Unsure of Java/Gnome/MatLab interactions

KAYVEN RIESE kayve at sfsu.edu
Tue Feb 9 08:37:37 UTC 2010 

I just installed a fresh new Ubuntu last week.. 9.10

Script done, file is matlab.log
root at kayve-laptop:~/apt-gets# uname -a
Linux kayve-laptop 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 
UTC 2010 x86_64 GNU/Linux
root at kayve-laptop:~/apt-get

I bought MatLab and here are instructions given to me:
  Student Downloads
Linux (32-bit) Download and Installation Instructions

    1. Create a temporary directory into which you can download files, and 
then cd into it. For example, to install into the location 
/usr/local/temp, use these commands:

          cd /usr/local
         mkdir temp
         cd temp
         Subsequent instructions refer to this directory as $TEMP.
    2. Click the Download button for each product and save the file to your 
$TEMP directory. Some browsers, such as Firefox, save files to a default 
location, so you may need to configure your browser to prompt for the 
location to save downloaded files.

    3. In the $TEMP directory, run the command tar -xf 
matlab_installer_glnx86.tar to expand the installer.

    4. Once you have expanded the installer files in the $TEMP directory, 
run ./install to install the products. During the installation process, 
provide the information requested on each screen. For example, on the 
MATLAB Root Directory screen enter your installation location, such as 
/usr/local/matlab.

    5. When the installer asks if you want to proceed with activation, 
click Continue. Activating right after installation is recommended. To get 
help for any part of the process, click Help on that screen.


    Note: To see or hide the MD5 checksum, click the Show/Hide MD5 checksum 
link in the Filename column. Learn more

Product 	Filename
(Show/Hide MD5 checksum) 	Size
Installer Linux x86 7.8
 	matlab_installer_glnx86.tar
a46803046327e8da905276f97bba7dd4 	12.7 MB
MATLAB Linux x86 7.8
 	stu_matlab_glnx86.tar
aa13d7e695ca34ee0d707e58f1877da6 	246.2 MB
Simulink Linux x86 7.3
 	stu_simulink_glnx86.tar
59a0e855c87aac20bdff75ed992bc96b 	123.4 MB
Control System Toolbox Linux x86 8.3
 	stu_control_glnx86.tar
638758c6347c604727660168cbf431bc 	14.6 MB
Image Processing Toolbox Linux x86 6.3
 	stu_images_glnx86.tar
6294af3183e539bf735f92ef594a248a 	127.9 MB
Optimization Toolbox Linux x86 4.2
 	stu_optim_glnx86.tar
d430a337960f20ed8bb7d5ced56cb6c6 	4.4 MB
Partial Differential Equation Toolbox Linux x86 1.0.14
 	stu_pde_glnx86.tar
2a5230b6067326f9828db242d571dc82 	2.8 MB
Signal Processing Blockset Linux x86 6.9
 	stu_dspblks_glnx86.tar
6e074724ce04fc30dac0a39b63694823 	33.4 MB
Signal Processing Toolbox Linux x86 6.11
 	stu_signal_glnx86.tar
ae835dd35b2944d4b7c707969f36e2b7 	37.1 MB
Statistics Toolbox Linux x86 7.1
 	stu_stats_glnx86.tar
24b9e8f8cab7329266a7da69a98e4af6 	12.2 MB
Symbolic Math Toolbox Linux x86 5.2
 	stu_symbolic_glnx86.tar
a6e035376934db11fb6ee9340690222e 	132.2 MB

I did openjdk and here is what that looked like:

