The third release of littler as a CRAN package is now available, following in the now more than ten-year history as a package started by Jeff in the summer of 2006, and joined by me a few weeks later. littler is the first command-line interface for R and predates Rscript. It is still faster, and in my very biased eyes better as it allows for piping as well shebang scripting via #!, uses command-line arguments more consistently and still starts faster. It prefers to live on Linux and Unix, has its difficulties on OS X due to yet-another-braindeadedness there (who ever thought case-insensitive filesystems where a good idea?) and simply does not exist on Windows (yet -- the build system could be extended -- see RInside for an existence proof, and volunteers welcome!). This release brings several new examples script to run package checks, use the extraordinary R Hub, download RStudio daily builds, and more -- see below for details. No internals were changed. The NEWS file entry is below.

Changes in littler version 0.3.2 (2017-02-14)

• Changes in examples
  • New scripts getRStudioServer.r and getRStudioDesktop.r to download daily packages, currently defaults to Ubuntu amd64
  • New script c4c.r calling rhub::check_for_cran()
  • New script rd2md.r to convert Rd to markdown.
  • New script build.r to create a source tarball.
  • The installGitHub.r script now use package remotes (PR #44, #46)

Courtesy of CRANberries, there is a comparison to the previous release. Full details for the littler release are provided as usual at the ChangeLog page. The code is available via the GitHub repo, from tarballs off my littler page and the local directory here -- and now of course all from its CRAN page and via install.packages("littler"). Binary packages are available directly in Debian as well as soon via Ubuntu binaries at CRAN thanks to the tireless Michael Rutter. Comments and suggestions are welcome at the GitHub repo.

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

I got a new computer and wondered... How can I test it? One of those innocent questions that brings hours and hours of work and questionning...

A new desktop: Intel NUC devices After reading up on Jeff Atwood's blog and especially his article on the scooter computer, I have discovered a whole range of small computers that could answer my need for a faster machine in my office at a low price tag and without taking up too much of my precious desk space. After what now seems like a too short review I ended up buying a new Intel NUC device from NCIX.com, along with 16GB of RAM and an amazing 500GB M.2 hard drive for around 750$. I am very happy with the machine. It's very quiet and takes up zero space on my desk as I was able to screw it to the back of my screen. You can see my review of the hardware compatibility and installation report in the Debian wiki. I wish I had taken more time to review the possible alternatives - for example I found out about the amazing Airtop PC recently and, although that specific brand is a bit too expensive, the space of small computers is far and wide and deserves a more thorough review than just finding the NUC by accident while shopping for laptops on System76.com...

Reviving the Stressant project But this, and Atwood's Is Your Computer Stable? article, got me thinking about how to test new computers. It's one thing to build a machine and fire it up, but how do you know everything is actually really working? It is common practice to do a basic stress test or burn-in when you get a new machine in the industry - how do you proceed with such tests? Back in the days when I was working at Koumbit, I wrote a tool exactly for that purpose called Stressant. Since I am the main author of the project and I didn't see much activity on it since I left, I felt it would be a good idea to bring it under my personal wing again, and I have therefore moved it to my Gitlab where I hope to bring it back to life. Parts of the project's rationale are explained in an "Intent To Package" the "breakin" tool (Debian bug #707178), which, after closer examination, ended up turning into a complete rewrite. The homepage has a bit more information about how the tool works and its objectives, but generally, the idea is to have a live CD or USB stick that you can just plugin into a machine to run a battery of automated tests (memtest86, bonnie++, stress-ng and disk wiping, for example) or allow for interactive rescue missions on broken machines. At Koumbit, we had Debirf-based live images that we could boot off the network fairly easily that we would use for various purposes, although nothing was automated yet. The tool is based on Debian, but since it starts from boot, it should be runnable on any computer. I was able to bring the project back to life, to a certain extent, by switching to vmdebootstrap instead of debirf for builds, but that removed netboot support. Also, I hope that Gitlab could provide with an autobuilder for the images, but unfortunately there's a bug in Docker that makes it impossible to mount loop images in Docker images (which makes it impossible to build Docker in Docker, apparently).

Should I start yet another project? So there's still a lot of work to do in this project to get it off the ground. I am still a bit hesitant in getting into this, however, for a few reasons:

1. It's yet another volunteer job - which I am trying to reduce for health and obvious economic reasons. That's a purely personal reason and there isn't much you can do about it.
2. I am not sure the project is useful. It's one thing to build a tool that can do basic tests on a machine - I can probably just build an live image for myself that will do everything I need - it's another completely different thing to build something that will scale to multiple machines and be useful for more various use cases and users.

(A variation of #1 is how everything and everyone is moving to the cloud. It's become a common argument that you shouldn't run your own metal these days, and we seem to be fighting an uphill economic battle when we run our own datacenters, rack or even physical servers these days. I still think it's essential to have some connexion to metal to be autonomous in our communications, but I'm worried that focusing on such a project is another of my precious dead entreprises... ) Part #2 is obviously where you people come in. Here's a few questions I'd like to have feedback on:

1. (How) do you perform stress-testing of your machines before putting them in production (or when you find issues you suspect to be hardware-related)?
2. Would a tool like breakin or stressant be useful in your environment?
3. Which tools do you use now for such purposes?
4. Would you contribute to such a project? How?
5. Do you think there is room for such a project in the existing ecology of projects) or should I contribute to an existing project?

Any feedback here would be, of course, greatly appreciated.

Last week, Josh sent the call for papers to the R-SIG-Finance list making everyone aware that we will have our nineth annual R/Finance conference in Chicago in May. Please see the call for paper (at the link, below, or at the website) and consider submitting a paper. We are once again very excited about our conference, thrilled about upcoming keynotes and hope that many R / Finance users will not only join us in Chicago in May 2017 -- but also submit an exciting proposal. We also overhauled the website, so please see R/Finance. It should render well and fast on devices of all sizes: phones, tablets, desktops with browsers in different resolutions. The program and registration details still correspond to last year's conference and will be updated in due course. So read on below, and see you in Chicago in May!

