Archive for Linux

implementing reproducible research [short book review]

Posted in Books, Kids, pictures, R, Statistics, Travel, University life with tags , , , , , , , , , , , on July 15, 2014 by xi'an

As promised, I got back to this book, Implementing reproducible research (after the pigeons had their say). I looked at it this morning while monitoring my students taking their last-chance R exam (definitely last chance as my undergraduate R course is not reconoduced next year). The book is in fact an edited collection of papers on tools, principles, and platforms around the theme of reproducible research. It obviously links with other themes like open access, open data, and open software. All positive directions that need more active support from the scientific community. In particular the solutions advocated through this volume are mostly Linux-based. Among the tools described in the first chapter, knitr appears as an alternative to sweave. I used the later a while ago and while I like its philosophy. it does not extend to situations where the R code within takes too long to run… (Or maybe I did not invest enough time to grasp the entire spectrum of sweave.) Note that, even though the book is part of the R Series of CRC Press, many chapters are unrelated to R. And even more [unrelated] to statistics.

This limitation is somewhat my difficulty with [adhering to] the global message proposed by the book. It is great to construct such tools that monitor and archive successive versions of code and research, as anyone can trace back the research steps conducting to the published result(s). Using some of the platforms covered by the book establishes for instance a superb documentation principle, going much further than just providing an “easy” verification tool against fraudulent experiments. The notion of a super-wiki where notes and preliminary versions and calculations (and dead ends and failures) would be preserved for open access is just as great. However this type of research processing and discipline takes time and space and human investment, i.e. resources that are sparse and costly. Complex studies may involve enormous amounts of data and, neglecting the notions of confidentiality and privacy, the cost of storing such amounts is significant. Similarly for experiments that require days and weeks of huge clusters. I thus wonder where those resources would be found (journals, universities, high tech companies, …?) for the principle to hold in full generality and how transient they could prove. One cannot expect the research time to garantee availability of those meta-documents for remote time horizons. Just as a biased illustration, checking the available Bayes’ notebooks meant going to a remote part of London at a specific time and with a preliminary appointment. Those notebooks are not available on line for free. But for how long?

“So far, Bob has been using Charlie’s old computer, using Ubuntu 10.04. The next day, he is excited to find the new computer Alice has ordered for him has arrived. He installs Ubuntu 12.04″ A. Davison et al.

Putting their principles into practice, the authors of Implementing reproducible research have made all chapters available for free on the Open Science Framework. I thus encourage anyone interesting in those principles (and who would not be?!) to peruse the chapters and see how they can benefit from and contribute to open and reproducible research.

hiccups or death throes for pangolin?

Posted in Linux, Statistics, Travel, University life with tags , , , on October 25, 2013 by xi'an

screen shot with ubuntu 10.10Today my Ubuntu system had a strange pathology, almost freezing in any Internet connection, whether using a cable connection or wireless, even ping did not answer and nothing wrong on the process table… I checked the hardware by dual-booting on windows (for the first time since I installed Linux on this laptop) and seeing no such feature on Explorer. After a few reboots, it came back to normal. I wonder if this is an incomplete safety upgrade or a signal that my cheap laptop is coming close to the end of its life cycle. A life started right after Kyoto. Since I am leaving for Pittsburgh and Toronto next week, I should try to re-install a Linux version on another machine this weekend….

Vodafone USB Stick K3773

Posted in Travel with tags , , , , , on July 11, 2012 by xi'an

As the issue of having to pay a lot to connect to the Internet during my jetlagged night sessions was bothering me, I bought a 3G device in a nearby Vodafone shop to do the job (at the mere cost of four hours of connection!). It is a Vodafone USB Stick K3773 and I was unsure it would work under Linux (Ubuntu 12.04). When mounting the USB stick, I first saw there was a Linux directory on the stick, with the instruction to run ./install as root. I tried that and it did not work. I then checked the stick was working under windows, which was the case. I could not find helpful advices on the forums (fori!). So I fiddled for a few minutes and came with the idea of installing from my directory rather than from the (read-only) disk. Changed the attributes of the install file to executable. And ran it again. It surprisingly worked! The device is now recognised as a network wired connection (eth1) whenever I start my (Compaq) laptop.

