Notes about open source software, computers, other stuff.
After an upgrade of one of my Ubuntu server that runs Nagios, I ran into the following error message (again…) when I tried to issue a command from the web interface:
Error: Could not stat() command file ‘/var/lib/nagios3/rw/nagios.cmd’!
This post by Barry O’Donovan shows very nicely how this problem can/should be fixed in Ubuntu. Much cleaner than chmod/chown-ing the directories myself. Thanks Barry!
Sun Grid Engine (SGE) is a bath queue system that can be used to distribute computation intensive tasks across one or more servers/CPUs. SGE has a graphical configuration utility called qmon, but when you start it on a remote machine (using SSH), you may end up with errors like this:
Warning: Cannot convert string "-adobe-courier-medium-r-*--14-*-*-*-m-*-*-*" to type FontStruct Warning: Cannot convert string "-adobe-courier-bold-r-*--14-*-*-*-m-*-*-*" to type FontStruct Warning: Cannot convert string "-adobe-courier-medium-r-*--12-*-*-*-m-*-*-*" to type FontStruct X Error of failed request: BadName (named color or font does not exist) Major opcode of failed request: 45 (X_OpenFont) Serial number of failed request: 329 Current serial number in output stream: 340
The warnings are not really a problem, but the error is. It can be solved by running the following on the client (i.e. your local) machine (assuming it runs Debian or Ubuntu):
sudo apt-get install xfonts-75dpi xset +fp /usr/share/fonts/X11/75dpi xset fp rehash |
Some time ago I bought a ThinkPad T440s for work. It’s an amazing machine! Before that I used a ThinkPad X121, which served me very well on my daily commute. This machine was getting a bit old, and given that my new job (more about which in a later post) also requires me to have a better machine with more screen real estate, it was high time to upgrade.
Ubuntu (13.10 and 14.04) runs well on the T440s, only two things didn’t work as expected:
Fn-F5 and Fn-F6 keys, but only in a weird way: several key presses are needed for one unit of decrease/increase.This last bug can be fixed by booting with the following kernel argument:
acpi_backlight=vendor
Simply add this to the GRUB_CMDLINE_LINUX_DEFAULT line in /etc/default/grub:
GRUB_CMDLINE_LINUX_DEFAULT="acpi_backlight=vendor quiet splash"
and run sudo update-grub. Reboot and you will be able to change the backlight brightness in finer steps.
I found this solution somewhere on the internet a few weeks ago, wrote it down, but can’t remember anymore what the original URL was. My apologies.
After upgrading my Ubuntu 13.10 installation to 14.04, I noticed that the output of several git commands (e.g. git diff and git log) didn’t show colours as they used to, but showed ESC[ ANSI codes instead.
A quick internet search lead to this post on unix.stackexchange.com where the LESS environment variable was ‘blamed’. Indeed, I have my LESS variable (re-) defined in my .bashrc and .zshrc files.
The solution was to add -R to the environment variable, which allows raw control characters to be displayed. I now have the environment variable defined as:
LESS='--quiet -X -F -R' |
Note to self: if you want to be able to upgrade WordPress via the web interface using SSH, you need to have the libssh2-php package installed on Debian/Ubuntu Linux.
Don’t forget to restart Apache after installing the package. Reload the WordPress admin pages and you’ll see the SSH option added.
After upgrading to Ubuntu 13.10 some time ago I noticed that my compose key (i.e. the key that you press followed by e.g. c and , to create a ç) didn’t work anymore in Emacs. I found two bug reports on this issue [1, 2], both effectively suggesting the same solution: start Emacs like this
XMODIFIERS=@im=none emacs |
So I added the following line to my ~/.zshrc and ~/.bashrc files:
alias emacs='XMODIFIERS=@im=none emacs' |
(of course somewhere before I set my EDITOR variable). I also changed the command in the launcher I use (GLX-Dock/Cairo-Dock).
This doesn’t make it a system-wide (or even user-wide) fix, e.g. the Firefox add-on “It’s all text” doesn’t get it, but it covers most of my use cases.
During the Christmas holidays I released a new version of ProbABEL (v0.4.2). The official release announcement can be found here. ProbABEL is a toolset that allows running GWAS (Genome-Wide Association Studies) in a fast and efficient manner. It implements regression using the linear, logistic or Cox proportional hazards models.
This version is mostly a bug fix release. The most important user-visible change is the fact that the ‘official’ name for the wrapper script that runs a GWAS over a range of chromosomes is now called probabel instead of probabel.pl. This change was induced by my attempts to get ProbABEL packaged in the Debian Linux repositories. One of the warnings that occurred during the package creation process was a Lintian warning that said that scripts with ‘language extensions’ are not allowed. There are several reasons for that, but the one I found most compelling was the fact that the user shouldn’t be concerned with the programming/scripting language we used to write it in. Moreover, being ‘agnostic’ in this matter also allows us to write such a script in a different language.