So, I did not accomplish my reading goal for 2016 (reading and reviewing more books in 2016 than I did in 2015). Many things contributed to that, but the root cause was that I didn't make enough time for reading. Much of the time that could have gone to reading went to playing Hearthstone (a good thing) and obsessing over the 2016 US election (mostly a waste of time and particularly energy, although I'm not sure I could have stopped). That said, I did get quite a lot of reading done at the end of the year, and I'm hoping to keep up that momentum for next year. In 2016, I did a lot of re-reading and comfort reading. I'm probably going to continue with some of the re-reading in 2017, since I'm enjoying it, but my reading goal for the year is to get back to reading award nominees and previous award winners. There's so much great new stuff being published that I want to discover. I'm not going to set an explicit goal around number of books, but I am going to make an effort to carve out more time in my schedule for reading books (and less for reading on-line news). This was another year with two 10 out of 10 books. One of them was a re-read: Lord of Emperors, the second book of Guy Gavriel Kay's Sarantine Mosaic. (I also re-read the first book this year, Sailing to Sarantium, and gave it a 9.) I like nearly all of Kay's historical fantasies, but this duology is one of my personal favorites. The second 10 out of 10 book was a complete surprise: A Man Called Ove by Fredrik Backman (translated by Henning Koch). My mother found this book and suggested it to me, and I loved every moment of it. I will definitely be reading more of Backman's work. There were two more fiction standouts this year: Digger by Ursula Vernon, and The Philosopher Kings by Jo Walton. The first is a graphic novel about a wombat who is trying to make her way home from an unexpected detour into a mess of magic and gods. The second is the middle book in a trilogy about an attempt to construct Plato's Just City and all of the philosophical and social problems that ensue (with some bonus science fiction and fantasy elements). Both of them are excellent. Walton is consistently one of my favorite authors, and Ursula Vernon was my great discovery of a new author to read this year. (Not that I've followed through on that much, the year in reading being what it was, but I will be doing so.) My favorite non-fiction book of the year continues my interest in time management in general and Mark Forster's approaches in particular. Secrets of Productive People was the last book I reviewed this year (just a coincidence, not any intentional attempt to set things up for next year) and the best version of his overall approach to date. If you've not read any of Forster based on my previous recommendations, this is a good place to start. Also worth mentions were Jeffrey Toobin's The Run of His Life, on the O.J. Simpson case, and Andrew Groen's The Empires of EVE, on the history of player empires in the EVE Online MMORPG. I Kickstarted the latter and didn't regret it. The full analysis includes some additional personal reading statistics, probably only of interest to me.

Whilst I managed to read almost sixty books in 2016 here are ten of my favourites in no particular order. Disappointments this year include Stewart Lee's Content Provider (nothing like his stand-up), Christopher Hitchens' And Yet (his best essays are already published) and Heinlein's Stranger in a Strange Land (great exposition, bizarre conclusion). The worst book I finished, by far, was Mark Edward's Follow You Home. Animal QC Gary Bell, QC Subtitled My Preposterous Life, this rags-to-riches story about a working-class boy turned eminent lawyer would be highly readable as a dry and factual account but I am compelled to include it here for its extremely entertaining style of writing. Full of unsurprising quotes that take one unaware: would you really expect a now-Queen's Counsel to "heartily suggest that if you find yourself suffering from dysentery in foreign climes you do not medicate it with lobster thermidor and a bottle of Ecuadorian red?" A real good yarn.

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So You've Been Publically Shamed Jon Ronson The author was initially recommended to me by Brad but I believe I started out with the wrong book. In fact, I even had my doubts about this one, prematurely judging from the title that it was merely cashing-in on a fairly recent internet phenomenon like his more recent shallow take on Trump and the alt-Right but in the end I read Publically Shamed thrice in quick succession. I would particularly endorse the audiobook version: Ronson's deadpan drawl suits his writing perfectly.

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The Obstacle is the Way Ryan Holiday Whilst everyone else appears to be obligated to include Ryan's recent Ego is the Enemy in their Best of 2016 lists I was actually taken by his earlier "introduction by stealth" to stoic philosophy. Certainly not your typical self-help book, this is "a manual to turn to in troubling times". Returning to this work at least three times over the year even splashing out on the audiobook at some point I feel like I learned a great deal, although it is now difficult to pinpoint exactly what. Perhaps another read in 2017 is thus in order

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Layer Cake J.J. Connolly To judge a book in comparison to the film is to do both a disservice, but reading the book of Layer Cake really underscored just how well the film played to the strengths of that medium. All of the aspects that would not have worked had been carefully excised from the screenplay, ironically leaving more rewarding "layers" for readers attempting the book. A parallel adaption here might be No Country for Old Men - I would love to read (or write) a comparative essay between these two adaptions although McCarthy's novel is certainly the superior source material.

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Lying Sam Harris I've absorbed a lot of Sam Harris's uvre this year in the form of his books but moreover via his compelling podcast. I'm especially fond of Waking Up on spirituality without religion and would rank that as my favourite work of his. Lying is a comparatively short read, more of a long essay in fact, where he argues that we can radically simplify our lives by merely telling the truth in situations where others invariably lie. Whilst it would take a brave soul to adopt his approach his case is superlatively well-argued and a delight to read.

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Letters from a Stoic Seneca

Great pleasure is to be found not only in keeping up an old and established friendship but also in beginning and building up a new one. Reading this in a beautifully svelte hardback, I tackled a randomly-chosen letter per day rather than attempting to read it cover-to-cover. Breaking with a life-long tradition, I even decided to highlight sections in pen so I could return to them at ease. I hope it's not too hackneyed to claim I gained a lot from "building up" a relationship with this book. Alas, it is one of those books that is too easy to recommend given that it might make one appear wise and learned, but if you find yourself in a slump, either in life or in your reading habits, it certainly has my approval.

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Solo: A James Bond Novel William Boyd I must have read all of the canonical Fleming novels as a teenager and Solo really rewards anyone who has done so. It would certainly punish anyone expecting a Goldeneye or at least be a little too foreign to be enjoyed. Indeed, its really a pastiche of these originals, both in terms of the time period, general tone (Bond is more somber; more vulnerable) and in various obsessions of Fleming's writing, such as the overly-detailed description of the gambling and dining tables. In this universe, 007's restaurant expenses probably contributed signifcantly to the downfall of the British Empire, let alone his waistline. Bond flicking through a ornithological book at one point was a cute touch

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The Subtle Art of Not Giving A F*ck Mark Manson Certainly a wildcard to include here and not without its problems, The Subtle Art is a curious manifesto on how to approach life. Whilst Manson expouses an age-old philosophy of grounding yourself and ignoring the accumulation of flatscreen TVs, etc. he manages to do so in a fresh and provocative "21st-centry gonzo" style. Highly entertaining, at one point the author posits an alternative superhero ("Disappointment Panda") that dishes out unsolicited and uncomfortable truths to strangers before simply walking away: "You know, if you make more money, that s not going to make your kids love you," or: "What you consider friendship is really just your constant attempts to impress people." Ouch.

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The Fourth Protocol Frederick Forsyth I have a crystal-clear memory from my childhood of watching a single scene from a film in the dead of night: Pierce Brosnan sets a nuclear device to detonate after he can get away but a double-crossing accomplice surreptitiously brings the timetable forward in order that the bomb also disposes of him Anyway, at some point whilst reading The Fourth Protocol it dawned on me that this was that book. I might thus be giving the book more credit due to this highly satisfying connection but I think it stands alone as a superlative political page-turner and is still approachable outside the machinations of the Cold War.

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The Partner John Grisham After indulging in a bit too much non-fiction and an aborted attempt at The Ministry of Fear, I turned to a few so-called lower-brow writers such as Jeffrey Archer, etc. However, it was The Partner that turned out to be a real page-turner for somewhat undefinable reasons. Alas, it appears the rest of the author's output is unfortunately in the same vein (laywers, etc.) so I am hesitant to immediately begin others but judging from various lists online I am glad I approached this one first.

