release in January 2017, the 0.12.4 release in March 2016, the 0.12.5 release in May 2016, the 0.12.6 release in July 2016, the 0.12.7 release in September 2016, the 0.12.8 release in November 2016, the 0.12.9 release in January 2017, the 0.12.10.release in March 2017, the 0.12.11.release in May 2017, the 0.12.12 release in July 2017, the 0.12.13.release in late September 2017, the 0.12.14.release in November 2017, the 0.12.15.release in January 2018, the 0.12.16.release in March 2018, and the 0.12.17 release in May 2018 making it the twenty-second release at the steady and predictable bi-montly release frequency (which started with the 0.11.* series).

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1403 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with another 138 in the current BioConductor release 3.7.

A pretty decent number of changes, contributed by a number of Rcpp core team members as well as Rcpp user, went into this. Full details are below.

Changes in Rcpp version 0.12.18 (2018-07-21)

  • Changes in Rcpp API:

    • The StringProxy::operator== is now const correct (Romain in #855 fixing #854).

    • The Environment::new_child() is now const (Romain in #858 fixing #854).

    • Next eval codes now properly unwind (Lionel in the large and careful #859 fixing #807).

    • In debugging mode, more type information is shown on abort() (Jack Wasey in #860 and #882 fixing #857).

    • A new class was added which allow suspension of the RNG synchronisation to address an issue seen in RcppDE (Kevin in #862).

    • Evaluation calls now happen in the base environment (which may fix an issue seen between conflicted and some BioConductor packages) (Kevin in #863 fixing #861).

    • Call stack display on error can now be controlled more finely (Romain in #868).

    • The new Rcpp_fast_eval is used instead of Rcpp_eval though this still requires setting RCPP_USE_UNWIND_PROTECT before including Rcpp.h (Qiang Kou in #867 closing #866).

    • The Rcpp::unwindProtect() function extracts the unwinding from the Rcpp_fast_eval() function and makes it more generally available. (Lionel in #873 and #877).

    • The tm_gmtoff part is skipped on AIX too (#876).

  • Changes in Rcpp Attributes:

    • The sourceCpp() function now evaluates R code in the correct local environment in which a function was compiled (Filip Schouwenaars in #852 and #869 fixing #851).

    • Filenames are now sorted in a case-insenstive way so that the RcppExports files are more stable across locales (Jack Wasey in #878).

  • Changes in Rcpp Sugar:

    • The sugar functions min and max now recognise empty vectors (Dirk in #884 fixing #883).

Thanks to CRANberries, you can also look at a diff to the previous release. As always, details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads page, the browseable doxygen docs and zip files of doxygen output for the standard formats. 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.

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Sun, 15 Jul 2018

RcppClassic 0.9.11

A new maintenance release, now at version 0.9.11, 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.

Per another request from CRAN, we updated the source code in four places to no longer use dynamic exceptions specification. This is something C++11 deprecated, and g++-7 and above now complain about each use. No other changes were made.

CRANberries also reports the changes relative 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.

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Fri, 29 Jun 2018

RcppArmadillo 0.8.600.0.0

armadillo image

A new RcppArmadillo release 0.8.600.0.0, based on the new Armadillo release 8.600.0 from this week, just arrived on CRAN.

It follows our (and Conrad’s) bi-monthly release schedule. We have made interim and release candidate versions available via the GitHub repo (and as usual thoroughly tested them) but this is the real release cycle. A matching Debian release will be prepared in due course.

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) 479 other packages on CRAN.

A high-level summary of changes follows (which omits the two rc releases leading up to 8.600.0). Conrad did his usual impressive load of upstream changes, but we are also grateful for the RcppArmadillo fixes added by Keith O’Hara and Santiago Olivella.

Changes in RcppArmadillo version 0.8.600.0.0 (2018-06-28)

  • Upgraded to Armadillo release 8.600.0 (Sabretooth Rugrat)

    • added hess() for Hessenberg decomposition

    • added .row(), .rows(), .col(), .cols() to subcube views

    • expanded .shed_rows() and .shed_cols() to handle cubes

    • expanded .insert_rows() and .insert_cols() to handle cubes

    • expanded subcube views to allow non-contiguous access to slices

    • improved tuning of sparse matrix element access operators

    • faster handling of tridiagonal matrices by solve()

    • faster multiplication of matrices with differing element types when using OpenMP

Changes in RcppArmadillo version 0.8.500.1.1 (2018-05-17) [GH only]

  • Upgraded to Armadillo release 8.500.1 (Caffeine Raider)

    • bug fix for banded matricex
  • Added slam to Suggests: as it is used in two unit test functions [CRAN requests]

  • The RcppArmadillo.package.skeleton() function now works with example_code=FALSE when pkgKitten is present (Santiago Olivella in #231 fixing #229)

  • The LAPACK tests now cover band matrix solvers (Keith O'Hara in #230).

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.

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Sun, 10 Jun 2018

RcppZiggurat 0.1.5

ziggurats

A maintenance release 0.1.5 of RcppZiggurat is now on the CRAN network for R.

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

Per a request from CRAN, we changed the vignette to accomodate pandoc 2.* just as we did with the most recent pinp release two days ago. No other changes were made. Other changes that have been pending are a minor rewrite of DOIs in DESCRIPTION, a corrected state setter thanks to a PR by Ralf Stubner, and a tweak for function registration to have user_norm_rand() visible.

The NEWS file entry below lists all changes.

Changes in version 0.1.5 (2018-06-10)

  • Description rewritten using doi for references.

  • Re-setting the Ziggurat generator seed now correctly re-sets state (Ralf Stubner in #7 fixing #3)

  • Dynamic registration reverts to manual mode so that user_norm_rand() is visible as well (#7).

  • The vignette was updated to accomodate pandoc 2* [CRAN request].

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

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RcppGSL 0.3.6

A maintenance update 0.3.6 of RcppGSL is now on CRAN. The RcppGSL package provides an interface from R to the GNU GSL using the Rcpp package.

