Value of an R object in an expression

Just wanted to create an expression, existing of some mathematical annotation and a value of an R object. Wasn’t that intuitive!

Each single goal is easy to reach, for example to combine a value of an R object with text just use paste :

> n = 5
> paste ("n=", n, "!")
[1] "n= 5 !"

To have a plot title with an \(\alpha_1\) you can use expression :

> plot(1:5, runif(5, 1, 4), main=expression("this is a " * alpha[1] * " example"))

But to let the the title of a plot contain objects and Greek letters isn’t that easy. Those of you who think it’s just about combining paste and expression might try it on their own and come back head-ached after few minutes of unsuccessful testings.

The problem is, that expression interprets chars as expression and not as object identifier, of course, how should it know whether you mean the var alpha or the Greek letter!? The solution is called substitute ! With substitute you can replace objects inline, here is a small example:

> var=10
> substitute(paste("here is the content: ", v), list(v=var))
paste("here is the content: ", 10)

You see, substitute got a list what to substitute and replaces the v in paste with the content of var . Run eval to evaluate to result:

> var=10
> eval(substitute(paste("here is the content: ", v), list(v=var)))
[1] "here is the content:  10"

Now it’s easy to create a more complex plot title:

> var=10
> plot(1:5, runif(5, 1, 4), main=substitute(paste("here ", lambda[1], "=", v, " and ", epsilon^2, "=", b, "!"), list(v=var, b=var^2)))

Go out and produce imposing graphs! (-;

Too much at once

Just installed a new Grml system, annoyingly from a bit too far outdated image so aptitude fails to handle everything at once…

Here is the error:

Reading package fields... 52%/usr/lib/ruby/1.8/debian/utils.rb:47:in 'pipe': Too many open files (Errno::EMFILE)
        from /usr/lib/ruby/1.8/debian/utils.rb:47:in 'pipeline'
        from /usr/lib/ruby/1.8/debian/utils.rb:86:in 'tar'
        from /usr/lib/ruby/1.8/debian.rb:142:in 'load'
        from /usr/lib/ruby/1.8/debian/utils.rb:75:in 'gunzip'
        from /usr/lib/ruby/1.8/debian/utils.rb:40:in 'pipeline'
        from /usr/lib/ruby/1.8/debian/utils.rb:72:in 'gunzip'
        from /usr/lib/ruby/1.8/debian.rb:141:in 'load'
        from /usr/lib/ruby/1.8/debian/ar.rb:150:in 'open'
        from /usr/lib/ruby/1.8/debian/ar.rb:147:in 'each'
        from /usr/lib/ruby/1.8/debian/ar.rb:147:in 'open'
        from /usr/lib/ruby/1.8/debian.rb:140:in 'load'
        from /usr/lib/ruby/1.8/debian.rb:82:in 'field'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:733:in 'field'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:751:in 'create'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:743:in 'each_index'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:743:in 'create'
        from /usr/sbin/apt-listbugs:323
/usr/lib/ruby/1.8/debian.rb:198:in 'parseFields': E: required field Package not found in  (Debian::FieldError)
        from /usr/lib/ruby/1.8/debian.rb:196:in 'each'
        from /usr/lib/ruby/1.8/debian.rb:196:in 'parseFields'
        from /usr/lib/ruby/1.8/debian.rb:439:in 'initialize'
        from /usr/lib/ruby/1.8/debian.rb:150:in 'new'
        from /usr/lib/ruby/1.8/debian.rb:150:in 'load'
        from /usr/lib/ruby/1.8/debian.rb:82:in 'field'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:733:in 'field'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:751:in 'create'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:743:in 'each_index'
        from /usr/share/apt-listbugs/apt-listbugs/logic.rb:743:in 'create'
        from /usr/sbin/apt-listbugs:323
E: Failed to fetch 404  Not Found
E: Sub-process /usr/sbin/apt-listbugs apt || exit 10 returned an error code (10)
E: Failure running script /usr/sbin/apt-listbugs apt || exit 10
A package failed to install.  Trying to recover:
Press return to continue.

Aha, too many open files.. So I had to install everything piecewise in a disturbing manner..

Btw. updating iptables 1.4.6-2 -> 1.4.10-1 before xtables-addons-common 1.23-1 -> 1.26-2 is a bad idea and fails for some reasons. So try to do it the other way round.

Crypto off

if you haven’t noticed yet: SSL is turned off…

Of course it isn’t really turned off, all content is still available through encrypted connections (all links are still working), but it’s disabled by default.