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Shogun: The First Novel of the Asian saga James Clavell Despite its length, I simply couldn't resist returning to Shogun this year although it did fatigue me to the point that I have still yet to commence on its sequel, Tai-Pan. Like any good musical composition, one is always rewarded by returning to a book and I took great delight in uncovering more symbolism throughout (such as noticing that one of the first words Blackthorne learns in Japanese is "truth") but also really savouring the tragic arcs that run throughout the novel, some beautiful phrases ("The day seemed to lose its warmth ") and its wistful themes of inevitability and karma.

It's been a while since I've done one of these. danah boyd It's Complicated (non-fiction)
Jeffrey A. Carver Eternity's End (sff)
Becky Chambers A Closed and Common Orbit (sff)
Stephen Deas The Adamantine Palace (sff)
Robert Heinlein The Green Hills of Earth / The Menace from Earth (sff)
Robert Heinlein Revolt in 2100 / Methuselah's Children (sff)
Marjorie M. Liu The Iron Hunt (sff)
Larry Niven The Ringworld Engineers (sff)
Don Norman The Design of Everyday Things (non-fiction)
Kurt Vonnegut Slaughterhouse-Five (sff)
Jo Walton Necessity (sff)
Eileen Wilks Tempting Danger (sff) I picked up some extra used books since I was placing a book order to pick up Necessity anyway, and fleshed out my early Heinlein novels mostly out of curiousity. I've already reviewed The Design of Everyday Things, which I got from the work book club.

The second release of littler as a CRAN package is now available, following in the now more than ten-year history as a package started by Jeff in the summer of 2006, and joined by me a few weeks later. littler is the first command-line interface for R and predates Rscript. It is still faster, and in my very biased eyes better as it allows for piping as well shebang scripting via #!, uses command-line arguments more consistently and still starts faster. It prefers to live on Linux and Unix, has its difficulties on the OS X due yet-another-braindeadedness there (who ever thought case-insensitive filesystems where a good idea?) and simply does not exist on Windows (yet -- the build system could be extended -- see RInside for an existence proof, and volunteers welcome!). This release brings us fixes and enhancements from three other contributors, a couple new example scripts, more robust builds, extended documentation and more -- see below for details. The NEWS file entry is below.

Changes in littler version 0.3.1 (2016-08-06)

• Changes in examples
  • install2.r now passes on extra options past -- to R CMD INSTALL (PR #37 by Steven Pav)
  • Added rcc.r to run rcmdcheck::rcmdcheck()
  • Added (still simple) render.r to render (R)markdown
  • Several examples now support the -x or --usage flag to show extended help.
• Changes in build system
  • The AM_LDFLAGS variable is now set and used too (PR #38 by Mattias Ellert)
  • Three more directories, used when an explicit installation directory is set, are excluded (also #38 by Mattias)
  • Travis CI is now driven via run.sh from our fork, and deploys all packages as .deb binaries using our PPA where needed
• Changes in package
  • SystemRequirements now mentions the need for libR, i.e. an R built with a shared library so that we can embed R.
  • The docopt and rcmdcheck packages are now suggested, and added to the Travis installation.
  • A new helper function r() is now provided and exported so that the package can be imported (closes #40).
  • URL and BugReports links were added to DESCRIPTION.
• Changes in documentation
  • The help output for installGithub.r was corrected (PR #39 by Brandon Bertelsen)

Full details for the littler release are provided as usual at the ChangeLog page. The code is available via the GitHub repo, from tarballs off my littler page and the local directory here -- and now of course all from its CRAN page and via install.packages("littler"). Binary packages are available directly in Debian as well as soon via Ubuntu binaries at CRAN thanks to the tireless Michael Rutter. will probably have new Comments and suggestions are welcome 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.

Review: The Run of His Life, by Jeffrey Toobin

Publisher:	Random House
Copyright:	1996, 1997
Printing:	2015
ISBN:	0-307-82916-2
Format:	Kindle
Pages:	498