Per a request from CRAN, we changed the vignette to accomodate pandoc 2.* just as we did with the most recent pinp release two days ago. No other changes were made. The (this time really boring) NEWS file entry follows:

Changes in version 0.3.6 (2018-06-10)

  • The vignette was updated to accomodate pandoc 2* [CRAN request].

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

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

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RcppClassic 0.9.10

A maintenance release RcppClassic 0.9.9 is now at CRAN. This package provides a maintained version of the otherwise deprecated first Rcpp API; no new projects should use it.

Per a request from CRAN, we changed the vignette to accomodate pandoc 2.* just as we did with the most recent pinp release two days ago. No other changes were made.

CRANberries also reports the changes relative 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.

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Sat, 09 Jun 2018

RcppDE 0.1.6

Another maintenance release, now at version 0.1.6, of our RcppDE package is now on CRAN. It follows the most recent (unblogged, my bad) 0.1.5 release in January 2016 and the 0.1.4 release in September 2015.

RcppDE is a "port" of DEoptim, a popular package for derivative-free optimisation using differential evolution optimization, to C++. By using RcppArmadillo, the code becomes a lot shorter and more legible. Our other main contribution is to leverage some of the excellence we get for free from using Rcpp, in particular the ability to optimise user-supplied compiled objective functions which can make things a lot faster than repeatedly evaluating interpreted objective functions as DEoptim (and, in fairness, just like most other optimisers) does.

That is also what lead to this upload: Kyle Baron noticed an issue when nesting a user-supplied compiled function inside a user-supplied compiled objective function -- and when using the newest Rcpp. This has to do with some cleanups we made for how RNG state is, or is not, set and preserved. Kevin Ushey was (once again) a real trooper here and added a simple class to Rcpp (in what is now the development version 0.12.17.2 available on the Rcpp drat repo) and used that here to (selectively) restore behaviour similarly to what we had in Rcpp (but which created another issue for another project). So all that is good now in all use cases. We also have some other changes contributed by Yi Kang some time ago for both JADE style randomization and some internal tweaks. Some packaging details were updated, and that sums up release 0.1.6.

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.

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Sun, 20 May 2018

Rcpp 0.12.17: More small updates

Another bi-monthly update and the seventeenth release in the 0.12.* series of Rcpp landed on CRAN late on Friday following nine (!!) days in gestation in the incoming/ directory of CRAN. And no complaints: we just wish CRAN were a little more forthcoming with what is happenening when, and/or would let us help supplying additional test information. I do run a fairly insane amount of backtests prior to releases, only to then have to wait another week or more is ... not ideal. But again, we all owe CRAN and immense amount of gratitude for all they do, and do so well.

So once more, this release follows the 0.12.0 release from July 2016, the 0.12.1 release in September 2016, the 0.12.2 release in November 2016, the 0.12.3 release in January 2017, the 0.12.4 release in March 2016, the 0.12.5 release in May 2016, the 0.12.6 release in July 2016, the 0.12.7 release in September 2016, the 0.12.8 release in November 2016, the 0.12.9 release in January 2017, the 0.12.10.release in March 2017, the 0.12.11.release in May 2017, the 0.12.12 release in July 2017, the 0.12.13.release in late September 2017, the 0.12.14.release in November 2017, the 0.12.15.release in January 2018 and the 0.12.16.release in March 2018 making it the twenty-first release at the steady and predictable bi-montly release frequency.

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1362 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with another 138 in the current BioConductor release 3.7.

Compared to other releases, this release contains again a relatively small change set, but between Kevin and Romain cleaned a few things up. Full details are below.

Changes in Rcpp version 0.12.17 (2018-05-09)

  • Changes in Rcpp API:

    • The random number Generator class no longer inhreits from RNGScope (Kevin in #837 fixing #836).

    • A spurious parenthesis was removed to please gcc8 (Dirk fixing #841)

    • The optional Timer class header now undefines FALSE which was seen to have side-effects on some platforms (Romain in #847 fixing #846).

    • Optional StoragePolicy attributes now also work for string vectors (Romain in #850 fixing #849).

Thanks to CRANberries, you can also look at a diff to the previous release. As always, details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads page, the browseable doxygen docs and zip files of doxygen output for the standard formats. 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.

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Sat, 19 May 2018

RcppGSL 0.3.5

A maintenance update of RcppGSL just brought version 0.3.5 to CRAN, a mere twelve days after the RcppGSL 0.3.4. release. Just like yesterday's upload of inline 0.3.15 it was prompted by a CRAN request to update the per-package manual page; see the inline post for details.

The RcppGSL package provides an interface from R to the GNU GSL using the Rcpp package.

No user-facing new code or features were added. The NEWS file entries follow below:

Changes in version 0.3.5 (2018-05-19)

  • Update package manual page using references to DESCRIPTION file [CRAN request].

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

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

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Mon, 07 May 2018

RcppGSL 0.3.4

A minor update version 0.3.4 of RcppGSL is now on CRAN. It contains an improved Windows build system (thanks, Jeroen!) and updates the C++ headers by removing dynamic exception specifications which C++11 frowns upon, and the compilers lets us know that in no uncertain terms. Builds using RcppGSL will now be more quiet. And as always, an extra treat for Solaris.

The RcppGSL package provides an interface from R to the GNU GSL using the Rcpp package.

No user-facing new code or features were added. The NEWS file entries follow below:

Changes in version 0.3.4 (2018-05-06)

  • Windows builds were updated (Jeroen Ooms in #16).

  • Remove dynamic exception specifications which are deprecated with C++11 or later (Dirk in #17).

  • Accomodate Solaris by being more explicit about sqrt.

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

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

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Sun, 06 May 2018

RcppMsgPack 0.2.2

Am maintenance release of RcppMsgPack got onto CRAN this afternoon. It contains a single static_cast fix to address a warning which g++-8.1 shows whereas older compilers remained silent---and CRAN asked us to address this.

MessagePack itself is an efficient binary serialization format. It lets you exchange data among multiple languages like JSON. But it is faster and smaller. Small integers are encoded into a single byte, and typical short strings require only one extra byte in addition to the strings themselves. RcppMsgPack brings both the C++ headers of MessagePack as well as clever code (in both R and C++) Travers wrote to access MsgPack-encoded objects directly from R.

