## Damn scoping in R

Ok, R is very well-considered in certain respects, but there are also some things annoying me… This time it’s scoping…

Let’s have a look to the following code:

First it looks damn unspectacular. But wait, whats that:

Taking a closer look to the function shows that the returned value is randomly chosen from local ( runif(1) > .5 ) or global scope ( runif(1) <= .5 ). So you can’t expect a result from this function. Nasty, especially while debugging external code, isn’t it? :-)

So again my advise: Think about such specific features! This won’t happen in any sensible language…

## Auth issues

Sitting on an almost well configured host, I experienced some authentication issues the last few days…

So for example I’m using xtrlock as default X locking mechanism, but if I try to run it on this machine I got the following error:

Mmh, that is crap. My workaround to temporarily avoid this problem: Connecting to another host via SSH, running xtrlock within a GNU screen session ;-) But that’s no solution for a longer time… So I started debugging. First of all I grabbed the sources from the apt repository and searched for this error message. Turned out to be this piece of code (beginning with line 94 of xtrlock.c ):

Ok, seems that the provided password(-hash) is shorter than 13 characters… Going on debugging, the content of pw comes from getpwuid(getuid()) and seems to be ok (matches my users profile like it can be found in /etc/passwd ). At this time (line 1) pw->pw_passwd contains only an single x , more information can’t be retrieved from the passwd -file.. Next the code checks whether SHADOW_PWD is defined, means whether we use an additional shadow -file. Since thats the case this code is executed and the variable sp gets the broken-out fields of the record in the shadow password database that matches the username pw->pw_name (validated, my user). Checking this sp variable I recognized that it is null ! So pw->pw_passwd won’t be updated and still contains the single x from the passwd entry… First I thought about a bug in the getspnam () function, such things might happen due to the Debian unstable release I’m using, but after some further thoughts I checked the shadow file itself:

In comparison with other systems with working xtrlock instances I figured out, that this file shouldn’t only be owned by root. Instead the group has to be shadow! So here is the solution to this issue:

And everything is working fine again. Have no idea what or who changed the permissions for the shadow-file…

Update: By the way, afterwards I tried to use Xscreensaver instead of xtrlock, but I wasn’t able to unlock the screen when the shadow rights are wrong. The /var/log/auth.log held messages like that:

But this is just for google-searchers ;-)

## Open Source DNA

Yesterday I was a bit confused when I read this tweet. Manu Sporny, founder and CEO of Digital Bazaar, announced in his blog that he has published his genome..

He send some saliva to 23andme, they analyzed his DNA and provided his genetic code to him (let’s neglect the discussion whether data from 23andme-chips represent a fully sequenced genome..). This process is very smart and not expensive, so this part of his announcement is not spectacular. Lot’s of people are doing so.

The interesting part of this article: He published the results (roughly 1 million SNP markers) from 23andme as open source project to github, licensed under CC0! So he has released all his rights on this data.

In general a very impressing step, he might be the first person who published its DNA under such a license. His intentions are more than exemplary, providing access to genetic data to everyone that wants to work with it, i.e. researchers.

So far, so good, but there are some disadvantages, he still dealt with some of it. For example, what if anybody uses this information against him? I.e. healthcare provider, they might deny him to avoid high costs because they detected some pre-existing conditions in his DNA. It may also affect employment and can lead to discrimination. His reaction:

I’ve thought long and hard about each of those questions and the many more that you ask yourself before publishing this sort of personal data. There are large privacy implications in doing this. However, speaking solely for myself, I think the benefits outweigh the drawbacks.

Very nice, but there are also some ugly implications he apparently didn’t thought about! All these disadvantages don’t only affect himself, they may also affect relatives (children, parents, siblings..). Did they all agree with this publication?

I can’t see the advantages to an anonymously publication. Attach some demographic information like age, gender, educational background and everyone is satisfied. Then you don’t have to bear any consequences with bugs in your DNA.

With all due respect for his engagement, I think this step is not really sophisticated.

## Valentine's Day

Yes, it’s that time again, Feb 14th.. It’s Valentine’s Day.

Don’t know who has told my wife, but now I have to do some love, uuurgh..

