Ubuntu 12.4 installation issues

1
Hi All,

After finally giving up the struggle with Windows, i got our IT people to install Ubuntu on one of our lab machines, a reasonably new Dell laptop, 8Gb RAM, Intel i5 2.6Ghz quad core

They installed Ubuntu 64 bit 12.4 (they said 12.10 wouldn't install for some reason) with 64 bit matlab 2010b. My account is admin.

I'm very new to Linux so i hope I followed installation instructions correctly:

I used NeuroDebian to install both versions of psychtoolbox 3 (the 'free' and non-free versions). This appears to be installed in the folder 'usr/share/psychtoolbox-3' as I asked for it to install for all users. I added all of these subfolders to matlab path.

I also installed the Octave version of psychtoolbox via Terminal, as noted in one of teh Installation help pages.

then I run, in Matlab, DownloadAdditionsForNeurodebian which, if I understand, somehow ties the Matlab to the Octave versions?

when I do run that command, with a target directory on my user desktop, I get the follwoing errors:



DownloadAdditionsForNeuroDebian('/home/jim/Desktop','trunk')
Requested flavor is: trunk
Requested location for the NeuroDebian additions folder is inside: /home/jim/Desktop

Good. Your privileges suffice for the requested installation into folder /home/jim/Desktop.

The following EXPORT command asks the Subversion client to
download the few additional bits of Psychtoolbox:
svn export --force -N -r https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/ "/home/jim/Desktop/PsychtoolboxAddons"
Downloading. It's a few megabytes, which can take a bit of time.
Alas there may be no output to this window to indicate progress until the download is complete.
Please be patient ...
If you see some message asking something like "accept certificate (p)ermanently, (t)emporarily? etc."
then please press the p key on your keyboard, possibly followed by pressing the ENTER key.

svn: Syntax error in revision argument 'https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/'
Sorry, the download command "EXPORT" failed with error code 1:
For reason, see output above.
The download failure might be due to temporary network or server problems. You may want to try again in a
few minutes. It could also be that the subversion client was not (properly) installed.
??? Error using ==> DownloadAdditionsForNeuroDebian at 250
Download failed.




** END PASTE

So that doesn't work. And attempting to run Screen in any fashion gives the error:

>> screen
??? Invalid MEX-file
'/usr/share/octave/site/m/psychtoolbox-3/PsychBasic/Screen.mexa64': libraw1394.so.8:
cannot open shared object file: No such file or directory.

That file IS there in that folder, if, again, I understand this correctly....


As I said, I'm new to Ubuntu etc so perhaps I went wrong with some aspects of teh installation (I've been rushing as I'm on a tight deadline to get this up and running!). Have I made a mistake installing the Matlab psychtoolbox to the usr/share folder? If I made a mistake in the PTB install somewhere, how can I roll back everything I've attempted and start again?

thans for any help on this! I'm really looking forward to ditching Win fully!
2
Just for additional info, Subversion seems up to date, i.e,

sudo apt-get install subversions says it's the newest version!

--- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@...> wrote:
>
> Hi All,
>
> After finally giving up the struggle with Windows, i got our IT people to install Ubuntu on one of our lab machines, a reasonably new Dell laptop, 8Gb RAM, Intel i5 2.6Ghz quad core
>
> They installed Ubuntu 64 bit 12.4 (they said 12.10 wouldn't install for some reason) with 64 bit matlab 2010b. My account is admin.
>
> I'm very new to Linux so i hope I followed installation instructions correctly:
>
> I used NeuroDebian to install both versions of psychtoolbox 3 (the 'free' and non-free versions). This appears to be installed in the folder 'usr/share/psychtoolbox-3' as I asked for it to install for all users. I added all of these subfolders to matlab path.
>
> I also installed the Octave version of psychtoolbox via Terminal, as noted in one of teh Installation help pages.
>
> then I run, in Matlab, DownloadAdditionsForNeurodebian which, if I understand, somehow ties the Matlab to the Octave versions?
>
> when I do run that command, with a target directory on my user desktop, I get the follwoing errors:
>
>
>
> DownloadAdditionsForNeuroDebian('/home/jim/Desktop','trunk')
> Requested flavor is: trunk
> Requested location for the NeuroDebian additions folder is inside: /home/jim/Desktop
>
> Good. Your privileges suffice for the requested installation into folder /home/jim/Desktop.
>
> The following EXPORT command asks the Subversion client to
> download the few additional bits of Psychtoolbox:
> svn export --force -N -r https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/ "/home/jim/Desktop/PsychtoolboxAddons"
> Downloading. It's a few megabytes, which can take a bit of time.
> Alas there may be no output to this window to indicate progress until the download is complete.
> Please be patient ...
> If you see some message asking something like "accept certificate (p)ermanently, (t)emporarily? etc."
> then please press the p key on your keyboard, possibly followed by pressing the ENTER key.
>
> svn: Syntax error in revision argument 'https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/'
> Sorry, the download command "EXPORT" failed with error code 1:
> For reason, see output above.
> The download failure might be due to temporary network or server problems. You may want to try again in a
> few minutes. It could also be that the subversion client was not (properly) installed.
> ??? Error using ==> DownloadAdditionsForNeuroDebian at 250
> Download failed.
>
>
>
>
> ** END PASTE
>
> So that doesn't work. And attempting to run Screen in any fashion gives the error:
>
> >> screen
> ??? Invalid MEX-file
> '/usr/share/octave/site/m/psychtoolbox-3/PsychBasic/Screen.mexa64': libraw1394.so.8:
> cannot open shared object file: No such file or directory.
>
> That file IS there in that folder, if, again, I understand this correctly....
>
>
> As I said, I'm new to Ubuntu etc so perhaps I went wrong with some aspects of teh installation (I've been rushing as I'm on a tight deadline to get this up and running!). Have I made a mistake installing the Matlab psychtoolbox to the usr/share folder? If I made a mistake in the PTB install somewhere, how can I roll back everything I've attempted and start again?
>
> thans for any help on this! I'm really looking forward to ditching Win fully!
>
3
And one other piece of info, if it matters:

when I boot matlab a terminal window opens in the background as part of the launch, and it displays the message:

home/jim/MATLAB/R2010bSP2/bin/matlab: 1: /home/jim/MATLAB/R2010bSP2/bin/util/os
check.sh: /lib64/libc.so.6: not found


Is that anything major??


--- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@...> wrote:
>
> Just for additional info, Subversion seems up to date, i.e,
>
> sudo apt-get install subversions says it's the newest version!
>
> --- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@> wrote:
> >
> > Hi All,
> >
> > After finally giving up the struggle with Windows, i got our IT people to install Ubuntu on one of our lab machines, a reasonably new Dell laptop, 8Gb RAM, Intel i5 2.6Ghz quad core
> >
> > They installed Ubuntu 64 bit 12.4 (they said 12.10 wouldn't install for some reason) with 64 bit matlab 2010b. My account is admin.
> >
> > I'm very new to Linux so i hope I followed installation instructions correctly:
> >
> > I used NeuroDebian to install both versions of psychtoolbox 3 (the 'free' and non-free versions). This appears to be installed in the folder 'usr/share/psychtoolbox-3' as I asked for it to install for all users. I added all of these subfolders to matlab path.
> >
> > I also installed the Octave version of psychtoolbox via Terminal, as noted in one of teh Installation help pages.
> >
> > then I run, in Matlab, DownloadAdditionsForNeurodebian which, if I understand, somehow ties the Matlab to the Octave versions?
> >
> > when I do run that command, with a target directory on my user desktop, I get the follwoing errors:
> >
> >
> >
> > DownloadAdditionsForNeuroDebian('/home/jim/Desktop','trunk')
> > Requested flavor is: trunk
> > Requested location for the NeuroDebian additions folder is inside: /home/jim/Desktop
> >
> > Good. Your privileges suffice for the requested installation into folder /home/jim/Desktop.
> >
> > The following EXPORT command asks the Subversion client to
> > download the few additional bits of Psychtoolbox:
> > svn export --force -N -r https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/ "/home/jim/Desktop/PsychtoolboxAddons"
> > Downloading. It's a few megabytes, which can take a bit of time.
> > Alas there may be no output to this window to indicate progress until the download is complete.
> > Please be patient ...
> > If you see some message asking something like "accept certificate (p)ermanently, (t)emporarily? etc."
> > then please press the p key on your keyboard, possibly followed by pressing the ENTER key.
> >
> > svn: Syntax error in revision argument 'https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/'
> > Sorry, the download command "EXPORT" failed with error code 1:
> > For reason, see output above.
> > The download failure might be due to temporary network or server problems. You may want to try again in a
> > few minutes. It could also be that the subversion client was not (properly) installed.
> > ??? Error using ==> DownloadAdditionsForNeuroDebian at 250
> > Download failed.
> >
> >
> >
> >
> > ** END PASTE
> >
> > So that doesn't work. And attempting to run Screen in any fashion gives the error:
> >
> > >> screen
> > ??? Invalid MEX-file
> > '/usr/share/octave/site/m/psychtoolbox-3/PsychBasic/Screen.mexa64': libraw1394.so.8:
> > cannot open shared object file: No such file or directory.
> >
> > That file IS there in that folder, if, again, I understand this correctly....
> >
> >
> > As I said, I'm new to Ubuntu etc so perhaps I went wrong with some aspects of teh installation (I've been rushing as I'm on a tight deadline to get this up and running!). Have I made a mistake installing the Matlab psychtoolbox to the usr/share folder? If I made a mistake in the PTB install somewhere, how can I roll back everything I've attempted and start again?
> >
> > thans for any help on this! I'm really looking forward to ditching Win fully!
> >
>
4
Yeah, so, I went and RTFM, specifically here :
http://psychtoolbox.org/usingpsychtoolboxonubuntu
with help from here
http://www.kiwwito.com/article/installing-opengl-glut-libraries-in-ubuntu