Changes in version 0.2.2 (2018-05-06)

  • Apply a static_cast from upstream to suppress a warning from g++-8.1 as requested by CRAN.

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

More information is on the RcppRedis 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.

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Mon, 30 Apr 2018

RcppArmadillo 0.8.500.0

armadillo image

RcppArmadillo release 0.8.500.0, originally prepared and uploaded on April 21, has hit CRAN today (after having already been available via the RcppCore drat repo). A corresponding Debian release will be prepared as well. This RcppArmadillo release contains Armadillo release 8.500.0 with a number of rather nice changes (see below for details), and continues our normal bi-monthly CRAN release cycle.

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) 472 other packages on CRAN.

A high-level summary of changes follows.

Changes in RcppArmadillo version 0.8.500.0 (2018-04-21)

  • Upgraded to Armadillo release 8.500 (Caffeine Raider)

    • faster handling of sparse matrices by kron() and repmat()

    • faster transpose of sparse matrices

    • faster element access in sparse matrices

    • faster row iterators for sparse matrices

    • faster handling of compound expressions by trace()

    • more efficient handling of aliasing in submatrix views

    • expanded normalise() to handle sparse matrices

    • expanded .transform() and .for_each() to handle sparse matrices

    • added reverse() for reversing order of elements

    • added repelem() for replicating elements

    • added roots() for finding the roots of a polynomial

  • Fewer LAPACK compile-time guards are used, new unit tests for underlying features have been added (Keith O'Hara in #211 addressing #207).

  • The configure check for LAPACK features has been updated accordingly (Keith O'Hara in #214 addressing #213).

  • The compile-time check for g++ is now more robust to minimal shell versions (#217 addressing #216).

  • Compiler tests to were added for macOS (Keith O'Hara in #219).

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.

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Thu, 22 Mar 2018

RcppCNPy 0.2.9

Another minor maintenance release of the RcppCNPy package arrived on CRAN this evening.

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

There is only small code change: a path is now checked before an attempt to save. Thanks to Wush for the suggestion. I also added a short new vignette showing how reticulate can be used for NumPy data.

Changes in version 0.2.9 (2018-03-22)

  • The npySave function has a new option to check the path in the given filename.

  • A new vignette was added showing how the reticulate package can be used instead.

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

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

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Sun, 18 Mar 2018

RcppSMC 0.2.1: A few new tricks

A new release, now at 0.2.1, of the RcppSMC package arrived on CRAN earlier this afternoon (and once again as a very quick pretest-publish within minutes of submission).

RcppSMC provides Rcpp-based bindings to R for the Sequential Monte Carlo Template Classes (SMCTC) by Adam Johansen described in his JSS article. Sequential Monte Carlo is also referred to as Particle Filter in some contexts .

This releases contains a few bug fixes and one minor rearrangment allowing header-only use of the package from other packages, or via a Rcpp plugin. Many of these changes were driven by new contributors, which is a wonderful thing to see for any open source project! So thanks to everybody who helped with. Full details below.

Changes in RcppSMC version 0.2.1 (2018-03-18)

  • The sampler now has a copy constructor and assignment overload (Brian Ni in #28).

  • The SMC library component can now be used in header-only mode (Martin Lysy in #29).

  • Plugin support was added for use via cppFunction() and other Rcpp Attributes (or inline functions (Dirk in #30).

  • The sampler copy ctor/assigment operator is now copy-constructor safe (Martin Lysy In #32).

  • A bug in state variance calculation was corrected (Adam in #36 addressing #34).

  • History getter methods are now more user-friendly (Tiberiu Lepadatu in #37).

  • Use of pow with atomic types was disambiguated to std::pow) to help the Solaris compiler (Dirk in #42).

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

More information is on the RcppSMC page. Issues and bugreports should go to the GitHub issue tracker.

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

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Fri, 16 Mar 2018

RcppClassicExamples 0.1.2

Per a CRAN email sent to 300+ maintainers, this package (just like many others) was asked to please register its S3 method. So we did, and also overhauled a few other packagaging standards which changed since the previous uploads in December of 2012 (!!).

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

Changes in version 0.1.2 (2018-03-15)

  • Registered S3 print method [per CRAN request]

  • Added src/init.c with registration and updated all .Call usages taking advantage of it

  • Updated http references to https

  • Updated DESCRIPTION conventions

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

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Tue, 13 Mar 2018

Rcpp 0.12.16: A small update

The sixteenth update the 0.12.* series of Rcpp landed on CRAN earlier this evening after a few days of gestation in incoming/ at CRAN.

Once again, this release follows the 0.12.0 release from July 2016, the 0.12.1 release in September 2016, the 0.12.2 release in November 2016, the 0.12.3 release in January 2017, the 0.12.4 release in March 2016, the 0.12.5 release in May 2016, the 0.12.6 release in July 2016, the 0.12.7 release in September 2016, the 0.12.8 release in November 2016, the 0.12.9 release in January 2017, the 0.12.10.release in March 2017, the 0.12.11.release in May 2017, the 0.12.12 release in July 2017, the 0.12.13.release in late September 2017, the 0.12.14.release in November 2017, and the 0.12.15.release in January 2018 making it the twentieth release at the steady and predictable bi-montly release frequency.

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1316 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with another 91 in BioConductor.

Compared to other releases, this release contains a relatively small change set, but between Kirill, Kevin and myself a few things got cleaned up and solidified. Full details are below.

Changes in Rcpp version 0.12.16 (2018-03-08)

  • Changes in Rcpp API:

    • Rcpp now sets and puts the RNG state upon each entry to an Rcpp function, ensuring that nested invocations of Rcpp functions manage the RNG state as expected (Kevin in #825 addressing #823).

    • The R::pythag wrapper has been commented out; the underlying function has been gone from R since 2.14.0, and ::hypot() (part of C99) is now used unconditionally for complex numbers (Dirk in #826).