root at kayve-laptop:~/apt-gets# cat openjdk.makesplat
su: Authentication failure
kayve at kayve-laptop:~$ su -
Password:
root at kayve-laptop:~# apt-get install openjdk-6-jre
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer 
required:
   linux-headers-2.6.31-14 linux-headers-2.6.31-14-generic
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
   ca-certificates-java icedtea-6-jre-cacao java-common 
libaccess-bridge-java
   libaccess-bridge-java-jni libjline-java openjdk-6-jre-headless
   openjdk-6-jre-lib rhino tzdata-java
Suggested packages:
   equivs libjline-java-doc icedtea6-plugin sun-java6-fonts 
ttf-kochi-gothic
   ttf-sazanami-gothic ttf-kochi-mincho ttf-sazanami-mincho 
ttf-telugu-fonts
   ttf-oriya-fonts ttf-kannada-fonts ttf-bengali-fonts rhino-doc
The following NEW packages will be installed:
   ca-certificates-java icedtea-6-jre-cacao java-common 
libaccess-bridge-java
   libaccess-bridge-java-jni libjline-java openjdk-6-jre 
openjdk-6-jre-headless
   openjdk-6-jre-lib rhino tzdata-java
0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
Need to get 31.7MB of archives.
After this operation, 89.7MB of additional disk space will be used.
Do you want to continue [Y/n]? y
Get:1 http://us.archive.ubuntu.com karmic-updates/main openjdk-6-jre-lib 
6b16-1.6.1-3ubuntu1 [4,772kB]
Get:2 http://us.archive.ubuntu.com karmic/main ca-certificates-java 
20090928 [101kB]
Get:3 http://us.archive.ubuntu.com karmic-updates/main tzdata-java 
2009u-0ubuntu0.9.10 [143kB]
Get:4 http://us.archive.ubuntu.com karmic-updates/main libjline-java 
0.9.94-5~ubuntu1 [68.3kB]
Get:5 http://us.archive.ubuntu.com karmic/main rhino 1.7R2-1ubuntu1 
[739kB]
Get:6 http://us.archive.ubuntu.com karmic/main java-common 0.30ubuntu5 
[80.3kB]
Get:7 http://us.archive.ubuntu.com karmic-updates/main 
openjdk-6-jre-headless 6b16-1.6.1-3ubuntu1 [24.8MB]
Get:8 http://us.archive.ubuntu.com karmic/main libaccess-bridge-java 
1.26.2-1ubuntu1 [409kB]
Get:9 http://us.archive.ubuntu.com karmic/main libaccess-bridge-java-jni 
1.26.2-1ubuntu1 [8,652B]
Get:10 http://us.archive.ubuntu.com karmic-updates/main openjdk-6-jre 
6b16-1.6.1-3ubuntu1 [271kB]
Get:11 http://us.archive.ubuntu.com karmic-updates/main 
icedtea-6-jre-cacao 6b16-1.6.1-3ubuntu1 [331kB]
Fetched 31.7MB in 1min 43s (308kB/s)
Selecting previously deselected package openjdk-6-jre-lib.
(Reading database ... 138811 files and directories currently installed.)
Unpacking openjdk-6-jre-lib (from 
.../openjdk-6-jre-lib_6b16-1.6.1-3ubuntu1_all.deb) ...
Selecting previously deselected package ca-certificates-java.
Unpacking ca-certificates-java (from 
.../ca-certificates-java_20090928_all.deb) ...
Selecting previously deselected package tzdata-java.
Unpacking tzdata-java (from .../tzdata-java_2009u-0ubuntu0.9.10_all.deb) 
...
Selecting previously deselected package libjline-java.
Unpacking libjline-java (from .../libjline-java_0.9.94-5~ubuntu1_all.deb) 
...
Selecting previously deselected package rhino.
Unpacking rhino (from .../rhino_1.7R2-1ubuntu1_all.deb) ...
Selecting previously deselected package java-common.
Unpacking java-common (from .../java-common_0.30ubuntu5_all.deb) ...
Selecting previously deselected package openjdk-6-jre-headless.
Unpacking openjdk-6-jre-headless (from 
.../openjdk-6-jre-headless_6b16-1.6.1-3ubuntu1_amd64.deb) ...
Selecting previously deselected package libaccess-bridge-java.
Unpacking libaccess-bridge-java (from 
.../libaccess-bridge-java_1.26.2-1ubuntu1_all.deb) ...
Selecting previously deselected package libaccess-bridge-java-jni.
Unpacking libaccess-bridge-java-jni (from 
.../libaccess-bridge-java-jni_1.26.2-1ubuntu1_amd64.deb) ...
Selecting previously deselected package openjdk-6-jre.
Unpacking openjdk-6-jre (from 
.../openjdk-6-jre_6b16-1.6.1-3ubuntu1_amd64.deb) ...
Selecting previously deselected package icedtea-6-jre-cacao.
Unpacking icedtea-6-jre-cacao (from 
.../icedtea-6-jre-cacao_6b16-1.6.1-3ubuntu1_amd64.deb) ...
Processing triggers for man-db ...
Processing triggers for doc-base ...
Processing 2 added doc-base file(s)...
Registering documents with scrollkeeper...
Processing triggers for desktop-file-utils ...
Processing triggers for hicolor-icon-theme ...
Setting up tzdata-java (2009u-0ubuntu0.9.10) ...
Setting up java-common (0.30ubuntu5) ...

Setting up openjdk-6-jre-lib (6b16-1.6.1-3ubuntu1) ...
Setting up openjdk-6-jre-headless (6b16-1.6.1-3ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/java to 
provide /usr/bin/java (java) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/keytool to 
provide /usr/bin/keytool (keytool) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/pack200 to 
provide /usr/bin/pack200 (pack200) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/rmid to 
provide /usr/bin/rmid (rmid) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/rmiregistry 
to provide /usr/bin/rmiregistry (rmiregistry) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/unpack200 
to provide /usr/bin/unpack200 (unpack200) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/orbd to 
provide /usr/bin/orbd (orbd) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/servertool 
to provide /usr/bin/servertool (servertool) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/tnameserv 
to provide /usr/bin/tnameserv (tnameserv) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/lib/jexec to 
provide /usr/bin/jexec (jexec) in auto mode.