Here are my commands, in case it helps:

 xian$ mkdir QuickStart
 xian$ cp /media/QuickStart\ 3.7/linux_mbb_install/* QuickStart/.
 xian$ cd QuickStart
 xian$ chmod +x install
 xian$ sudo ./install

It is rather slow (20 Kb/s) but this may a good way to manage my time on line!

quick impressions from Japan

Posted in pictures, Running, Travel with tags , , , , , , , , , on July 9, 2012 by xi'an

Just like last year trip to Shanghai was my first visit to China, this trip to Kyoto was my first time in Japan. I found the experience so exhilarating that I am already considering a trip back next year! (Especially since I could have lost all of my Kyoto pictures with my hard drive!) The mix of tradition and modernity, of history and high-tech, of chaotic architecture and smooth interactions, of rice fields in the shade of high-rises and of houses in the shade of expressways; all those snapshots, caught from the train as much as from the few hours I spent exploring the modern part of the city, are starting to blur already and I feel a need to go beyond to get a broader and deeper perspective on this fascinating country! Continue reading

Dennis Ritchie 1941-2011

Posted in Books, R, University life with tags , , , , , on October 29, 2011 by xi'an

I just got the “news” that Dennis Ritchie died, although this happened on October 12… The announcement was surprisingly missing from my information channels and certainly got little media coverage, compared with Steve Jobs‘ demise. (I did miss the obituaries in the New York Times and in the Guardian. The Economist has the most appropriate heading, printf(“goodbye, Dennis”); !!!) Still, Dennis Ritchie contributed to computer science to extents comparable to Steve Jobs’, if on a lesser commercial plane: he is a founding father of both the C language and the Unix operating system. I remember spending many days perusing over his reference book, The C programming language, co-written with Brian Kernighan. (I kept trying programming in C until Olivier Cappé kindly pointed out to me that I was merely translating my Pascal vision into C code, missing most of the appeal of the language!) And, of course, I also remember discovering Unix when arriving at Purdue as a logical and much more modern operating system: just tfour years after programming principal components on punched card and in SAS, this was a real shock! I took a few evening classes at Purdue run by the Computer Department and I still carry around the Purdue University UNIX Pocket Guide. Although I hardly ever use it, it is there on the first shelf on top of my desk… As is The C programming language even though I have not opened it in years!

So we (geeks, computer users, Linuxians, R users, …) owe a lot to Dennis Ritchie and it is quite sad both that he passed away by himself and that his enormous contribution was not better acknowledged. Thus, indeed,

for (i=0; i<ULONG_LONG_MAX; i++)
    printf("thanks a lot, Dennis")

A new series of mishaps

Posted in Kids, R, University life with tags , , , , , on March 13, 2011 by xi'an

Following the slight difficulties of last week, I had a hard week on the computer front: indeed, on Monday, I received my 2007 macbook from the repair shop, with a new video card, courtesy of Apple. Unfortunately, this started a series of problems. First, the old macbook stopped recognizing the NVIDIA video and, while it worked under VESA, the system got unstable to the point that I had no choice but to install Maverick Meerkat (Ubuntu 10.10) to make it work again… This proved rather unsuccessful in that the new installment is periodically login me out, especially when I am under Firefox or Acrobat… (Most items are working, though, including the bluetooth Apple mouse… Anyway, Pierre kindly offered to take a look over the weekend.) This was not the end of my worries, though, as I stupidly typed sudo chown xian on my new macbook while on / (when I thought I was on /home/xian). This was very very s.t.u.p.i.d. (I committed this major error during Pierre’s talk two days ago, while typing my post on SMC²!) and it also ruined the whole system, despite a manual attempt at recreating the ownership of the system directories… This also ended in a reinstallation of Maverick Meerkat from the start, which surprisingly did not produce the same outcome as the first time, with hardly anything working. Even under the minimal Ubuntu configuration. So this morning I once again started from scratch, using the whole disk and letting the installation CD make all the decisions. Except for the sound (!), everything seems to be working now. Including the webcam as shown above. (Once I installed Isight.) Then tonight, the hinge of the macbook Air I keep at home (and often borrowed by my daughter) broke, a frequent problem with macbook air‘s as I brought one from the department to the repair shop on Monday in exchange for my repaired macbook… And to make the day complete, this morning a neighbouring car kindly pointed out to me a flat tire on my car! I am glad I recovered my bike with a new axis earlier this week…

Maverick Meerkat [10.10]

Posted in Linux with tags , , , on December 16, 2010 by xi'an

About one year after I failed to install Ubuntu 9.10 on my Macbook pro, I had another try with Ubuntu 10.10 (Maverick Meerkat!) Here is a copy of the screen:

The nice thing is that it worked right out of the installation CD. No add-on for wireless to install. (This post was made with the new Mac!) The only remaining difficulty is to work out how to cut-and-paste with the touchpad, as the sound isssue has been solved thanks to the special MacBookPro/Maverick page. Moving from Ubuntu to Kubuntu was about as seamless,

and while I still have a few items to install, including acrobat, both R and LaTeX are working fine. This is a constant conclusion with Linux: it eventually works out if one wait for the right version, with the obvious drawback that new material does not fit this scheme!


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