    • The long long type can now be used on 64-bit Windows (Kevin in #811 and again in #829 addressing #804).

  • Changes in Rcpp Attributes:

    • Code generated with cppFunction() now uses .Call() directly (Kirill Mueller in #813 addressing #795).
  • Changes in Rcpp Documentation:

    • The Rcpp FAQ vignette is now indexed as 'Rcpp-FAQ'; a stale Gmane reference was removed and entry for getting compilers under Conda was added.

    • The top-level README.md now has a Support section.

    • The Rcpp.bib reference file was refreshed to current versions.

Thanks to CRANberries, you can also look at a diff to the previous release. As always, details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads page, the browseable doxygen docs and zip files of doxygen output for the standard formats. 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.

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Thu, 01 Mar 2018

RcppArmadillo 0.8.400.0.0

armadillo image

RcppArmadillo release 0.8.400.0.0, originally prepared and uploaded on February 19, finally hit CRAN today (after having been available via the RcppCore drat repo for a number of days). A corresponding Debian release was prepared and uploaded as well. This RcppArmadillo release contains Armadillo release 8.400.0 with a number of nice changes (see below for details), and continues our normal bi-monthly CRAN release cycle (slight delayes in CRAN processing notwithstanding).

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) 450 other packages on CRAN.

A high-level summary of changes follows.

Changes in RcppArmadillo version 0.8.400.0.0 (2018-02-19)

  • Upgraded to Armadillo release 8.400.rc2 (Entropy Bandit)

    • faster handling of sparse matrices by repmat()

    • faster loading of CSV files

    • expanded kron() to handle sparse matrices

    • expanded index_min() and index_max() to handle cubes

    • expanded randi(), randu(), randn(), randg() to output single scalars

    • added submatrix & subcube iterators

    • added normcdf()

    • added mvnrnd()

    • added chi2rnd()

    • added wishrnd() and iwishrnd()

  • The configure generated header settings for LAPACK and OpenMP can be overridden by the user.

  • This release was preceded by two release candidates which were tested extensively.

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.

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Wed, 07 Feb 2018

RcppEigen 0.3.3.4.0

A new minor release 0.3.3.4.0 of RcppEigen hit CRAN earlier today, and just went to Debian as well. It brings Eigen 3.3.4 to R.

Yixuan once again did the leg-work of bringing the most recent Eigen release in along with the small set of patches we have carried forward for a few years.

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 uses 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 0.3.3.4.0 (2018-02-05)

  • Updated to version 3.3.4 of Eigen (Yixuan in #49)

  • Also carried over on new upstream (Yixuan, addressing #48)

  • As before, condition long long use on C++11.

  • Pragmas for g++ & clang to suppress diagnostics messages are disabled per CRAN Policy; use -Wno-ignored-attributes to quieten.

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.

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Sat, 20 Jan 2018

Rcpp 0.12.15: Numerous tweaks and enhancements

The fifteenth release in the 0.12.* series of Rcpp landed on CRAN today after just a few days of gestation in incoming/.

This release follows the 0.12.0 release from July 2016, the 0.12.1 release in September 2016, the 0.12.2 release in November 2016, the 0.12.3 release in January 2017, the 0.12.4 release in March 2016, the 0.12.5 release in May 2016, the 0.12.6 release in July 2016, the 0.12.7 release in September 2016, the 0.12.8 release in November 2016, the 0.12.9 release in January 2017, the 0.12.10.release in March 2017, the 0.12.11.release in May 2017, the 0.12.12 release in July 2017, the 0.12.13.release in late September 2017, and the 0.12.14.release in November 2017 making it the nineteenth release at the steady and predictable bi-montly release frequency.

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1288 packages on CRAN depend on Rcpp for making analytical code go faster and further, along with another 91 in BioConductor.

This release contains a pretty large number of pull requests by a wide variety of authors. Most of these pull requests are very focused on a particular issue at hand. One was larger and ambitious with some forward-looking code for R 3.5.0; however this backfired a little on Windows and is currently "parked" behind a #define. Full details are below.

Changes in Rcpp version 0.12.15 (2018-01-16)

  • Changes in Rcpp API:

    • Calls from exception handling to Rf_warning() now correctly set an initial format string (Dirk in #777 fixing #776).

    • The 'new' Date and Datetime vectors now have is_na methods too. (Dirk in #783 fixing #781).

    • Protect more temporary SEXP objects produced by wrap (Kevin in #784).

    • Use public R APIs for new_env (Kevin in #785).

    • Evaluation of R code is now safer when compiled against R 3.5 (you also need to explicitly define RCPP_PROTECTED_EVAL before including Rcpp.h). Longjumps of all kinds (condition catching, returns, restarts, debugger exit) are appropriately detected and handled, e.g. the C++ stack unwinds correctly (Lionel in #789). [ Committed but subsequently disabled in release 0.12.15 ]

    • The new function Rcpp_fast_eval() can be used for performance-sensitive evaluation of R code. Unlike Rcpp_eval(), it does not try to catch errors with tryEval in order to avoid the catching overhead. While this is safe thanks to the stack unwinding protection, this also means that R errors are not transformed to an Rcpp::exception. If you are relying on error rethrowing, you have to use the slower Rcpp_eval(). On old R versions Rcpp_fast_eval() falls back to Rcpp_eval() so it is safe to use against any versions of R (Lionel in #789). [ Committed but subsequently disabled in release 0.12.15 ]

    • Overly-clever checks for NA have been removed (Kevin in #790).

    • The included tinyformat has been updated to the current version, Rcpp-specific changes are now more isolated (Kirill in #791).

    • Overly picky fall-through warnings by gcc-7 regarding switch statements are now pre-empted (Kirill in #792).

    • Permit compilation on ANDROID (Kenny Bell in #796).

    • Improve support for NVCC, the CUDA compiler (Iñaki Ucar in #798 addressing #797).

    • Speed up tests for NA and NaN (Kirill and Dirk in #799 and #800).

    • Rearrange stack unwind test code, keep test disabled for now (Lionel in #801).