Setting up libaccess-bridge-java (1.26.2-1ubuntu1) ...
Setting up libaccess-bridge-java-jni (1.26.2-1ubuntu1) ...

Setting up openjdk-6-jre (6b16-1.6.1-3ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/javaws to 
provide /usr/bin/javaws (javaws) in auto mode.
update-alternatives: using 
/usr/lib/jvm/java-6-openjdk/jre/bin/pluginappletviewer to provide 
/usr/bin/pluginappletviewer (pluginappletviewer) in auto mode.
update-alternatives: using /usr/lib/jvm/java-6-openjdk/jre/bin/policytool 
to provide /usr/bin/policytool (policytool) in auto mode.

Setting up icedtea-6-jre-cacao (6b16-1.6.1-3ubuntu1) ...
Setting up ca-certificates-java (20090928) ...
creating /etc/ssl/certs/java/cacerts...
done.

Setting up libjline-java (0.9.94-5~ubuntu1) ...
Setting up rhino (1.7R2-1ubuntu1) ...
update-alternatives: using /usr/bin/rhino to provide /usr/bin/js (js) in 
auto mode.

Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
root at kayve-laptop:~#

root at kayve-laptop:~/apt-gets#

I wasn't really sure how to follow the instructions on this webpage:

https://help.ubuntu.com/community/Java

So here is what I did:

root at kayve-laptop:~/apt-gets# cat java-update.log

t at kayve-laptop:~# mkdir apt-gets
root at kayve-laptop:~# cd apt-gets/
root at kayve-laptop:~/apt-gets# vi openjdk.makesplat
root at kayve-laptop:~/apt-gets# update-java-alternatives -l
java-6-openjdk 1061 /usr/lib/jvm/java-6-openjdk
root at kayve-laptop:~/apt-gets# java -version
java version "1.6.0_0"
OpenJDK Runtime Environment (IcedTea6 1.6.1) (6b16-1.6.1-3ubuntu1)
OpenJDK 64-Bit Server VM (build 14.0-b16, mixed mode)
root at kayve-laptop:~/apt-gets# update-java-alternatives -s java-6-openjdk
update-alternatives: error: no alternatives for appletviewer.
update-alternatives: error: no alternatives for apt.
update-alternatives: error: no alternatives for extcheck.
update-alternatives: error: no alternatives for idlj.
update-alternatives: error: no alternatives for jar.
update-alternatives: error: no alternatives for jarsigner.
update-alternatives: error: no alternatives for javac.
update-alternatives: error: no alternatives for javadoc.
update-alternatives: error: no alternatives for javah.
update-alternatives: error: no alternatives for javap.
update-alternatives: error: no alternatives for jconsole.
update-alternatives: error: no alternatives for jdb.
update-alternatives: error: no alternatives for jhat.
update-alternatives: error: no alternatives for jinfo.
update-alternatives: error: no alternatives for jmap.
update-alternatives: error: no alternatives for jps.
update-alternatives: error: no alternatives for jrunscript.
update-alternatives: error: no alternatives for jsadebugd.
update-alternatives: error: no alternatives for jstack.
update-alternatives: error: no alternatives for jstat.
update-alternatives: error: no alternatives for jstatd.
update-alternatives: error: no alternatives for mozilla-javaplugin.so.
update-alternatives: error: no alternatives for native2ascii.
update-alternatives: error: no alternatives for rmic.
update-alternatives: error: no alternatives for schemagen.
update-alternatives: error: no alternatives for serialver.
update-alternatives: error: no alternatives for wsgen.
update-alternatives: error: no alternatives for wsimport.
update-alternatives: error: no alternatives for xjc.
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/appletviewer
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/apt
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/extcheck
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/idlj
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jarsigner
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jar
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/javac
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/javadoc
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/javah
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/javap
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jconsole
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jdb
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jhat
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jinfo
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jmap
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jps
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jrunscript
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jsadebugd
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jstack
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jstatd
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/jstat
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/native2ascii
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/rmic
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/schemagen
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/serialver
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/wsgen
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/wsimport
update-java-alternatives: jdk alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/bin/xjc
update-java-alternatives: plugin alternative does not exist: 
/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/IcedTeaPlugin.so

Not really sure that looks right.

