Installation of Package ‘rggobi’ requires GGobi

30 08 2009

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

30 08 2009

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.


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Cannot find sprng 2.0 header file

10 08 2009

Trying to
install.packages("rsprng")
fails because
Cannot find sprng 2.0 header file.

The development package of the SPRNG (Scalable Parallel Random Number Generator) library which provides several RNGs that are suitable for use in parallel computing are missing:

sudo aptitude install libsprng2-dev

fixes it.


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Install R Package XML with Ubuntu amd64

8 08 2009

install.packages("XML")

failed while complaining

Cannot find xml2-config

Seth Falcon pointed out library libxml2-dev – Development files for the GNOME XML library – where missing.

sudo aptitude install libxml2-dev

fixed the problem.


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Installing RODBC with Ubuntu/Debian amd64

8 08 2009

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


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.dmrc Beeing Ignored

30 07 2009

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.


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Add Firefox Shiretoko (3.5) to Ubuntu Jaunty (9.04)

24 07 2009

To install the latest Firefox 3.5 (final) or Firefox 3.6 in Ubuntu, open a terminal and:

sudo sh -c "echo 'deb http://ppa.launchpad.net/ubuntu-mozilla-daily/ppa/ubuntu jaunty main' >> /etc/apt/sources.list"

Then add the Launchpad PPA GPG key:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 247510BE

And finally, install Firefox 3.5:

sudo aptitude update && sudo aptitude install firefox-3.5


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Things2do after Ubuntu Fresh Install

19 07 2009

Some very important things are missing having installed a fresh cup of Ubuntu – so called proprietary software with copyrights and stuff. Heretics! But the true believer has to fight evil with its own means :D

.. anyway I like to have the media codecs for “research purposes” and Adobes Reader and Googles stuff (desktop search engine, Picasa Image Gallery, Google-Earth …) …

so there is something to do. I just collected the things down here on other blogs a while ago, so I do not recall the links unfortunately.

I changed them a bit and not everything is working! Just to get an idea what to do and where to search…

1. Add the Medibuntu Repository

Medibutu stands for Multimedia, Entertainment & Distractions In Ubuntu and is a repository of packages that cannot be included in Ubuntu due to legal reasons. We need to add this repository to enable MP3, DVD playback, install certain codecs etc.

Take a terminal and enter:

sudo wget http://www.medibuntu.org/sources.list.d/intrepid.list --output-document=/etc/apt/sources.list.d/medibuntu.list && sudo apt-get update && sudo apt-get install medibuntu-keyring && sudo apt-get update

Now we’ll enable all repositories (including Universe and Multiverse repositories) that Ubuntu provides. Take a terminal and enter:

sudo sed -i -e "s/# deb/deb/g" /etc/apt/sources.list && sudo apt-get update

2. Enable Playback of Encrypted DVDs in Ubuntu 8.10

Once the Medibuntu repository has been added as said above, take a terminal and enter:

sudo apt-get install libdvdcss2

3. Playing MP3, WMA, Real and Apple QuickTime Files in Ubuntu 8.10

Once the Medibuntu repository has been added as said above, take a terminal and enter:

For a 32 bit machine:

sudo apt-get install w32codecs

For a 64 bit machine:

sudo apt-get install w64codecs

For a PPC machine:

sudo apt-get install ppc-codecs

4. Install Skype in Ubuntu 8.10

Once the Medibuntu repository has been added as said above, take a terminal and enter:

sudo apt-get install skype

5. Install Adobe Acrobat Reader in Ubuntu 8.10

Once the Medibuntu repository has been added as said above, take a terminal and enter:

sudo apt-get install acroread

6. Install Google Earth in Ubuntu 8.10

Take a terminal and enter:

wget http://dl.google.com/earth/client/current/GoogleEarthLinux.bin && chmod +x GoogleEarthLinux.bin && ./GoogleEarthLinux.bin

7. Install VLC Player in Ubuntu 8.10

VLC is the media player that is said to play all media formats under the sky. Install it by running the following command from a terminal:

sudo apt-get install vlc

8. Install Flash Plugin for Firefox in Ubuntu 8.10

The latest flash plugin (Flash player 10) can be installed using this command:

sudo apt-get install flashplugin-nonfree

9. Install Google Picasa in Ubuntu 8.10

F-Spot sucks if compared to Google Picasa. Run this command from a terminal to get Google Picasa:

sudo echo 'deb http://dl.google.com/linux/deb/ stable non-free' >> /etc/apt/sources.list && sudo apt-get update && sudo apt-get install picasa


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Ubuntu Alternate Installation from USB-disk

14 07 2009

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!


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Ubuntu Installation from USB-disk

14 07 2009

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…


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