    • Further condition away protect unwind behind #define (Dirk in #802).

  • Changes in Rcpp Attributes:

    • Addressed a missing Rcpp namespace prefix when generating a C++ interface (James Balamuta in #779).
  • Changes in Rcpp Documentation:

    • The Rcpp FAQ now shows Rcpp::Rcpp.plugin.maker() and not the outdated ::: use applicable non-exported functions.

Thanks to CRANberries, you can also look at a diff to the previous release. As always, details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads page, the browseable doxygen docs and zip files of doxygen output for the standard formats. 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

Tue, 16 Jan 2018

RcppMsgPack 0.2.1

Am update of RcppMsgPack got onto CRAN today. It contains a number of enhancements Travers had been working on, as well as one thing CRAN asked us to do in making a suggested package optional.

MessagePack itself is an efficient binary serialization format. It lets you exchange data among multiple languages like JSON. But it is faster and smaller. Small integers are encoded into a single byte, and typical short strings require only one extra byte in addition to the strings themselves. RcppMsgPack brings both the C++ headers of MessagePack as well as clever code (in both R and C++) Travers wrote to access MsgPack-encoded objects directly from R.

Changes in version 0.2.1 (2018-01-15)

  • Some corrections and update to DESCRIPTION, README.md, msgpack.org.md and vignette (#6).

  • Update to c_pack.cpp and tests (#7).

  • More efficient packing of vectors (#8).

  • Support for timestamps and NAs (#9).

  • Conditional use of microbenchmark in tests/ as required for Suggests: package [CRAN request] (#10).

  • Minor polish to tests relaxing comparison of timestamp, and avoiding a few g++ warnings (#12 addressing #11).

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

More information may be on the RcppMsgPack 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.

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Sat, 06 Jan 2018

RcppCNPy 0.2.8

A minor maintenance release of the RcppCNPy package arrived on CRAN this week.

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

There is no code change here. But to process the vignette we rely on knitr which sees Python here and (as of its most recent release) wants the (excellent !!) reticulate package. Which is of course overkill just to process a short pdf document, so we turned this off.

Changes in version 0.2.8 (2018-01-04)

  • Vignette sets knitr option python.reticulate=FALSE to avoid another depedency just for the vignette [CRAN request]

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

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

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Wed, 06 Dec 2017

RcppArmadillo 0.8.300.1.0

armadillo image

Another RcppArmadillo release hit CRAN today. Since our last 0.8.100.1.0 release in October, Conrad kept busy and produced Armadillo releases 8.200.0, 8.200.1, 8.300.0 and now 8.300.1. We tend to now package these (with proper reverse-dependency checks and all) first for the RcppCore drat repo from where you can install them "as usual" (see the repo page for details). But this actual release resumes within our normal bi-monthly CRAN release cycle.

These releases improve a few little nags on the recent switch to more extensive use of OpenMP, and round out a number of other corners. See below for a brief summary.

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) 405 other packages on CRAN.

A high-level summary of changes follows.

Changes in RcppArmadillo version 0.8.300.1.0 (2017-12-04)

  • Upgraded to Armadillo release 8.300.1 (Tropical Shenanigans)

    • faster handling of band matrices by solve()

    • faster handling of band matrices by chol()

    • faster randg() when using OpenMP

    • added normpdf()

    • expanded .save() to allow appending new datasets to existing HDF5 files

  • Includes changes made in several earlier GitHub-only releases (versions 0.8.300.0.0, 0.8.200.2.0 and 0.8.200.1.0).

  • Conversion from simple_triplet_matrix is now supported (Serguei Sokol in #192).

  • Updated configure code to check for g++ 5.4 or later to enable OpenMP.

  • Updated the skeleton package to current packaging standards

  • Suppress warnings from Armadillo about missing OpenMP support and -fopenmp flags by setting ARMA_DONT_PRINT_OPENMP_WARNING

Courtesy of CRANberries, there is a diffstat report. 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.

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Tue, 28 Nov 2017

Rcpp now used by 1250 CRAN packages

1250 Rcpp packages

Earlier today Rcpp passed 1250 reverse-dependencies on CRAN as another big milestone. The graph is on the left depicts the growth of Rcpp usage (as measured by Depends, Imports and LinkingTo, but excluding Suggests) over time.

Rcpp cleared 300 packages in November 2014. It passed 400 packages in June 2015 (when I only tweeted about it), 500 packages in late October 2015, 600 packages last March, 700 packages last July, 800 packages last October, 900 packages early January, and 1000 packages in April. 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 kept on this page.

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 and then cracked ten percent this summer.

1250 user packages is staggering. We can use the progression of CRAN itself compiled by Henrik in a series of posts and emails to the main development mailing list. A decade ago CRAN itself did not have 1250 packages, and here we are approaching 12k with Rcpp at 10% and growing steadily. Amazeballs.

This puts a whole lot of responsibility on us in the Rcpp team as we continue to keep Rcpp as performant and reliable as it has been.

And with that, and as always, a very big 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.

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Fri, 24 Nov 2017

Rcpp 0.12.14: Some deprecation and minor updates

The fourteenth release in the 0.12.* series of Rcpp landed on CRAN yesterday after a somewhat longer-than-usual gestation period (and word is it may have been due to some unrelated disturbances from lots of changes within the main r-devel build).

This release follows the 0.12.0 release from July 2016, the 0.12.1 release in September 2016, the 0.12.2 release in November 2016, the 0.12.3 release in January 2017, the 0.12.4 release in March 2016, the 0.12.5 release in May 2016, the 0.12.6 release in July 2016, the 0.12.7 release in September 2016, the 0.12.8 release in November 2016, the 0.12.9 release in January 2017, the 0.12.10.release in March 2017, the 0.12.11.release in May 2017, the 0.12.12 release in July 2017 and the 0.12.13.release in late September 2017 making it the eighteenth release at the steady and predictable bi-montly release frequency.

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1246 packages (and hence 77 more since the last release) on CRAN depend on Rcpp for making analytical code go faster and further, along with another 91 in BioConductor.