The O.J. Simpson trial needs little introduction to anyone who lived through it in the United States, but a brief summary for those who didn't. O.J. Simpson is a Hall of Fame football player and one of the best running backs to ever play the game. He's also black, which is very relevant much of what later happened. After he retired from professional play, he became a television football commentator and a spokesperson for various companies (particularly Hertz, a car rental business). In 1994, he was arrested for the murder of two people: his ex-wife, Nicole Brown Simpson, and Ron Goldman (a friend of Nicole's). The arrest happened after a bizarre low-speed police chase across Los Angeles in a white Bronco that was broadcast live on network television. The media turned the resulting criminal trial into a reality TV show, with live cable television broadcasts of all of the court proceedings. After nearly a full year of trial (with the jury sequestered for nine months more on that later), a mostly black jury returned a verdict of not guilty after a mere four hours of deliberation. Following the criminal trial, in an extremely unusual legal proceeding, Simpson was found civilly liable for Ron Goldman's death in a lawsuit brought by his family. Bizarre events surrounding the case continued long afterwards. A book titled If I Did It (with "if" in very tiny letters on the cover) was published, ghost-written but allegedly with Simpson's input and cooperation, and was widely considered a confession. Another legal judgment let the Goldman family get all the profits from that book's publication. In an unrelated (but also bizarre) incident in Las Vegas, Simpson was later arrested for kidnapping and armed robbery and is currently in prison until at least 2017. It is almost impossible to have lived through the O.J. Simpson trial in the United States and not have formed some opinion on it. I was in college and without a TV set at the time, and even I watched some of the live trial coverage. Reactions to the trial were extremely racially polarized, as you might have guessed. A lot of black people believed at the time that Simpson was innocent (probably fewer now, given subsequent events). A lot of white people thought he was obviously guilty and was let off by a black jury for racial reasons. My personal opinion, prior to reading this book, was a common "third way" among white liberals: Simpson almost certainly committed the murders, but the racist Los Angeles police department decided to frame him for a crime that he did commit by trying to make the evidence stronger. That's a legitimate reason in the US justice system for finding someone innocent: the state has an obligation to follow correct procedure and treat the defendant fairly in order to get a conviction. I have a strong bias towards trusting juries; frequently, it seems that the media second-guesses the outcome of a case that makes perfect sense as soon as you see all the information the jury had (or didn't have). Toobin's book changed my mind. Perhaps because I wasn't watching all of the coverage, I was greatly underestimating the level of incompetence and bad decision-making by everyone involved: the prosecution, the defense, the police, the jury, and the judge. This court case was a disaster from start to finish; no one involved comes away looking good. Simpson was clearly guilty given the evidence presented, but the case was so badly mishandled that it gave the jury room to reach the wrong verdict. (It's telling that, in the far better managed subsequent civil case, the jury had no trouble reaching a guilty verdict.) The Run of His Life is a very detailed examination of the entire Simpson case, from the night of the murder through the end of the trial and (in an epilogue) the civil case. Toobin was himself involved in the media firestorm, breaking some early news of the defense's decision to focus on race in The New Yorker and then involved throughout the trial as a legal analyst, and he makes it clear when he becomes part of the story. But despite that, this book felt objective to me. There are tons of direct quotes, lots of clear description of the evidence, underlying interviews with many of the people involved to source statements in the book, and a comprehensive approach to the facts. I think Toobin is a bit baffled by the black reaction to the case, and that felt like a gap in the comprehensiveness and the one place where he might be accused of falling back on stereotypes and easy judgments. But other than hole, Toobin applies his criticism even-handedly and devastatingly to all parties. I won't go into all the details of how Toobin changed my mind. It was a cumulative effect across the whole book, and if you're curious, I do recommend reading it. A lot was the detailed discussion of the forensic evidence, which was undermined for the jury at trial but looks very solid outside the hothouse of the case. But there is one critical piece that I would hope would be handled differently today, twenty years later, than it was by the prosecutors in that case: Simpson's history of domestic violence against Nicole. With what we now know about patterns of domestic abuse, the escalation to murder looks entirely unsurprising. And that history of domestic abuse was exceedingly well-documented: multiple external witnesses, police reports, and one actual prior conviction for spousal abuse (for which Simpson did "community service" that was basically a joke). The prosecution did a very poor job of establishing this history and the jury discounted it. That was a huge mistake by both parties. I'll mention one other critical collection of facts that Toobin explains well and that contradicted my previous impression of the case: the relationship between Simpson and the police. Today, in the era of Black Lives Matter, the routine abuse of black Americans by the police is more widely known. At the time of the murders, it was less recognized among white Americans, although black Americans certainly knew about it. But even in 1994, the Los Angeles police department was notorious as one of the most corrupt and racist big-city police departments in the United States. This is the police department that beat Rodney King. Mark Fuhrman, one of the police officers involved in the case (although not that significantly, despite his role at the trial), was clearly racist and had no business being a police officer. It was therefore entirely believable that these people would have decided to frame a black man for a murder he actually committed. What Toobin argues, quite persuasively and with quite a lot of evidence, is that this analysis may make sense given the racial tensions in Los Angeles but ignores another critical characteristic of Los Angeles politics, namely a deference to celebrity. Prior to this trial, O.J. Simpson largely followed the path of many black athletes who become broadly popular in white America: underplaying race and focusing on his personal celebrity and connections. (Toobin records a quote from Simpson earlier in his life that perfectly captures this approach: "I'm not black, I'm O.J.") Simpson spent more time with white businessmen than the black inhabitants of central Los Angeles. And, more to the point, the police treated him as a celebrity, not as a black man. Toobin takes some time to chronicle the remarkable history of deference and familiarity that the police showed Simpson. He regularly invited police officers to his house for parties. The police had a long history of largely ignoring or downplaying his abuse of his wife, including not arresting him in situations that clearly seemed to call for that, showing a remarkable amount of deference to his side of the story, not pursuing clear violations of the court judgment after his one conviction for spousal abuse, and never showing much inclination to believe or protect Nicole. Even on the night of the murder, they started following a standard playbook for giving a celebrity advance warning of investigations that might involve them before the news media found out about them. It seems clear, given the evidence that Toobin collected, that the racist Los Angeles police didn't focus that animus at Simpson, a wealthy celebrity living in Brentwood. He wasn't a black man in their eyes; he was a rich Hall of Fame football player and a friend. This obviously raises the question of how the jury could return an innocent verdict. Toobin provides plenty of material to analyze that question from multiple angles in his detailed account of the case, but I can tell you my conclusion: Judge Lance Ito did a horrifically incompetent job of managing the case. He let the lawyers wander all over the case, interacted bizarrely with the media coverage (and was part of letting the media turn it into a daytime drama), was not crisp or clear about his standards of evidence and admissibility, and, perhaps worst of all, let the case meander on at incredible length. With a fully sequestered jury allowed only brief conjugal visits and no media contact (not even bookstore shopping!). Quite a lot of anger was focused on the jury after the acquittal, and I do think they reached the wrong conclusion and had all the information they would have needed to reach the correct one. But Toobin touches on something that I think would be very hard to comprehend without having lived through it. The jury and alternate pool essentially lived in prison for nine months, with guards and very strict rules about contact with the outside world, in a country where compensation for jury duty is almost nonexistent. There were a lot of other factors behind their decision, including racial tensions and the sheer pressure from judging a celebrity case about which everyone has an opinion, but I think it's nearly impossible to underestimate the psychological tension and stress from being locked up with random other people under armed guard for three quarters of a year. It's hard for jury members to do an exhaustive and careful deliberation in a typical trial that takes a week and doesn't involve sequestration. People want to get back to their lives and families. I can only imagine the state I would be in after nine months of this, or how poor psychological shape I would be in to make a careful and considered decision. Similarly, for those who condemned the jury for profiting via books and media appearances after the trial, the current compensation for jurors is $15 per day (not hour). I believe at the time it was around $5 per day. There are a few employers who will pay full salary for the entire jury service, but only a few; many cap the length at a few weeks, and some employers treat all jury duty as unpaid leave. The only legal requirement for employers in the United States is that employees that serve on a jury have their job held for them to return to, but compensation is pathetic, not tied to minimum wage, and employers do not have to supplement it. I'm much less inclined to blame the jurors than the system that badly mistreated them. As you can probably tell from the length of this review, I found The Run of His Life fascinating. If I had followed the whole saga more closely at the time, this may have been old material, but I think my vague impressions and patchwork of assumptions were more typical than not among people who were around for the trial but didn't invest a lot of effort into following it. If you are like me, and you have any interest in the case or the details of how the US criminal justice system works, this is a fascinating case study, and Toobin does a great job with it. Recommended. Rating: 8 out of 10

Here is my monthly update covering a large part of what I have been doing in the free software world (previously):

• Updates to tickle-me-email, my Getting Things Done-inspired email toolbox:
  • Added the ability to inject arbitrary headers into draft messages. (#5)
  • Merged a documentation fix from Will Thompson. (#5)
• Improved my Chrome extension for the FastMail web interface:
  • Support appending arbitrary text in the Compose textarea to the subject via a context menu. (#4)
  • Avoid brittle parsing of the page and use the Javascript API instead. (diff)
• Updated my Strava Enhancement Suite, a Chrome extension that improves and fixes annoyances in the web interface of the Strava cycling and running tracker:
  • Merge support from Jeff Schuler to support "Flyby" activity defaults. (#50)
  • Correctly fallback to the default value after introducing a new value. (diff)
• Made a quick and dirty Kindle version of Derek Siver's book reviews. (repo)
• Improved my stravabot IRC bot to be more resilient on service failure. (diff)

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Book reading is happening, and more book review posting will be happening. I'm a bit behind in writing reviews, but the holiday weekend is a good opportunity to do a bit of catching up. In the meantime, here are some new acquisitions: Roxanne J. Coady & Joy Johannessen (ed.) The Books That Changed My Life (nonfiction)
James S.A. Corey Caliban's War (sff)
James S.A. Corey Abaddon's Gate (sff)
Max Gladstone Full Fathom Five (sff)
Max Gladstone Last First Snow (sff)
N.K. Jemisin The Fifth Season (sff)
Guy Gavriel Kay Children of Earth and Sky (sff)
Naomi Novik Uprooted (sff)
Ada Palmer Too Like the Lightning (sff)
Graydon Saunders Safely You Deliver (sff)
Neal Stephenson Seveneves (sff)
Jeff VanderMeer Annihilation (sff) This is mostly catching up on books that were nominated for awards. I want to read the (legitimate) nominees for Hugo best novel this year if I can find the time, and VanderMeer won the Nebula last year. The rest of Gladstone's series to date was on sale, and I really liked the first book. And of course a new Guy Gavriel Kay is buy on sight. I'm currently re-reading The Sarantine Mosaic, since I read that before I started writing reviews and Children of Earth and Sky is apparently set in historical contact with it. (It's possible all of Kay's historical fantasies are set in the same universe, but they're usually fairly disconnected.)