So.  Unsurprisingly, when I followed the MatLab instructions this is what 
happened:


Script started on Mon 08 Feb 2010 11:43:03 PM PST
root at kayve-laptop:~/apt-gets# date
Mon Feb  8 23:43:04 PST 2010
root at kayve-laptop:~/apt-gets# pushd /usr/local
/usr/local ~/apt-gets
root at kayve-laptop:/usr/local# mkdir temp
mkdir: cannot create directory `temp': File exists
root at kayve-laptop:/usr/local# ls temp
root at kayve-laptop:/usr/local# cd temp
root at kayve-laptop:/usr/local/temp# ls
root at kayve-laptop:/usr/local/temp# cp /home/kayve/src/matlab/* .
root at kayve-laptop:/usr/local/temp# tar -xf matlab_installer_glnx86.tar
root at kayve-laptop:/usr/local/temp# ls
activate.ini                 readme.txt              stu_pde_glnx86.tar
install                      stu_control_glnx86.tar  stu_signal_glnx86.tar
inst_doc.pdf                 stu_dspblks_glnx86.tar 
stu_simulink_glnx86.tar
license.txt                  stu_images_glnx86.tar   stu_stats_glnx86.tar
mac_install_guide.pdf        stu_matlab_glnx86.tar 
stu_symbolic_glnx86.tar
matlab_installer_glnx86.tar  stu_optim_glnx86.tar    update
root at kayve-laptop:/usr/local/temp# ./install

Extracting student file stu_control_glnx86.tar
Extracting student file stu_dspblks_glnx86.tar
Extracting student file stu_images_glnx86.tar
Extracting student file stu_matlab_glnx86.tar
Extracting student file stu_optim_glnx86.tar
Extracting student file stu_pde_glnx86.tar
Extracting student file stu_signal_glnx86.tar
Extracting student file stu_simulink_glnx86.tar
Extracting student file stu_stats_glnx86.tar
Extracting student file stu_symbolic_glnx86.tar

Extracting ftp files . . . [please wait]
Extracting matlab.common
Extracting matlab.glnx86
Extracting tbx.simulink.common
Extracting tbx.simulink.glnx86
Extracting tbx.control.common
Extracting tbx.control.glnx86
Extracting tbx.optim.common
Extracting tbx.optim.glnx86
Extracting tbx.signal.common
Extracting tbx.signal.glnx86
Extracting tbx.symbolic.common
Extracting tbx.symbolic.glnx86
Extracting tbx.images.common
Extracting tbx.images.glnx86
Extracting tbx.stats.common
Extracting tbx.stats.glnx86
Extracting tbx.dspblks.common
Extracting tbx.dspblks.glnx86
Extracting tbx.pde
Finished extracting ftp files.
Starting installer ...
-------------------------------------------------------------------

     An error status was returned by the program 'xsetup',
     the X Window System version of 'install'. The following
     messages were written to standard error:

         /usr/local/temp/update/install/main.sh: 178: 
/usr/local/temp/update/bin/glnxa64/xsetup: not found

     Attempt to fix the problem and try again. If X is not available
     or 'xsetup' cannot be made to work then try the terminal
     version of 'install' using the command:

             install* -t    or    INSTALL* -t

-------------------------------------------------------------------

     Sorry! Setup aborted . . .

root at kayve-laptop:/usr/local/temp# ls
activate.ini                 stu_control_glnx86.tar   tbx.control.common 
tbx.signal.glnx86
install                      stu_dspblks_glnx86.tar   tbx.control.glnx86 
tbx.simulink.common
inst_doc.pdf                 stu_images_glnx86.tar    tbx.dspblks.common 
tbx.simulink.glnx86
licenses                     stu_matlab_glnx86.tar    tbx.dspblks.glnx86 
tbx.stats.common
license.txt                  stu_optim_glnx86.tar     tbx.images.common 
tbx.stats.glnx86
mac_install_guide.pdf        stu_pde_glnx86.tar       tbx.images.glnx86 
tbx.symbolic.common
matlab.common                stu_signal_glnx86.tar    tbx.optim.common 
tbx.symbolic.glnx86
matlab.glnx86                stu_simulink_glnx86.tar  tbx.optim.glnx86 
update
matlab_installer_glnx86.tar  stu_stats_glnx86.tar     tbx.pde
readme.txt                   stu_symbolic_glnx86.tar  tbx.signal.common
root at kayve-laptop:/usr/local/temp# popd
~/apt-gets
root at kayve-laptop:~/apt-gets# exit
exit

Script done on Tue 09 Feb 2010 12:13:52 AM PST
root at kayve-laptop:~/apt-gets#


Is it stating the obvious that I am trying to Get MaTLab working?


*----------------------------------------------------------*
   Kayven Riese, BSCS, MS (Physiology and Biophysics)
   (415) 902 5513 cellular
   http://kayve.net
   Webmaster http://ChessYoga.org
*----------------------------------------------------------*

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