Installation of Package ‘rggobi’ requires GGobi

Installation of package ‘rggobi’ had non-zero exit status on my way to solve all the rattle dependencies.

rggobi is an interface from R to GGobi – an open source visualization program for exploring high-dimensional data. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Plots are interactive and linked with brushing and identification (from the package description).

When trying to install rggobi R complained accordingly error: Package requirements (ggobi >= 2.1.6) were not met: No package 'ggobi' found

and the fix is not hard to figure out:
sudo aptitude install ggobi

rggobi also depends on RGtk2 which in turn requires libglade. That was another post.


libglade not found – Installation of package ‘RGtk2’ had non-zero exit status

Both R-packages rattle and rggobi depend on RGtk2. Trying to install RGtk2 threw an error: WARNING: libglade not found

sudo aptitude install libglade2-dev
installs the development files for libglade, which allows to load externally stored user interfaces into programs. This development file is needed for the graphical user interfaces of both rggobi and rattle.

Installing RODBC with Ubuntu/Debian amd64

Trying to install RODBC in Ubuntu with
failed throwing an error message
ODBC headers sql.h and sqlext.h not found

A glance at the r-help showed that it had to do with something called unixODBC – an ODBC driver manager.

The package was installed, but not the development package and thus not the headers which R complained about.

Again a not-so-obvious-for-the-newbee-Linux-Unix-Shell-goblish thing. The fix is
sudo aptitude install unixodbc-dev

.dmrc Beeing Ignored

After installing the Fluxbox desktop in addition to the default Xfce4 in Xubuntu a persistent error message started to show up:

User's $home/.dmrc file is being ignored. This prevents the default session and language from being saved. File should be owned by user and have 644 permission. User's $home directory must be owned by user and not writable by other user's.

It seems to be a bug in Ubuntu. It turned out that the same error message appeared on a Ubuntu Jaunty (Gnome) fresh install and on my Linux Mint 7 (based on Ubuntu Jaunty) fresh install. From time to time it shows up and I have not figured out how to (re-)produce it.

chmod 644 .dmrc
chmod o-w /home/USER

does the job, where USER has to be replaced by you username.

Ubuntu Alternate Installation from USB-disk

Writing the Alternate Installation Disk of Xubuntu 8.04 Hardy Heron to an USB-disk is not as straightforward as doing it with the desktop version.

You would follow the same procedure as with the desktop version, but when you boot the computer from the usb-disk you run into an error:
No common CD-drive detected

… and there it stops. You might find some forums suggesting to toggle into the console and do some “creating folders” and “links” and “mounting” them. Do not read them. It does not work.

It is a bug. You have to change a file named cdrom-detect.postinst. Pretty obvious name. There is a patch from Hans Deragon.

I assume it would be more elegant to download and run the patch
patch YourFile2BePatched
… anyway I did not bother, opened a text editor and pasted the addition instead. The part of the code is quite at the beginning of cdrom-detect.postinst.

Nice try, but FIRST you have to FIND the file to change:

cdrom-detect.postinst is located inside an archive inside a compressed folder called initrd.gz. The initrd.gz file is actually a compressed archive containing all of the executables, libraries, and configuration files needed during boot.


Open a terminal and create a folder extract in your home directory, change into this folder and extract initrd.gz into it:
mkdir extract
cd extract
zcat /media/USBdisk/install/initrd.gz | cpio -i

Note that in this example the installation USB-disk is found at /media/USBdisk. Change it according to your situation.

Now it is time to find /var/lib/dpkg/info/cdrom-detect.postinst and exchange the lines


devices="$(list-devices cd; list-devices maybe-usb-floppy)"
for device in $devices; do
if mount -t iso9660 -o ro,exec $device /cdrom; then
log "CD-ROM mount succeeded: device=$device"
db_set cdrom-detect/cdrom_device $device



devices="$(list-devices cd; list-devices partition; list-devices maybe-usb-floppy)"
for device in $devices; do
if mount -t iso9660 -o ro,exec $device /cdrom || \
mount -t vfat -o ro,exec $device /cdrom ; then
log "CD-ROM mount succeeded: device=$device"
db_set cdrom-detect/cdrom_device $device

Repackage the initrd.gz file and put it on the USB drive:

find . | cpio -o --format='newc' | gzip -9 > /media/USBdisk/install/initrd.gz

Now you can remove your temporary extraction folder:
cd ..
rm -R extract

and restart use the Alternate Install USB-disk.


Ubuntu Installation from USB-disk

First, it is no longer neccessary to burn CDs in order to install Ubuntu (as any other Linux flavor i assume).

If one has a running Ubuntu install present, it is very easy:

  1. download the desired distribution (e.g. the Xubuntu 64-bit Desktop release to your harddrive
  2. sudo aptitude install usb-creator
  3. plug in a USB-disk with 1GB capacity at least
  4. open Menu – System – USB Startup Disk Creator and
  5. follow the menu instructions.

Doing this you end up with a desktop realease of Xubuntu on a USB-disk. You can boot and try out Xubuntu from the disk without changing anything on the host-computer. Or: you can start the installer to have the operating system permanently on harddisk.

But: if you might want to have an alternate installation USB-disk you have to undergo a more difficult task.

Why would you do this? The alternate install offers more flexibility concerning crypted partitions or installing just a command line “barebone” version of ubuntu. I started this task since the fluxbox is my favorite desktop manager and I wanted to play around a bit with creating my own Ubuntu flavour…

Install R packages without internet connection

You might have no internet connection or as in my case you have one, but the firewall prevents anything beside Windows IE to access the net. Grrr.

Ok. It takes more time, but is possible. Lets have an example:
Installing the package ‘gam’ for R-2.9 on Windows being in Norway (with as the nearest and fastest “Comprehensive R Archive Network”.

  1. Find another place with internet connection or as in my case, the browser works, so use the browser.
  2. Find the package on the repository corresponding to your operating system and your version of R in our above example here
  3. klick on the link, download it and save it (e.g. using an USB disk). Remember the path to the file (in our example in the folder H:/DATA/).
  4. Open R and write install.packages("H:/DATA/", repos=NULL) at the command line.

Thats it.

Difficulties installing rgl

rgl is a R package for three-dimensional visualisation using OpenGL. The package provides functions implementing a new graphics device suitable for visualisation of R objects in three dimensions using the OpenGL libraries.

It can be installed from the Ubuntu repostitories with

sudo aptitude install r-cran-rgl

or on all platforms inside R with



It depends on some GL libraries installed, which do not get installed by default. So you might expect unsuccessful installation, with an error message like
missing required header GL/gl.h.

The solution is to install the missing library manually with

sudo aptitude install libglu1-mesa-dev

… one of those inconveniences preventing mainstream users switching to OpenSource software – it seems to me.