But why!? I got a lot of mails during the last weeks, telling me that there is a problem with my SSL cert. Yes, your browser is completely right, my cert isn’t valid because I’ve signed it by myself.. To get a trusted certificate that your browser recognizes to be valid is very expensive. For a cheap one I still have to pay about $100, that’s neither worthy nor affordable for me and my private blog. But I’m always interested in ideally offering secure mechanisms, so I tried to provide SSL. Another reason for SSL was my auth stuff. Wordpress doesn’t provide both SSL and SSL-free access. In an installation you have to decide whether to use https://... or http://... for URL’s. So all links are either to SSL encrypted content or the next click is unencrypted. Don’t ask me why they don’t check whether SSL was turned on/off for the last query and decide afterwards on using SSL for all further links.. However, I didn’t want to authenticate myself unencrypted and so I enabled SSL by default.

To be congenial to my visitors I turned off SSL, until somebody sponsors a valid certificate. There are also many disgusting tools having problems with my website, so it might be the better way to deliver unencrypted contend. The information on my site isn’t that secret ;-)

As a consequences you aren’t able to register/login anymore. I scripted a little bit to find a secure way for authenticating myself, but you aren’t allowed to take this path :-P Nevertheless, comments are still open and doesn’t require any authentication.

If you can find any SSL zombies please inform me!

ShortCut[siblings]: tail and its derivatives

Every text-tool-user should know about tail! You can print the last few lines of a file or watch it growing. But there are three improved derivatives, just get into it.

I think there is no need for further explanation of tail itself, so lets begin with the first derivative.


colortail is based on tail with support for colors, so it helps to keep track of important content. Common options and parameters are resembled closely to them of tail, so it won’t be a big adjustment to new circumstances for tail fans. The content that it presents is of course the same as if it comes from tail, but colorized ;) With -k you can additional submit a configuration file that defines some regular expressions and its colors. On a Debian some examples can be found in /usr/share/doc/colortail/examples/ . In figure 1 you can see an example output of colortail on the syslog of a virtual machine.


The second tool in this article is multitail. Like colortail it can colorize the output, but all is presented in a ncurses based user interface so it is able to create multiple windows on your console. If you open a file in multitail it’s automatically in a following mode ( -f in case of tail and colortail). If you are monitoring multiple log files your console is split horizontal or vertical or a mix of both. You can pause the output, search for regular expressions and a lot more. Enter F1 to get a small help window. Figure 2 presents a sample output. Its project page keeps much more information.


logtail pursues a different goal. It’s not interested in prettifying the output, it remembers the content that was still displayed and just prints the differences to the last run. So it is an ideal tool for log analyzer, log messages doesn’t have to be parsed multiple times. logtail is written in perl, you can also monitor logfiles on different machines.

I hope I could give you some smart inspirations.

OpenNIC DNS network

DNS look-ups are a very sensible topic. Of course you want very fast name-to-IP resolutions, but should you always use Google’s DNS server? After all they can keep track of all your network motion profile unless you are surfing by IP! Today I read about the OpenNIC Project and ran some speed tests. It’s very interesting and worthy to know about!

The project about itself:

OpenNIC (a.k.a. "The OpenNIC Project") is an organization of hobbyists who run an alternative DNS network. [...] Our goal is to provide you with quick and reliable DNS services and access to domains not administered by ICANN.

Ok, I gave it a try and implemented a Perl-script that checks the speed. It throws a dice to call one of my often used domains and digs1 each of my predefined DNS servers to save the query time. I tested the following DNS server:

  • : one server of the OpenNIC project, located in Germany
  • : one server of the OpenNIC project, located in Germany (NRW)
  • : Google’s public DNS server, proven to be fast and reliable
  • : my ISP’s server
  • : name server of our university

Find the Perl code attached.

And here are the results after 10000 qeuries:

IPProvider10000 queries ISP131989 ms ms ms ms of uni-halle.de394134 ms

As you can see, my ISP’s DNS server is the fastest, they may have optimized their internal infrastructure to provide very fast look-ups to its customers. But it is also nice to see, that there is one OpenNIC server that is faster than google! And this server comes with another feature: It doesn’t track any logs! Isn’t that great!?

To find some servers near you just check their server list. Some of them don’t record logs or anonymize them, and of course all of them are independent from ICANN administrations.

I can’t recommend to use any special DNS server, but I want to advise to test them and find the best one for your demands! Feel free to post your own test results via comment or trackback.

1 dig is part of the larger ISC BIND distribution

Download: Perl: pipapo/scripts/ (Please take a look at the man-page. Browse bugs and feature requests.)

Martin Scharm

stuff. just for the records.

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