Archive for Linux

LaTeX issues from Vienna

Posted in Books, Statistics, University life with tags , , , , , , , , , , , on September 21, 2017 by xi'an

When working on the final stage of our edited handbook on mixtures, in Vienna, I came across unexpected practical difficulties! One was that by working on Dropbox with Windows users, files and directories names suddenly switched from upper case to lower cases letters !, making hard-wired paths to figures and subsections void in the numerous LaTeX files used for the book. And forcing us to change to lower cases everywhere. Having not worked under Windows since George Casella gave me my first laptop in the mid 90’s!, I am amazed that this inability to handle both upper and lower names is still an issue. And that Dropbox replicates it. (And that some people see that as a plus.)

The other LaTeX issue that took a while to solve was that we opted for one chapter one bibliography, rather than having a single bibliography at the end of the book, mainly because CRC Press asked for this feature in order to sell chapters individually… This was my first encounter with this issue and I found the solutions to produce individual bibliographies incredibly heavy handed, whether through chapterbib or bibunits, since one has to bibtex one .aux file for each chapter. Even with a one line bash command, this is annoying to the extreme!

web [mis-]content

Posted in Statistics with tags , , , on March 7, 2017 by xi'an

For the past two weeks, I have noticed a web content process on my computer, process that eats a lot of my CPU! And I have not found any final solution when looking on Linux/Ubuntu fora/forums… Moving to a new [and neat] laptop [as the older one broke an hinge that could not be fixed!] did not help, while killing the process by itself saw this very tab vanish on Firefox and the process reappear a few seconds later. Solving this issue seems beyond my reach!

Extending R

Posted in Books, Kids, R, Statistics with tags , , , , , , , , , , , , , , , , , on July 13, 2016 by xi'an

As I was previously unaware of this book coming up, my surprise and excitement were both extreme when I received it from CRC Press a few weeks ago! John Chambers, one of the fathers of S, precursor of R, had just published a book about extending R. It covers some reflections of the author on programming and the story of R (Parts 2 and 1),  and then focus on object-oriented programming (Part 3) and the interfaces from R to other languages (Part 4). While this is “only” a programming book, and thus not strictly appealing to statisticians, reading one of the original actors’ thoughts on the past, present, and future of R is simply fantastic!!! And John Chambers is definitely not calling to simply start over and build something better, as Ross Ihaka did in this [most read] post a few years ago. (It is also great to see the names of friends appearing at times, like Julie, Luke, and Duncan!)

“I wrote most of the original software for S3 methods, which were useful for their application, in the early 1990s.”

In the (hi)story part, Chambers delves into the details of the evolution of S at Bells Labs, as described in his [first]  “blue book” (which I kept on my shelf until very recently, next to the “white book“!) and of the occurrence of R in the mid-1990s. I find those sections fascinating maybe the more because I am somewhat of a contemporary, having first learned Fortran (and Pascal) in the mid-1980’s, before moving in the early 1990s to C (that I mostly coded as translated Pascal!), S-plus and eventually R, in conjunction with a (forced) migration from Unix to Linux, as my local computer managers abandoned Unix and mainframe in favour of some virtual Windows machines. And as I started running R on laptops with the help of friends more skilled than I (again keeping some of the early R manuals on my shelf until recently). Maybe one of the most surprising things about those reminiscences is that the very first version of R was dated Feb 29, 2000! Not because of Feb 29, 2000 (which, as Chambers points out, is the first use of the third-order correction to the Gregorian calendar, although I would have thought 1600 was the first one), but because I would have thought it appeared earlier, in conjunction with my first Linux laptop, but this memory is alas getting too vague!

As indicated above, the book is mostly about programming, which means in my case that some sections are definitely beyond my reach! For instance, reading “the onus is on the person writing the calling function to avoid using a reference object as the argument to an existing function that expects a named list” is not immediately clear… Nonetheless, most sections are readable [at my level] and enlightening about the mottoes “everything that exists is an object” and “everything that happens is a function” repeated throughout.  (And about my psycho-rigid ways of translating Pascal into every other language!) I obviously learned about new commands and notions, like the difference between

x <- 3


x <<- 3

(but I was disappointed to learn that the number of <‘s was not related with the depth or height of the allocation!) In particular, I found the part about replacement fascinating, explaining how a command like

diag(x)[i] = 3

could modify x directly. (While definitely worth reading, the chapter on R packages could have benefited from more details. But as Chambers points out there are whole books about this.) Overall, I am afraid the book will not improve my (limited) way of programming in R but I definitely recommend it to anyone even moderately skilled in the language.