This release is relatively minor compared to other releases, but follows through on the deprecattion of the old vectors for Date and Datetime (which were terrible: I was influenced by the vector design in QuantLib at the time and didn't really understand yet how a SEXP vector should work) we announced with Rcpp 0.12.8 a year ago. So now the new vectors are the default, but you can flip back if you need to with #define.

Otherwise Dan rounded a corner with the improved iterators he contributed, and Kirill improved the output stream implementation suppressing a warning with newer compilers.

Changes in Rcpp version 0.12.14 (2017-11-17)

  • Changes in Rcpp API:

    • New const iterators functions cbegin() and cend() added to MatrixRow as well (Dan Dillon in #750).

    • The Rostream object now contains a Buffer rather than allocating one (Kirill Müller in #763).

    • New DateVector and DatetimeVector classes are now the default fully deprecating the old classes as announced one year ago.

  • Changes in Rcpp Package:

    • DESCRIPTION file now list doi information per CRAN suggestion.
  • Changes in Rcpp Documentation:

    • Update CITATION file with doi information and PeerJ preprint.

Thanks to CRANberries, you can also look at a diff to the previous release. As always, details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads page, the browseable doxygen docs and zip files of doxygen output for the standard formats. A local directory has source and documentation too. 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, 19 Nov 2017

RcppEigen 0.3.3.3.1

A maintenance release 0.3.3.3.1 of RcppEigen is now on CRAN (and will get to Debian soon). It brings Eigen 3.3.* to R.

The impetus was a request from CRAN to change the call to Rcpp::Rcpp.plugin.maker() to only use :: as the function has in fact been exported and accessible for a pretty long time. So now the usage pattern catches up. Otherwise, Haiku-OS is now supported and a minor Travis tweak was made.

The complete NEWS file entry follows.

Changes in RcppEigen version 0.3.3.3.1 (2017-11-19)

  • Compilation under Haiku-OS is now supported (Yu Gong in #45).

  • The Rcpp.plugin.maker helper function is called via :: as it is in fact exported (yet we had old code using :::).

  • A spurious argument was removed from an example call.

  • Travis CI now uses https to fetch the test runner script.

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

RcppClassic 0.9.9

A maintenance release RcppClassic 0.9.9 is now at CRAN. This package provides a maintained version of the otherwise deprecated first Rcpp API; no new projects should use it.

Per a request from CRAN, we changed the call to Rcpp::Rcpp.plugin.maker() to only use :: as the function has in fact been exported and accessible for a pretty long time. So now the usage pattern catches up.

Courtesy of CRANberries, there are changes relative 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.

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Mon, 06 Nov 2017

RcppQuantuccia 0.0.2

A first maintenance release of RcppQuantuccia got to CRAN earlier today.

RcppQuantuccia brings the Quantuccia header-only subset / variant of QuantLib to R. At present it mostly offers calendaring, but Quantuccia just got a decent amount of new functions so hopefully we can offer more here too.

This release was motivated by the upcoming Rcpp release which will deprecate the okd Date and Datetime vectors in favours of newer ones. So this release of RcppQuantuccia switches to the newer ones.

Other changes are below:

Changes in version 0.0.2 (2017-11-06)

  • Added calendars for Canada, China, Germany, Japan and United Kingdom.

  • Added bespoke and joint calendars.

  • Using new date(time) vectors (#6).

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.

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Wed, 11 Oct 2017

RcppArmadillo 0.8.100.1.0

armadillo image

We are thrilled to announce a new big RcppArmadillo release! Conrad recently moved Armadillo to the 8.* series, with significant improvements and speed ups for sparse matrix operations, and more. See below for a brief summary.

This also required some changes at our end which Binxiang Ni provided, and Serguei Sokol improved some instantiations. We now show the new vignette Binxiang Ni wrote for his GSoC contribution, and I converted it (and the other main vignette) to using the pinp package for sleeker pdf vignettes.

This release resumes our bi-monthly CRAN release cycle. I may make interim updates available at GitHub "as needed". And this time I managed to mess up the reverse depends testing, and missed one sync() call on the way back to R---but all that is now taken care of.

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) 405 other packages on CRAN.

A high-level summary of changes follows.

Changes in RcppArmadillo version 0.8.100.1.0 (2017-10-05)

  • Upgraded to Armadillo release 8.100.1 (Feral Pursuits)

    • faster incremental construction of sparse matrices via element access operators

    • faster diagonal views in sparse matrices

    • expanded SpMat to save/load sparse matrices in coord format

    • expanded .save(),.load() to allow specification of datasets within HDF5 files

    • added affmul() to simplify application of affine transformations

    • warnings and errors are now printed by default to the std::cerr stream

    • added set_cerr_stream() and get_cerr_stream() to replace set_stream_err1(), set_stream_err2(), get_stream_err1(), get_stream_err2()

    • new configuration options ARMA_COUT_STREAM and ARMA_CERR_STREAM

  • Constructors for sparse matrices of types dgt, dtt amd dst now use Armadillo code for improved performance (Serguei Sokol in #175 addressing #173)

  • Sparse matrices call .sync() before accessing internal arrays (Binxiang Ni in #171)

  • The sparse matrix vignette has been converted to Rmarkdown using the pinp package, and is now correctly indexed. (#176)

Courtesy of CRANberries, there is a diffstat report. 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.

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Thu, 28 Sep 2017

Rcpp 0.12.13: Updated vignettes, and more

The thirteenth release in the 0.12.* series of Rcpp landed on CRAN this morning, following a little delay because Uwe Ligges was traveling and whatnot. We had announced its availability to the mailing list late last week. As usual, a rather substantial amount of testing effort went into this release so you should not expect any surprise.

This release follows the 0.12.0 release from July 2016, the 0.12.1 release in September 2016, the 0.12.2 release in November 2016, the 0.12.3 release in January 2017, the 0.12.4 release in March 2016, the 0.12.5 release in May 2016, the 0.12.6 release in July 2016, the 0.12.7 release in September 2016, the 0.12.8 release in November 2016, the 0.12.9 release in January 2017, the 0.12.10.release in March 2017, the 0.12.11.release in May 2017, and the 0.12.12 release in July 2017 making it the seventeeth release at the steady and predictable bi-montly release frequency.