The primary change in this release is porting the remctl extension to PHP 7. PHP 7.0 included a major change to the PHP API for binary extensions, which required quite a lot of porting (contributed by Nish Aravamudan). Due to the depth of the changes, the extension has been forked and the PHP 5 version of the extension should be considered frozen. Currently, they both provide the same functionality, but expect new functionality to be released only for PHP 7 or later. This release also includes numerous portability fixes for older versions of Heimdal and numerous fixes to the RPM spec, both thanks to Jeffrey Hutzelman. You can get the latest release from the remctl distribution page.

Review: The Oath, by Jeffrey Toobin

Publisher:	Anchor
Copyright:	2012
Printing:	June 2013
ISBN:	0-307-39071-3
Format:	Trade paperback
Pages:	298

Jeffrey Toobin is a legal analyst for CNN and The New Yorker and plays a similar role for the intricacies of the legal system as popular science writers play for physics. I'd previously read and reviewed his The Nine, an excellent history of the Rehnquist Supreme Court. The Oath is half sequel and half extension, bringing the same analysis to the first four years of the Obama presidency and the appointments of Sonia Sotomayor and Elena Kagan. Sequels to popular history books that are not explicitly multi-volume works are a tricky publishing niche. People expect them to stand alone; I doubt it would work to tell people "read The Nine before reading this book," and regardless, Toobin did not take that approach. But the court profiled in The Oath only differs by two justices than that in The Nine. There was therefore a fair bit of repetition, since Toobin felt obligated to repeat his profiles of the five members of the court he had already deeply analyzed in the previous book. He even retold the story of Sandra Day O'Conner leaving the court despite it falling outside the focus of this book. I think these 300 pages could have been 150 pages of additional material in The Nine if Toobin had started this project later. That said, if you enjoyed The Nine (and I very much did), this is more of the same. Toobin picks up with Obama's inauguration ceremony and a fascinating bit of legal trivia over the oath of office, and then provides a detailed profile of the Roberts court and the major decisions of the first four years of Obama's presidency. His discussion of the nomination process and Obama's judicial philosophy rang very true following the death of Scalia: Obama's nomination of Merrick Garland is exactly what one would predict from Toobin's discussion. And, as with the previous book, I discovered that I had a lot of misconceptions about both Sotomayor and Kagan that Toobin cleared up. He does a great job showing the complexities of the interplay between law, politics, apparently unlikely friendships (such as Scalia and Ginsburg), and the executive and judicial branch. Worth particular mention is Toobin's discussion of the office of Solicitor General of the United States. I had no idea the role it plays in Supreme Court decisions. If I had given it any thought at all, I would have assumed it was essentially a variation on White House Counsel crossed with the Attorney General's office. But it's quite a bit more than that, as Elena Kagan's profile shows. If you, like I, raised an eyebrow at Obama's nomination of Elena Kagan to the Supreme Court from Solicitor General, wondering if that was at all similar to Bush's nomination of Harriet Miers, this section will be very informative. White House Counsel and Solicitor General are very, very different positions. However, The Oath has one major drawback that The Nine didn't: it's partisan. Now, Toobin is a liberal, with a clear preference towards the progressive side of the court. This was also true in The Nine, and I don't think that's a serious problem. Everyone writes from a particular perspective; stating it is more honest than concealing it, and it's the reader's responsibility to weigh multiple sides. But I thought Toobin was largely fair to those he disagreed with in The Nine. Even Thomas received some defense against popular misconceptions. It probably helped that much of that book focuses on conservatives who became liberals as the court shifted, people like Sandra Day O'Conner for whom Toobin has clear respect. I commented in my review of the previous book that it didn't feel quite balanced, but it felt like Toobin was trying hard to be fair. The Oath does not give that same feeling. Toobin hates the direction of the Roberts court, hates most of its 5-4 decisions, and strongly disagrees with the judicial philosophies of both Roberts and Alito. But more than that, he is clearly dubious that they even have coherent judicial philosophies. Maybe that's a legitimate critique, maybe it's not; regardless, I don't think he proves his case. The tone of much of the book is disgusted and angry rather than deliberate and relentless. Where Toobin engages with the thought process of Alito or, particularly, Roberts, the primary focus is to disagree with it rather than explain it. This happens to match my own emotional reaction, but I doubt it will be persuasive to someone who doesn't already agree with Toobin, and it hurts the quality of the history. I suspect this would have been a better book if Toobin had waited ten years before writing it (still covering the same time frame). Some distance from the subject helps provide a more complete and thoughtful history. But, of course, it likely wouldn't have sold as well. That said, one of the themes of this book is how the conservatives on the Roberts court are currently playing the role of radicals from the perspective of the judicial tradition, overturning settled case law and calling into question precedents that have been used to decide numerous cases. The liberals, in contrast, are currently mostly playing the role of conservatives: standing up for the principle of stare decisis, trying to maintain consistency with past decisions, trying to minimize disruptive change. Conservatives will argue (correctly) that this depends on one's time frame and that they're trying to overturn radical past decisions, but those radical decisions, whatever their merits, are now often more than fifty years into the past. I hadn't thought about the current Supreme Court ideological battles from that perspective and found it eye-opening. It also ties in well with Obama's judicial philosophy as Toobin presents it: preferring democracy, laws, and change from the ballot box, and with little appetite for controversial court decisions. Obama is a judicial conservative. He therefore favors the liberal wing as the court is currently constructed, but not because he has much appetite for pushing forward civil rights in the courts. This is not the book The Nine was. It's repetitive if you've read the previous book (which you should, as it's the better book of the two), and I thought Toobin's critical balance was off. But it has a lot of interesting things to say about Obama's approach to the law, how the executive branch interacts with the Supreme Court, and the philosophy and approaches of the newer justices on the court. Recommended, although not as strongly. Rating: 7 out of 10

Almost seven years since the last time we saw him here, Brad Mehldau returned to the CSO for a concert on Friday eve in his standard trio setup with Larry Grenadier on bass and Jeff Ballard on drums. The material mostly (all?) new and drawn from the upcoming album Blues and Ballads. The morning of the concert---which happened to be the final one in their tour---he retweeted a bit from this review in the Boston Globe

[Brad Mehldau] flashed facets of his renowned pianism: crystalline touch, deep lyricism, harmonic sophistication, adroit use of space, and the otherworldly independence of his right and left hands.