How ever, this one is for my little valentine:

Love you soo much, of course! ;-)

PS. If you are able to catch one of these flower or praline seller: beat the living daylights out of them!!

## java.lang.OutOfMemoryError: Java heap space

I was just contacted concerning this Java memory problem, here is how you can get rid of it.

The amount of Ram for an Java application is limited by the JVM. To provide more memory to a single application you can start your Java process with two more parameters, like:

This allows Java to use up to 1024 MB. Here -Xms specifies the initial heap size, while -Xmx determines the maximum size. For machines with much more mem you might use g instead of m to set the size in gig’s. So -Xmx10g limits the amount of RAM to 10 GB.

Of course it’s annoying to apply these parameters to all your Java runs, so to change this behavior user-wide, you may create an alias like:

or better: Tell it to the Java Plugin Control Panel! Using Xfce you can find this tool in your panel’s menu in the Settings section. Gnome users may look in System > Preferences. If you don’t want to move your mouse you can also run ControlPanel from your terminal. This opens a window, default parameters can be applied in the tab Java, click View… and add your parameters to the Runtime Parameters column. This tool afterwards writes something like the following line to \$HOME/.java/deployment/deployment.properties :

So advanced users craving for trouble may edit this file on it’s own :-P

## MySQL upgrade failed

Still upgrading some of our servers from lenny to squeeze, actually I run into MySQL trouble…

While upgrading from the package mysql-server 5.0.51a-24+lenny5 -> 5.1.49-3 aptitude told me the following:

Mmh, a look into the /var/log/syslog pointed to the following errors:

Many messages at once.. To make a long story short the main problem is this line:

So edit your /etc/mysql/my.cnf and comment the following line (in my configuration it’s line 94):

That’s it, retry to configure the new version and everything will turn out all right.

## Apache not parsing PHP files

I just had a confusing problem: instead of interpreting PHP-scripts in our webserver’s userdir apache serves them for download!

It’s caused by an upgrade from lenny to squeeze and I spend a lot of ours with fixing.

This is really a serious problem, these sites aren’t able to read for those people/search engines etc. that are browsing and, more fatal, if clients are able to access the PHP code of our students/staff they might explore security issues or passwords stored in these PHP files, so first of all I disabled the public access to the webserver.

So what was the problem? When I recognized that phpMyAdmin and other not userdir related stuff still works fine, I searched for issues that differ for userdirs. At long last I took a look into the libapache2-mod-php5 config file located in /etc/apache2/mods-available/php5.conf :

As you can see, PHP is disabled if the userdir module was enabled… Disgusting! Commenting these lines out switched PHP for users on. Very annoying!

## It's squeeezzed

Yes, Debian’s 6th release, codename squeeze, has become stable yesterday!

Those of you following Debian on twitter should have noticed yet, they announced it in about 4 million tweets ;-)

To mark the occasion the also redesigned the whole web presence, just take a look at their new layout!

This article is just a small THANK YOU to the whole Debian team, they are working hard to make your life much more comfortable! Great work guys!

By the way I send some greetings to all the administrators out there running Debian. Just have a look at figure 1 :-P

## freiesMagazin 02/2011 published

The journal freiesMagazin just published it’s February issue, describing all the bots that took part in the programming contest.

Those of you that aren’t convinced by this topic, they also have a nice article about VirtualBox and KVM! So go out and grab a copy!

## X deletes input devices

Today I restarted my notebook to boot into another kernel. Unfortunately I couldn’t log-in to the desktop because neither the mouse nor the keyboard was working. The Xorg.log gave me a hint what happened.

That all affected my GRML installation. Unfortunately you can’t change to a virtual terminal while there is no keyboard control, so to change anything you have to connect via SSH or boot from live CD or USB. The error reported in /var/log/Xorg.0.log looks like:

So you see, all input device are turned off. Annoying!! To avoid this problem you have to add the following section to your /etc/X11/xorg.conf :

That should solve the problem. If you don’t have a xorg.conf yet you can create one with:

This will create /root/xorg.conf.new , so you just have to copy it to /etc/X11/xorg.conf .

Since it was the first reboot for about 30 days and I updated/installed a lot of new software, so I’m not able to blame anyone generating this bug. But if you are feel free to do so ;-)