and it *seems* to be working now. so feel free to delete my messages here, or just leave them up as a warning to daft people :-)




--- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@...> wrote:
>
>
> And one other piece of info, if it matters:
>
> when I boot matlab a terminal window opens in the background as part of the launch, and it displays the message:
>
> home/jim/MATLAB/R2010bSP2/bin/matlab: 1: /home/jim/MATLAB/R2010bSP2/bin/util/os
> check.sh: /lib64/libc.so.6: not found
>
>
> Is that anything major??
>
>
> --- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@> wrote:
> >
> > Just for additional info, Subversion seems up to date, i.e,
> >
> > sudo apt-get install subversions says it's the newest version!
> >
> > --- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@> wrote:
> > >
> > > Hi All,
> > >
> > > After finally giving up the struggle with Windows, i got our IT people to install Ubuntu on one of our lab machines, a reasonably new Dell laptop, 8Gb RAM, Intel i5 2.6Ghz quad core
> > >
> > > They installed Ubuntu 64 bit 12.4 (they said 12.10 wouldn't install for some reason) with 64 bit matlab 2010b. My account is admin.
> > >
> > > I'm very new to Linux so i hope I followed installation instructions correctly:
> > >
> > > I used NeuroDebian to install both versions of psychtoolbox 3 (the 'free' and non-free versions). This appears to be installed in the folder 'usr/share/psychtoolbox-3' as I asked for it to install for all users. I added all of these subfolders to matlab path.
> > >
> > > I also installed the Octave version of psychtoolbox via Terminal, as noted in one of teh Installation help pages.
> > >
> > > then I run, in Matlab, DownloadAdditionsForNeurodebian which, if I understand, somehow ties the Matlab to the Octave versions?
> > >
> > > when I do run that command, with a target directory on my user desktop, I get the follwoing errors:
> > >
> > >
> > >
> > > DownloadAdditionsForNeuroDebian('/home/jim/Desktop','trunk')
> > > Requested flavor is: trunk
> > > Requested location for the NeuroDebian additions folder is inside: /home/jim/Desktop
> > >
> > > Good. Your privileges suffice for the requested installation into folder /home/jim/Desktop.
> > >
> > > The following EXPORT command asks the Subversion client to
> > > download the few additional bits of Psychtoolbox:
> > > svn export --force -N -r https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/ "/home/jim/Desktop/PsychtoolboxAddons"
> > > Downloading. It's a few megabytes, which can take a bit of time.
> > > Alas there may be no output to this window to indicate progress until the download is complete.
> > > Please be patient ...
> > > If you see some message asking something like "accept certificate (p)ermanently, (t)emporarily? etc."
> > > then please press the p key on your keyboard, possibly followed by pressing the ENTER key.
> > >
> > > svn: Syntax error in revision argument 'https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/'
> > > Sorry, the download command "EXPORT" failed with error code 1:
> > > For reason, see output above.
> > > The download failure might be due to temporary network or server problems. You may want to try again in a
> > > few minutes. It could also be that the subversion client was not (properly) installed.
> > > ??? Error using ==> DownloadAdditionsForNeuroDebian at 250
> > > Download failed.
> > >
> > >
> > >
> > >
> > > ** END PASTE
> > >
> > > So that doesn't work. And attempting to run Screen in any fashion gives the error:
> > >
> > > >> screen
> > > ??? Invalid MEX-file
> > > '/usr/share/octave/site/m/psychtoolbox-3/PsychBasic/Screen.mexa64': libraw1394.so.8:
> > > cannot open shared object file: No such file or directory.
> > >
> > > That file IS there in that folder, if, again, I understand this correctly....
> > >
> > >
> > > As I said, I'm new to Ubuntu etc so perhaps I went wrong with some aspects of teh installation (I've been rushing as I'm on a tight deadline to get this up and running!). Have I made a mistake installing the Matlab psychtoolbox to the usr/share folder? If I made a mistake in the PTB install somewhere, how can I roll back everything I've attempted and start again?
> > >
> > > thans for any help on this! I'm really looking forward to ditching Win fully!
> > >
> >
>
5
Spoke a little too soon. Now I;m having Matlab/PTB related Java issues:

