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.

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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

Fix:
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
install.packages("RODBC")
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.

Anyway:
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.

SO DO THIS:

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

do
mounted=0

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"
mounted=1
db_set cdrom-detect/cdrom_device $device

with

do
mounted=0

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"
mounted=1
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.

Whew!