I cannot really describe his style any better than this. If you get a chance to see him, go!

Let's see if I can scrounge through all of my now-organized directories of ebooks and figure out what I haven't recorded here yet. At least the paper books make that relatively easy, since I don't shelve them until I post them. (Yeah, yeah, I should actually make a database.) Hugh Aldersey-Williams Periodic Tales (nonfiction)
Sandra Ulbrich Almazan SF Women A-Z (nonfiction)
Radley Balko Rise of the Warrior Cop (nonfiction)
Peter V. Brett The Warded Man (sff)
Lois McMaster Bujold Gentleman Jole and the Red Queen (sff)
Fred Clark The Anti-Christ Handbook Vol. 2 (nonfiction)
Dave Duncan West of January (sff)
Karl Fogel Producing Open Source Software (nonfiction)
Philip Gourevitch We Wish to Inform You That Tomorrow We Will Be Killed With Our Families (nonfiction)
Andrew Groen Empires of EVE (nonfiction)
John Harris @ Play (nonfiction)
David Hellman & Tevis Thompson Second Quest (graphic novel)
M.C.A. Hogarth Earthrise (sff)
S.L. Huang An Examination of Collegial Dynamics... (sff)
S.L. Huang & Kurt Hunt Up and Coming (sff anthology)
Kameron Hurley Infidel (sff)
Kevin Jackson-Mead & J. Robinson Wheeler IF Theory Reader (nonfiction)
Rosemary Kirstein The Lost Steersman (sff)
Rosemary Kirstein The Language of Power (sff)
Merritt Kopas Videogames for Humans (nonfiction)
Alisa Krasnostein & Alexandra Pierce (ed.) Letters to Tiptree (nonfiction)
Mathew Kumar Exp. Negatives (nonfiction)
Ken Liu The Grace of Kings (sff)
Susan MacGregor The Tattooed Witch (sff)
Helen Marshall Gifts for the One Who Comes After (sff collection)
Jack McDevitt Coming Home (sff)
Seanan McGuire A Red-Rose Chain (sff)
Seanan McGuire Velveteen vs. The Multiverse (sff)
Seanan McGuire The Winter Long (sff)
Marc Miller Agent of the Imperium (sff)
Randal Munroe Thing Explainer (graphic nonfiction)
Marguerite Reed Archangel (sff)
J.K. Rowling Harry Potter: The Complete Collection (sff)
K.J. Russell Tides of Possibility (sff anthology)
Robert J. Sawyer Starplex (sff)
Bruce Schneier Secrets & Lies (nonfiction)
Mike Selinker (ed.) The Kobold Game to Board Game Design (nonfiction)
Douglas Smith Chimerascope (sff collection)
Jonathan Strahan Fearsome Journeys (sff anthology)
Nick Suttner Shadow of the Colossus (nonfiction)
Aaron Swartz The Boy Who Could Change the World (essays)
Caitlin Sweet The Pattern Scars (sff)
John Szczepaniak The Untold History of Japanese Game Developers I (nonfiction)
John Szczepaniak The Untold History of Japanese Game Developers II (nonfiction)
Jeffrey Toobin The Run of His Life (nonfiction)
Hayden Trenholm Blood and Water (sff anthology)
Coen Teulings & Richard Baldwin (ed.) Secular Stagnation (nonfiction)
Ursula Vernon Book of the Wombat 2015 (graphic nonfiction)
Ursula Vernon Digger (graphic novel) Phew, that was a ton of stuff. A bunch of these were from two large StoryBundle bundles, which is a great source of cheap DRM-free ebooks, although still rather hit and miss. There's a lot of just fairly random stuff that's been accumulating for a while, even though I've not had a chance to read very much. Vacation upcoming, which will be a nice time to catch up on reading.

It s been a while since my last what s been happening behind the scenes e-mail so I m here to report on what has been happening within the GNOME Infrastructure, its future plans and my personal sensations about a challenge that started around three (3) years ago when Sriram Ramkrishna and Jeff Schroeder proposed my name as a possible candidate for coordinating the team that runs the systems behind the GNOME Project. All this followed by the official hiring achieved by Karen Sandler back in February 2013. The GNOME Infrastructure has finally reached stability both in terms of reliability and uptime, we didn t have any service disruption this and the past year and services have been running smoothly as they were expected to in a project like the one we are managing. As many of you know service disruptions and a total lack of maintenance were very common before I joined back in 2013, I m so glad the situation has dramatically changed and developers, users, passionates are now able to reach our websites, code repositories, build machines without experiencing slowness, downtimes or
unreachability. Additionally all these groups of people now have a reference point they can contact in case they need help when coping with the infrastructure they daily use. The ticketing system allows users to get in touch with the members of the Sysadmin Team and receive support right away within a very short period of time (Also thanks to Pagerduty, service the Foundation is kindly sponsoring) Before moving ahead to the future plans I d like to provide you a summary of what has been done during these roughly three years so you can get an idea of why I define the changes that happened to the infrastructure a complete revamp:

1. Recycled several ancient machines migrating services off of them while consolidating them by placing all their configuration on our central configuration management platform ran by Puppet. This includes a grand total of 7 machines that were replaced by new hardware and extended warranties the Foundation kindly sponsored.
2. We strenghten our websites security by introducing SSL certificates everywhere and recently replacing them with SHA2 certificates.
3. We introduced several services such as Owncloud, the Commits Bot, the Pastebin, the Etherpad, Jabber, the GNOME Github mirror.
4. We restructured the way we backup our machines also thanks to the Fedora Project sponsoring the disk space on their backup facility. The way we were used to handle backups drastically changed from early years where a magnetic tape facility was in charge of all the burden of archiving our data to today where a NetApp is used together with rdiff-backup.
5. We upgraded Bugzilla to the latest release, a huge thanks goes to Krzesimir Nowak who kindly helped us building the migration tools.
6. We introduced the GNOME Apprentice program open-sourcing our internal Puppet repository and cleansing it (shallow clones FTW!) from any sensitive information which now lives on a different repository with restricted access.
7. We retired Mango and our OpenLDAP instance in favor of FreeIPA which allows users to modify their account information on their own without waiting for the Accounts Team to process the change.
8. We documented how our internal tools are customized to play together making it easy for future Sysadmin Team members to learn how the infrastructure works and supersede existing members in case they aren t able to keep up their position anymore.
9. We started providing hosting to the GIMP and GTK projects which now completely rely on the GNOME Infrastructure. (DNS, email, websites and other services infrastructure hosting)
10. We started providing hosting not only to the GIMP and GTK projects but to localized communities as well such as GNOME Hispano and GNOME Greece
11. We configured proper monitoring for all the hosted services thanks to Nagios and Check-MK
12. We migrated the IRC network to a newer ircd with proper IRC services (Nickserv, Chanserv) in place.
13. We made sure each machine had a configured management (mgmt) and KVM interface for direct remote access to the bare metal machine itself, its hardware status and all the operations related to it. (hard reset, reboot, shutdown etc.)
14. We upgraded MoinMoin to the latest release and made a substantial cleanup of old accounts, pages marked as spam and trashed pages.
15. We deployed DNSSEC for several domains we manage including gnome.org, guadec.es, gnomehispano.es, guadec.org, gtk.org and gimp.org
16. We introduced an account de-activation policy which comes into play when a contributor not committing to any of the hosted repositories at git.gnome.org since two years is caught by the script. The account in question is marked as inactive and the gnomecvs (from the old cvs days) and ftpadmin groups are removed.
17. We planned mass reboots of all the machines roughly every month for properly applying security and kernel updates.
18. We introduced Mirrorbrain (MB), the mirroring service serving GNOME and related modules tarballs and software all over the world. Before introducing MB GNOME had several mirrors located in all the main continents and at the same time a very low amount of users making good use of them. Many organizations and companies behind these mirrors decided to not host GNOME sources anymore as the statistics of usage were very poor and preferred providing the same service to projects that really had a demand for these resources. MB solved all this allowing a proper redirect to the closest mirror (through mod_geoip) and making sure the sources checksum matched across all the mirrors and against the original tarball uploaded by a GNOME maintainer and hosted at master.gnome.org.