Of course, we have left the original name in place (via a symlink) in order not to disrupt any current pipelines. If the user runs the script with the old name a warning appears, urging him/her to start using the new name and that the old name will be deprecated in the future.
In the mean time, ProbABEL v0.4.1 has been accepted in Debian (unstable) and as of today it is also available in Debian ‘testing’. Lots of thanks to the Debian Med team that helped me a lot in preparing the .deb package. Note that the package has been split up in probabel (architecture-dependent files) and probabel-examples (with architecture independent files: the examples). See the Debian Package Tracking System page for ProbABEL for more details of the package.
From Debian the package has trickled down to Ubuntu as well (Launchpad page here), so it will be available by default in the next Ubuntu release (14.04, a.k.a. Trusty Tahr).
After upgrading Puppet from versions < v3 to version 3.0.0 or higher, the main commands have changed, keep this in mind when reading my earlier post. From the ChangeLog:
| Pre-2.6 | Post-2.6 |
|---|---|
| puppetmasterd | puppet master |
| puppetd | puppet agent |
| puppet | puppet apply |
| puppetca | puppet cert |
| ralsh | puppet resource |
| puppetrun | puppet kick |
| puppetqd | puppet queue |
| filebucket | puppet filebucket |
| puppetdoc | puppet doc |
| pi | puppet describe |
To run puppet on a client puppetd --test is changed to:
puppet agent --test |
To show a list of clients waiting for signing of their certificates run the following on the master:
puppet cert list |
instead of puppet ca -l. To list all certificates, run (on the master):
puppet cert list --all |
To completely remove a client’s certificate on the master run:
puppet cert clean client.localdomain |
and to sign a client certificate on the master run:
puppet cert sign client.localdomain |
Ubuntu Linux uses the LightDM greeter (the login screen you see after booting). Since I’m using an LDAP server to store my user accounts and LightDM by default only shows local users I needed to tell LightDM to give me an ‘other user’ option where I can enter a user name and password (I first checked to see if my LDAP connection work by logging in with an LDAP user from the console (tty1).
LightDM is configured in /etc/lightdm/lightdm.conf, but also provides command line tools to set the options. To show the ‘other user’ use:
sudo /usr/lib/lightdm/lightdm-set-defaults --show-manual-login true |
This will disable the user list. It adds the line
greeter-show-manual-login=true |
to the lightdm.conf file.
If you only want to see the “Other” entry run:
sudo /usr/lib/lightdm/lightdm-set-defaults --hide-users true |
And lastly you can turn off guest:
sudo /usr/lib/lightdm/lightdm-set-defaults --allow-guest false |
Thanks to mfish at askubuntu.com!
Last week I released v0.4.1 of ProbABEL, just a few days after releasing v0.4.0, which contained a small, but irritating bug.
This release took quite some time to create, but features quite a few bug fixes, including a major one: for the first time since the filevector format was introduced somewhere in 2009/2010, the Cox proportional hazards regression module works with filevector/DatABEL files. This is a major step forward, because up till now we had to maintain two branches of code: trunk, with all the regular updates and improvements, and the old branch that contained the Cox PH module that was only capable of reading text files.
Another notable change is the incorporation of 
--mmscore option. The implementation was relatively easy, because part of the code was still there from previous versions; it was disabled however, because it didn’t deal with missing genotype data. Now it does. Using the LRT is also easier in the case of the 2df (or genotypic) genetic model, where using the Wald test is not straightforward.
The third user-visible change was a change in the [code]probabel.pl[/code] script that hides some of the details (e.g. the location of the files with genotype data) of running a regression for the user. Previously, using the -o option meant that the output file name was constructed from the name of the phenotype file, the argument of the -o option and a fixed extension that depends on the model(s) being run. Starting with v.0.4.0 this behaviour has changed. If the -o option is specified its argument is used as the start of the output file name, with only the fixed extension appended to it. This allows users to specify output in a different directory than the one where the phenotype file was created.
Packages for Ubuntu Linux (or one of its derivatives and probably also Debian) can be found in the GenABEL PPA (personal package archive). Previously we also released pre-compiled Windows binaries, but I’ve stopped doing that. They were never tested anyway, and I think there isn’t much demand for them anyway. Most people who do genome-wide association studies use Linux servers anyway.
Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!
User support for the GenABEL suite can be found at our forum.
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