Rcpp has become the most popular way of enhancing GNU R with C or C++ code. As of today, 1069 packages (and hence 73 more since the last release) on CRAN depend on Rcpp for making analytical code go faster and further, along with another 91 in BioConductor.

This releases contains a large-ish update to the documentation as all vignettes (apart from the unit test one, which is a one-off) now use Markdown and the (still pretty new) pinp package by James and myself. There is also a new vignette corresponding to the PeerJ preprint James and I produced as an updated and current Introduction to Rcpp replacing the older JSS piece (which is still included as a vignette too).

A few other things got fixed: Dan is working on const iterators you would expect with modern C++, Lei Yu spotted error in Modules, and more. See below for details.

Changes in Rcpp version 0.12.13 (2017-09-24)

  • Changes in Rcpp API:

    • New const iterators functions cbegin() and cend() have been added to several vector and matrix classes (Dan Dillon and James Balamuta in #748) starting to address #741).
  • Changes in Rcpp Modules:

    • Misplacement of one parenthesis in macro LOAD_RCPP_MODULE was corrected (Lei Yu in #737)
  • Changes in Rcpp Documentation:

    • Rewrote the macOS sections to depend on official documentation due to large changes in the macOS toolchain. (James Balamuta in #742 addressing issue #682).

    • Added a new vignette ‘Rcpp-introduction’ based on new PeerJ preprint, renamed existing introduction to ‘Rcpp-jss-2011’.

    • Transitioned all vignettes to the 'pinp' RMarkdown template (James Balamuta and Dirk Eddelbuettel in #755 addressing issue #604).

    • Added an entry on running 'compileAttributes()' twice to the Rcpp-FAQ (##745).

Thanks to CRANberries, you can also look at a diff to the previous release. As always, even fuller details are on the Rcpp Changelog page and the Rcpp page which also leads to the downloads page, the browseable doxygen docs and zip files of doxygen output for the standard formats. A local directory has source and documentation too. 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

Wed, 27 Sep 2017

RcppZiggurat 0.1.4

ziggurats

A maintenance release of RcppZiggurat is now on the CRAN network for R. It switched the vignette to the our new pinp package and its two-column pdf default.

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

The NEWS file entry below lists all changes.

Changes in version 0.1.4 (2017-07-27)

  • The vignette now uses the pinp package in two-column mode.

  • Dynamic symbol registration is now enabled.

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

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Tue, 26 Sep 2017

RcppAnnoy 0.0.10

A few short weeks after the more substantial 0.0.9 release of RcppAnnoy, we have a quick bug-fix update.

RcppAnnoy is our Rcpp-based R integration of the nifty Annoy library by Erik. Annoy is a small and lightweight C++ template header library for very fast approximate nearest neighbours.

Michaël Benesty noticed that our getItemsVector() function didn't, ahem, do much besides crashing. Simple bug, they happen--now fixed, and a unit test added.

Changes in this version are summarized here:

Changes in version 0.0.10 (2017-09-25)

  • The getItemsVector() function no longer crashes (#24)

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.

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Sun, 24 Sep 2017

RcppGSL 0.3.3

A maintenance update RcppGSL 0.3.3 is now on CRAN. It switched the vignette to the our new pinp package and its two-column pdf default.

The RcppGSL package provides an interface from R to the GNU GSL using the Rcpp package.

No user-facing new code or features were added. The NEWS file entries follow below:

Changes in version 0.3.3 (2017-09-24)

  • We also check for gsl-config at package load.

  • The vignette now uses the pinp package in two-column mode.

  • Minor other fixes to package and testing infrastructure.

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

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

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Sat, 23 Sep 2017

RcppCNPy 0.2.7

A new version of the RcppCNPy package arrived on CRAN yesterday.

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

This version updates internals for function registration, but otherwise mostly switches the vignette over to the shiny new pinp two-page template and package.

Changes in version 0.2.7 (2017-09-22)

  • Vignette updated to Rmd and use of pinp package

  • File src/init.c added for dynamic registration

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

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

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RcppClassic 0.9.8

A bug-fix release RcppClassic 0.9.8 for the very recent 0.9.7 release which fixes a build issue on macOS introduced in 0.9.7. No other changes.

Courtesy of CRANberries, there are changes relative 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.

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Sun, 17 Sep 2017

RcppClassic 0.9.7

A rather boring and otherwise uneventful release 0.9.7 of RcppClassic is now at CRAN. This package provides a maintained version of the otherwise deprecated first Rcpp API; no new projects should use it.

Once again no changes in user-facing code. But this makes it the first package to use the very new and shiny pinp package as the backend for its vignette, now converted to Markdown---see here for this new version. We also updated three sources files for tabs versus spaces as the current g++ version complained (correctly !!) about misleading indents. Otherwise a file src/init.c was added for dynamic registration, the Travis CI runner script was updated to using run.sh from our r-travis fork, and we now strip the library after they have been built. Again, no user code changes.

And no iterate: nobody should use this package. Rcpp is so much better in so many ways---this one is simply available as we (quite strongly) believe that APIs are contracts, and as such we hold up our end of the deal.

Courtesy of CRANberries, there are changes relative 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.

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Wed, 13 Sep 2017

RcppMsgPack 0.2.0

A new and much enhanced version of RcppMsgPack arrived on CRAN a couple of days ago. It came together following this email to the r-package-devel list which made it apparent that Travers Ching had been working on MessagePack converters for R which required the very headers I had for use from, inter alia, the RcppRedis package.

So we joined our packages. I updated the headers in RcppMsgPack to the current upstream version 2.1.5 of MessagePack, and Travers added his helper functions allow direct packing / unpacking of MessagePack objects at the R level, as well as tests and a draft vignette. Very exciting, and great to have a coauthor!

So now RcppMspPack provides R with both MessagePack header files for use via C++ (or C, if you must) packages such as RcppRedis --- and direct conversion routines at the R prompt.