I can keep the list going for dozens of other accomplished tasks but I m sure many of you are now more interested in what the future plans actually are in terms of where the GNOME Infrastructure should be in the next couple of years. One of the main topics we ve been discussing will be migrating our Git infrastructure away from cgit (which is mainly serving as a code browsing tool) to a more complete platform that is surely going to include a code review tool of some sort. (Gerrit, Gitlab, Phabricator) Another topic would be migrating our mailing lists to Mailman 3 / Hyperkitty. This also means we definitely need a staging infrastructure in place for testing these kind of transitions ideally bound to a separate Puppet / Ansible repository or branch. Having a different repository for testing purposes will also mean helping apprentices to test their changes directly on a live system and not on their personal computer which might be running a different OS / set of tools than the ones we run on the GNOME Infrastructure. What I also aim would be seeing GNOME Accounts being the only authentication resource in use within the whole GNOME Infrastructure. That means one should be able to login to a specific service with the same username / password in use on the other hosted services. That s been on my todo list for a while already and it s probably time to push it forward together with Patrick Uiterwijk, responsible of Ipsilon s development at Red Hat and GNOME Sysadmin. While these are the top priority items we are soon receiving new hardware (plus extended warranty renewals for two out of the three machines that had their warranty renewed a while back) and migrating some of the VMs off from the current set of machines to the new boxes is definitely another task I d be willing to look at in the next couple of months (one machine (ns-master.gnome.org) is being decommissioned giving me a chance to migrate away from BIND into NSD). The GNOME Infrastructure is evolving and it s crucial to have someone maintaining it. On this side I m bringing to your attention the fact the assigned Sysadmin funds are running out as reported on the Board minutes from the 27th of October. On this side Jeff Fortin started looking for possible sponsors and came up with the idea of making a brochure with a set of accomplished tasks that couldn t have been possible without the Sysadmin fundraising campaign launched by Stormy Peters back in June 2010 being a success. The Board is well aware of the importance of having someone looking at the infrastructure that runs the GNOME Project and is making sure the brochure will be properly reviewed and published. And now some stats taken from the Puppet Git Repository:

$ cd /git/GNOME/puppet && git shortlog -ns
3520 Andrea Veri
506 Olav Vitters
338 Owen W. Taylor
239 Patrick Uiterwijk
112 Jeff Schroeder
71 Christer Edwards
4 Daniel Mustieles
4 Matanya Moses
3 Tobias Mueller
2 John Carr
2 Ray Wang
1 Daniel Mustieles Garc a
1 Peter Baumgarten

and from the Request Tracker database (52388 being my assigned ID):

mysql> select count(*) from Tickets where LastUpdatedBy = '52388';
+----------+
  count(*)  
+----------+
  3613  
+----------+
1 row in set (0.01 sec)
mysql> select count(*) from Tickets where LastUpdatedBy = '52388' and Status = 'Resolved';
+----------+
  count(*)  
+----------+
  1596  
+----------+
1 row in set (0.03 sec)

It s been a long run which made me proud, for the things I learnt, for the tasks I ve been able to accomplish, for the great support the GNOME community gave me all the time and most of all for the same fact of being part of the team responsible of the systems hosting the GNOME Project. Thank you GNOME community for your continued and never ending backing, we daily work to improve how the services we host are delivered to you and the support we receive back is fundamental for our passion and enthusiasm to remain high!

A new major release of littler is now available. And for the first time in the nine years since 2006 when Jeff started the effort (which I joined not long after) we are now a CRAN package. This required a rewrite of the build system, foregoing the calls to aclocal, autoheader, automake and leaving just a simpler autoconf layer creating a configure script and a simple src/Makevars.in. Not only does R provide such a robust and well-understood build system (which I got to understand reasonably well given all my R packages, but being on CRAN and leveraging its mechanism for installation and upgrades is clearly worth the change. There may be a moment or two of transition. While we can create a binary in an R package, we cannot (generally) copy to /usr/bin or /usr/local/bin as part of the build process (for lack of write-rights to those directories). So if you do not have r in the $PATH and load the package, it makes a suggestion (which needs a linebreak which I added here):

R> library(littler)
The littler package provides 'r' as a binary.
You could link to the 'r' binary installed in
'/usr/local/lib/R/site-library/littler/bin/r' from
'/usr/local/bin' in order to use 'r' for scripting.
R> 

Similarly, you could copy (or softlink) r to ~/bin if that is in your $PATH. The Debian (and Ubuntu) packages will continue to provide /usr/bin/r as before. Note thah these packages will now be called r-cran-littler to match all other CRAN packages. The NEWS file entry is below.

Changes in littler version 0.3.0 (2015-10-29)

• Changes in build system
  • First CRAN Release as R package following nine years of source releases
  • Script configure, src/Makevars.in and remainder of build system rewritten to take advantage of the R package build infrastructure
  • Reproducible builds are better supported as the (changing) compilation timestamps etc are only inserted for 'verbose builds' directly off the git repo, but not for Debian (or CRAN) builds off the release tarballs
• Changes in littler functionality
  • Also source $R_HOME/etc/Rprofile.site and ~/.Rprofile if present
• Changes in littler documentation
  • Added new vignette with examples

Full details for the littler release are provided as usual at the ChangeLog page. The code is available via the GitHub repo, from tarballs off my littler page and the local directory here -- and now of course all from its CRAN page and via install.packages("littler"). A fresh package has gone to the incoming queue at Debian where it will a few days as the binary packages was renamed from littler to r-cran-littler matching all other CRAN packages. Michael Rutter will probably have new Ubuntu binaries at CRAN once the source package gets into Debian proper. Comments and suggestions are welcome 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.

Earlier today, Josh sent the text below in this message to the R-SIG-Finance list as the very first heads-up concerning the 2016 edition of our successful R/Finance series. We are once again very excited about our conference, thrilled about upcoming keynotes (some of which are confirmed and some of which are in the works), and hope that many R / Finance users will not only join us in Chicago in May 2016 -- but also submit an exciting proposal. So read on below, and see you in Chicago in May!