Ubuntu issues

Posted in Kids, Linux with tags , , , on February 28, 2015 by xi'an

screen shot with ubuntu 10.10It may be that weekends are the wrong time to tamper with computer OS… Last Sunday, I noticed my Bluetooth icon had a “turn off” option and since I only use Bluetooth for my remote keyboard and mouse when in Warwick, I turned it off, thinking I would turn it on again next week. This alas led to a series of problems, maybe as a coincidence since I also updated the Kubuntu 14.04 system over the weekend.

  1. I cannot turn Bluetooth on again! My keyboard and mouse are no longer recognised or detected. No Bluetooth adapter is found by the system setting. Similarly, sudo modprobe bluetooth shows nothing. I have installed a new interface called Blueman but to no avail. The fix suggested on forums to run rfkill unblock bluetooth does not work either… Actually rfkill list all only returns the wireless device. Which is working fine.
  2. My webcam vanished as well. It was working fine before the weekend.
  3. Accessing some webpages, including all New York Times articles, now takes forever on Firefox! If less on Chrome.

Is this a curse of sorts?!

As an aside, I also found this week that I cannot update Adobe reader from version 9 to version 11, as Adobe does not support Linux versions any more… Another bummer. If one wants to stick to acrobat.

Update [03/02]

Thanks to Ingmar and Thomas, I got  both my problems solved! The Bluetooth restarted after I shut down my unplugged computer, in connection with an USB over-current protection. And Thomas figured out my keyboard had a key to turn the webcam off and on, key that I had pressed when trying to restart the Bluetooth device. Et voilà!

Glibc GHOST vulnerability

Posted in Linux with tags , , , , , on January 28, 2015 by xi'an

screen shot with ubuntu 10.10Just heard about a security vulnerability on Linux machines running Red Hat version 5 to 7, Ubuntu 10.04 and 12.04, Debian version 7, Fedora versions 19 and older, and SUSE versions 11 and older. The vulnerability occurs through a buffer overflow from some functions in the C library Glibc, which allows for a remote code to execute, and the fix to the problem is indicated on that NixCRaft webpage. (It is also possible to run the GHOST C code if you want to live dangerously!)



BibTool on the air

Posted in Books, Linux, Travel, University life with tags , , , , , , , , , , on October 23, 2014 by xi'an

Yesterday night, just before leaving for Coventry, I realised I had about 30 versions of my “mother of all .bib” bib file, spread over directories and with broken links with the original mother file… (I mean, I always create bib files in new directories by a hard link,

    ln ~/mother.bib

but they eventually and inexplicably end up with a life of their own!) So I decided a Spring clean-up was in order and installed BibTool on my Linux machine to gather all those versions into a new encompassing all-inclusive bib reference. I did not take advantage of the many possibilities of the program, written by Gerd Neugebauer, but it certainly solved my problem: once I realised I had to set the variates

check.double = on
check.double.delete = on
pass.comments = off

all I had to do was to call

bibtool -s -i ../*/*.bib -o mother.bib
bibtool -d -i mother.bib -o mother.bib
bibtool -s -i mother.bib -o mother.bib

to merge all bib file and then to get rid of the duplicated entries in mother.bib (the -d option commented out the duplicates and the second call with -s removed them). And to remove the duplicated definitions in the preamble of the file. This took me very little time in the RER train from Paris-Dauphine (where I taught this morning, having a hard time to make the students envision the empirical cdf as an average of Dirac masses!) to Roissy airport, in contrast with my pedestrian replacement of all stray siblings of the mother bib into new proper hard links, one by one. I am sure there is a bash command that could have done it in one line, but I spent instead my flight to Birmingham switching all existing bib files, one by one…

echo vulnerable

Posted in Linux with tags , , , on October 3, 2014 by xi'an

screen shot with ubuntu 10.10Even though most people are now aware of the Shellshock security problem on the bash shell, here is a test to check whether your Unix system is at risk:

env x='() { :;}; echo vulnerable' bash -c 'echo hello'

if the prompt returns vulnerable, it means the system is vulnerable and needs to be upgraded with the proper security patch… For instance running

sudo apt-get update && sudo apt-get install --only-upgrade bash

for Debian/Ubuntu versions. Check Apple support page for Apple OS.