MessagePack itself is an efficient binary serialization format. It lets you exchange data among multiple languages like JSON. But it is faster and smaller. Small integers are encoded into a single byte, and typical short strings require only one extra byte in addition to the strings themselves.

Changes in version 0.2.0 (2017-09-07)

  • Added support for building on Windows

  • Upgraded to MsgPack 2.1.5 (#3)

  • New R functions to manipulate MsgPack objects: msgpack_format, msgpack_map, msgpack_pack, msgpack_simplify, mgspack_unpack (#4)

  • New R functions also available as msgpackFormat, msgpackMap, msgpackPack, msgpackSimplify, mgspackUnpack (#4)

  • New vignette (#4)

  • New tests (#4)

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

More information may be on the RcppMsgPack 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.

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RcppRedis 0.1.8

A new minor release of RcppRedis arrived on CRAN last week, following the release 0.2.0 of RcppMsgPack which brought the MsgPack headers forward to release 2.1.5. This required a minor and rather trivial change in the code. When the optional RcppMsgPack package is used, we now require this version 0.2.0 or later.

We made a few internal updates to the package as well.

Changes in version 0.1.8 (2017-09-08)

  • A new file init.c was added with calls to R_registerRoutines() and R_useDynamicSymbols()

  • Symbol registration is enabled in useDynLib

  • Travis CI was updated to using run.sh

  • The (optional MessagePack) code was updated for MsgPack 2.*

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

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Thu, 31 Aug 2017

RcppAnnoy 0.0.9

An new version 0.0.9 of RcppAnnoy, our Rcpp-based R integration of the nifty Annoy library by Erik, is now on CRAN. Annoy is a small and lightweight C++ template header library for very fast approximate nearest neighbours.

This release corrects an issue for Windows users discovered by GitHub user 'khoran' who later also suggested the fix of binary mode. It upgrades to Annoy release 1.9.1 and brings its new Manhattan distance to RcppAnnoy. A number of unit tests were added as well, and we updated some packaging internals such as symbol registration.

And I presume I had a good streak emailing with Uwe's robots as the package made it onto CRAN rather smoothly within ten minutes of submission:

RcppAnnou to CRAN 

Changes in this version are summarized here:

Changes in version 0.0.9 (2017-08-31)

  • Synchronized with Annoy upstream version 1.9.1

  • Minor updates in calls and tests as required by annoy 1.9.1

  • New Manhattan distance modules along with unit test code

  • Additional unit tests from upstream test code carried over

  • Binary mode is used for save (as suggested by @khoran in #21)

  • A new file init.c was added with calls to R_registerRoutines() and R_useDynamicSymbols()

  • Symbol registration is enabled in useDynLib

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.

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Tue, 29 Aug 2017

RcppArmadillo 0.7.960.1.2

armadillo image

A second fix-up release is needed following on the recent bi-monthly RcppArmadillo release as well as the initial follow-up as it turns out that OS X / macOS is so darn special that it needs an entire separate treatment for OpenMP. Namely to turn it off entirely...

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) 384 other packages on CRAN---an increase of 54 since the CRAN release in June!

Changes in RcppArmadillo version 0.7.960.1.2 (2017-08-29)

  • On macOS, OpenMP support is now turned off (#170).

  • The package is now compiling under the C++11 standard (#170).

  • The vignette dependency is correctly set (James and Dirk in #168 and #169)

Courtesy of CRANberries, there is a diffstat report. 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.

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Mon, 28 Aug 2017

RcppSMC 0.2.0

A new version 0.2.0 of the RcppSMC package arrived on CRAN earlier today (as a very quick pretest-publish within minutes of submission).

RcppSMC provides Rcpp-based bindings to R for the Sequential Monte Carlo Template Classes (SMCTC) by Adam Johansen described in his JSS article.

This release 0.2.0 is chiefly the work of Leah South, a Ph.D. student at Queensland University of Technology, who was during the last few months a Google Summer of Code student mentored by Adam and myself. It was pleasure to work with Leah on this, and see her progress. Our congratulations to Leah for a job well done!

Changes in RcppSMC version 0.2.0 (2017-08-28)

  • Also use .registration=TRUE in useDynLib in NAMESPACE

  • Multiple Sequential Monte Carlo extensions (Leah South as part of Google Summer of Code 2017)

    • Switching to population level objects (#2 and #3).

    • Using Rcpp attributes (#2).

    • Using automatic RNGscope (#4 and #5).

    • Adding multiple normalising constant estimators (#7).

    • Static Bayesian model example: linear regression (#10 addressing #9).

    • Adding a PMMH example (#13 addressing #11).

    • Framework for additional algorithm parameters and adaptation (#19 addressing #16; also #24 addressing #23).

    • Common adaptation methods for static Bayesian models (#20 addressing #17).

    • Supporting MCMC repeated runs (#21).

    • Adding adaptation to linear regression example (#22 addressing #18).

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

More information is on the RcppSMC page. Issues and bugreports should go to the GitHub issue tracker.

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

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Wed, 23 Aug 2017

Rcpp now used by 10 percent of CRAN packages

10 percent of CRAN packages

Over the last few days, Rcpp passed another noteworthy hurdle. It is now used by over 10 percent of packages on CRAN (as measured by Depends, Imports and LinkingTo, but excluding Suggests). As of this morning 1130 packages use Rcpp out of a total of 11275 packages. The graph on the left shows the growth of both outright usage numbers (in darker blue, left axis) and relative usage (in lighter blue, right axis).

Older posts on this blog took note when Rcpp passed round hundreds of packages, most recently in April for 1000 packages. The growth rates for both Rcpp, and of course CRAN, are still staggering. A big thank you to everybody who makes this happen, from R Core and CRAN to all package developers, contributors, and of course all users driving this. We have built ourselves a rather impressive ecosystem.

So with that a heartfelt Thank You! to all users and contributors of R, CRAN, and of course Rcpp, for help, suggestions, bug reports, documentation, encouragement, and, 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.

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