The annoucement below just went to the R-SIG-Finance list. More information is as usual at the R / Finance page. See you in Chicago in May!

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

Every now and then we get reports from CRAN about our packages failing a test there. A challenging one concerns UBSAN, or Undefined Behaviour Sanitizer. For background on UBSAN, see this RedHat blog post for gcc and this one from LLVM about clang. I had written briefly about this before in a blog post introducing the sanitizers package for tests, as well as the corresponding package page for sanitizers, which clearly predates our follow-up Rocker.org repo / project described in this initial announcement and when we became the official R container for Docker. Rocker had support for SAN testing, but UBSAN was not working yet. So following a recent CRAN report against our RcppAnnoy package, I was unable to replicate the error and asked for help on r-devel in this thread. Martyn Plummer and Jan van der Laan kindly sent their configurations in the same thread and off-list; Jeff Horner did so too following an initial tweet offering help. None of these worked for me, but further trials eventually lead me to the (already mentioned above) RedHat blog post with its mention of -fno-sanitize-recover to actually have an error abort a test. Which, coupled with the settings used by Martyn, were what worked for me: clang-3.5 -fsanitize=undefined -fno-sanitize=float-divide-by-zero,vptr,function -fno-sanitize-recover. This is now part of the updated Dockerfile of the R-devel-SAN-Clang repo behind the r-devel-ubsan-clang. It contains these settings, as well a new support script check.r for littler---which enables testing right out the box. Here is a complete example:

docker                              # run Docker (any recent version, I use 1.2.0)
  run                               # launch a container 
    --rm                            # remove Docker temporary objects when dome
    -ti                             # use a terminal and interactive mode 
    -v $(pwd):/mnt                  # mount the current directory as /mnt in the container
    rocker/r-devel-ubsan-clang      # using the rocker/r-devel-ubsan-clang container
  check.r                           # launch the check.r command from littler (in the container)
    --setwd /mnt                    # with a setwd() to the /mnt directory
    --install-deps                  # installing all package dependencies before the test
    RcppAnnoy_0.0.5.tar.gz          # and test this tarball

I know. It is a mouthful. But it really is merely the standard practice of running Docker to launch a single command. And while I frequently make this the /bin/bash command (hence the -ti options I always use) to work and explore interactively, here we do one better thanks to the (pretty useful so far) check.r script I wrote over the last two days. check.r does about the same as R CMD check. If you look inside check you will see a call to a (non-exported) function from the (R base-internal) tools package. We call the same function here. But to make things more interesting we also first install the package we test to really ensure we have all build-dependencies from CRAN met. (And we plan to extend check.r to support additional apt-get calls in case other libraries etc are needed.) We use the dependencies=TRUE option to have R smartly install Suggests: as well, but only one level (see help(install.packages) for details. With that prerequisite out of the way, the test can proceed as if we had done R CMD check (and additional R CMD INSTALL as well). The result for this (known-bad) package:

edd@max:~/git$ docker run --rm -ti -v $(pwd):/mnt rocker/r-devel-ubsan-clang check.r --setwd /mnt --install-deps RcppAnnoy_0.0.5.tar.gz 
also installing the dependencies  Rcpp ,  BH ,  RUnit 
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.3.tar.gz'
Content type 'application/x-gzip' length 2169583 bytes (2.1 MB)
opened URL
==================================================
downloaded 2.1 MB
trying URL 'http://cran.rstudio.com/src/contrib/BH_1.55.0-3.tar.gz'
Content type 'application/x-gzip' length 7860141 bytes (7.5 MB)
opened URL
==================================================
downloaded 7.5 MB
trying URL 'http://cran.rstudio.com/src/contrib/RUnit_0.4.28.tar.gz'
Content type 'application/x-gzip' length 322486 bytes (314 KB)
opened URL
==================================================
downloaded 314 KB
trying URL 'http://cran.rstudio.com/src/contrib/RcppAnnoy_0.0.4.tar.gz'
Content type 'application/x-gzip' length 25777 bytes (25 KB)
opened URL
==================================================
downloaded 25 KB
* installing *source* package  Rcpp  ...
** package  Rcpp  successfully unpacked and MD5 sums checked
** libs
clang++-3.5 -fsanitize=undefined -fno-sanitize=float-divide-by-zero,vptr,function -fno-sanitize-recover -I/usr/local/lib/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -pipe -Wall -pedantic -
g  -c Date.cpp -o Date.o
[...]
* checking examples ... OK
* checking for unstated dependencies in  tests  ... OK
* checking tests ...
  Running  runUnitTests.R 
 ERROR
Running the tests in  tests/runUnitTests.R  failed.
Last 13 lines of output:
  +     if (getErrors(tests)$nFail > 0)  
  +         stop("TEST FAILED!")
  +      
  +     if (getErrors(tests)$nErr > 0)  
  +         stop("TEST HAD ERRORS!")
  +      
  +     if (getErrors(tests)$nTestFunc < 1)  
  +         stop("NO TEST FUNCTIONS RUN!")
  +      
  +  
  
  
  Executing test function test01getNNsByVector  ... ../inst/include/annoylib.h:532:40: runtime error: index 3 out of bounds for type 'int const[2]'
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
   /tmp/RcppAnnoy/..Rcheck/00check.log 
for details.
root@a7687c014e55:/tmp/RcppAnnoy# 

The log shows that thanks to check.r, we first download and the install the required packages Rcpp, BH, RUnit and RcppAnnoy itself (in the CRAN release). Rcpp is installed first, we then cut out the middle until we get to ... the failure we set out to confirm. Now having a tool to confirm the error, we can work on improved code. One such fix currently under inspection in a non-release version 0.0.5.1 then passes with the exact same invocation (but pointing at RcppAnnoy_0.0.5.1.tar.gz):

edd@max:~/git$ docker run --rm -ti -v $(pwd):/mnt rocker/r-devel-ubsan-clang check.r --setwd /mnt --install-deps RcppAnnoy_0.0.5.1.tar.gz
also installing the dependencies  Rcpp ,  BH ,  RUnit 
[...]
* checking examples ... OK
* checking for unstated dependencies in  tests  ... OK
* checking tests ...
  Running  runUnitTests.R 
 OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
   /mnt/RcppAnnoy.Rcheck/00check.log 
for details.
edd@max:~/git$

This proceeds the same way from the same pristine, clean container for testing. It first installs the four required packages, and the proceeds to test the new and improved tarball. Which passes the test which failed above with no issues. Good. So we now have an "appliance" container anybody can download from free from the Docker hub, and deploy as we did here in order to have fully automated, one-command setup for testing for UBSAN errors. UBSAN is a very powerful tool. We are only beginning to deploy it. There are many more useful configuration settings. I would love to hear from anyone who would like to work on building this out via the R-devel-SAN-Clang GitHub repo. Improvements to the littler scripts are similarly welcome (and I plan on releasing an updated littler package "soon").

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