My error when my script first encounters a java based command is this:

PsychJavaTrouble: Will now try to add the PsychJava folder to Matlabs dynamic classpath...
PsychJavaTrouble: Added PsychJava folder to dynamic class path. Psychtoolbox Java commands should work now!
PTB-INFO: Display ':0.0' : X-Screen 0 : Assigning primary output as 0 with RandR-CRTC 0 and GPU-CRTC 0.

WARNING: Failed to load GetCharJava Java class. Most likely your Matlab
WARNING: classpath.txt file is not up to date. I will try to auto-fix this for
WARNING: the current session by executing the PsychJavaTrouble() command.
WARNING: This may have bad side-effects, like clearing all your scripts variables
WARNING: and functions! If it works, please read 'help PsychJavaTrouble'
WARNING: for a proper and permanent fix to the problem.

PsychJavaTrouble: Will now try to add the PsychJava folder to Matlabs dynamic classpath...
PsychJavaTrouble: Added PsychJava folder to dynamic class path. Psychtoolbox Java commands should work now!
INFO: Problem may be fixed for this session. Let's see...
Could not create a GetCharJava object. This may be due to any of the
reasons mentioned in 'help PsychJavaTrouble'. Another reason could be
that i do not have a matching GetCharJava implementation for your version
of Matlab. Will try now to compile a customized GetCharJava using the javac compiler.
This may or may not work...
Compile command is: javac /usr/share/octave/site/m/psychtoolbox-3/PsychJava/GetCharJava.java
/bin/bash: javac: command not found
Failed to built customized GetCharJava! This may be due to lack of
an installed Java SDK on your system. Read 'help PsychJavaTrouble'
for more info.

??? Error using ==> ListenChar at 121
Could not load Java class GetCharJava! Read 'help PsychJavaTrouble' for help.

Error in ==> New_game_03 at 44
ListenChar(0);

*********************
Checking the current version of Java seems OK, I *think*:

'java -version' in terminal gives me:

java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.3) (6b27-1.12.3-0ubuntu1~12.04.1)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)


**************

and working through some of the PTB help point relating to the message, I have successfully added this line to the end of classpath.txt:

/usr/share/psychtoolbox-3/PsychJava

(where my PTB folder is)

and restarted both the PC and Matlab since then, to no help!

any ideas to fix this thing?

--- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@...> wrote:
>
> Yeah, so, I went and RTFM, specifically here :
> http://psychtoolbox.org/usingpsychtoolboxonubuntu
> with help from here
> http://www.kiwwito.com/article/installing-opengl-glut-libraries-in-ubuntu
>
> and it *seems* to be working now. so feel free to delete my messages here, or just leave them up as a warning to daft people :-)
>
>
>
>
> --- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@> wrote:
> >
> >
> > And one other piece of info, if it matters:
> >
> > when I boot matlab a terminal window opens in the background as part of the launch, and it displays the message:
> >
> > home/jim/MATLAB/R2010bSP2/bin/matlab: 1: /home/jim/MATLAB/R2010bSP2/bin/util/os
> > check.sh: /lib64/libc.so.6: not found
> >
> >
> > Is that anything major??
> >
> >
> > --- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@> wrote:
> > >
> > > Just for additional info, Subversion seems up to date, i.e,
> > >
> > > sudo apt-get install subversions says it's the newest version!
> > >
> > > --- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@> wrote:
> > > >
> > > > Hi All,
> > > >
> > > > After finally giving up the struggle with Windows, i got our IT people to install Ubuntu on one of our lab machines, a reasonably new Dell laptop, 8Gb RAM, Intel i5 2.6Ghz quad core
> > > >
> > > > They installed Ubuntu 64 bit 12.4 (they said 12.10 wouldn't install for some reason) with 64 bit matlab 2010b. My account is admin.
> > > >
> > > > I'm very new to Linux so i hope I followed installation instructions correctly:
> > > >
> > > > I used NeuroDebian to install both versions of psychtoolbox 3 (the 'free' and non-free versions). This appears to be installed in the folder 'usr/share/psychtoolbox-3' as I asked for it to install for all users. I added all of these subfolders to matlab path.
> > > >
> > > > I also installed the Octave version of psychtoolbox via Terminal, as noted in one of teh Installation help pages.
> > > >
> > > > then I run, in Matlab, DownloadAdditionsForNeurodebian which, if I understand, somehow ties the Matlab to the Octave versions?
> > > >
> > > > when I do run that command, with a target directory on my user desktop, I get the follwoing errors:
> > > >
> > > >
> > > >
> > > > DownloadAdditionsForNeuroDebian('/home/jim/Desktop','trunk')
> > > > Requested flavor is: trunk
> > > > Requested location for the NeuroDebian additions folder is inside: /home/jim/Desktop
> > > >
> > > > Good. Your privileges suffice for the requested installation into folder /home/jim/Desktop.
> > > >
> > > > The following EXPORT command asks the Subversion client to
> > > > download the few additional bits of Psychtoolbox:
> > > > svn export --force -N -r https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/ "/home/jim/Desktop/PsychtoolboxAddons"
> > > > Downloading. It's a few megabytes, which can take a bit of time.
> > > > Alas there may be no output to this window to indicate progress until the download is complete.
> > > > Please be patient ...
> > > > If you see some message asking something like "accept certificate (p)ermanently, (t)emporarily? etc."
> > > > then please press the p key on your keyboard, possibly followed by pressing the ENTER key.
> > > >
> > > > svn: Syntax error in revision argument 'https://github.com/Psychtoolbox-3/Psychtoolbox-3/trunk/Psychtoolbox/PsychBasic/'
> > > > Sorry, the download command "EXPORT" failed with error code 1:
> > > > For reason, see output above.
> > > > The download failure might be due to temporary network or server problems. You may want to try again in a
> > > > few minutes. It could also be that the subversion client was not (properly) installed.
> > > > ??? Error using ==> DownloadAdditionsForNeuroDebian at 250
> > > > Download failed.
> > > >
> > > >
> > > >
> > > >
> > > > ** END PASTE
> > > >
> > > > So that doesn't work. And attempting to run Screen in any fashion gives the error:
> > > >
> > > > >> screen
> > > > ??? Invalid MEX-file
> > > > '/usr/share/octave/site/m/psychtoolbox-3/PsychBasic/Screen.mexa64': libraw1394.so.8:
> > > > cannot open shared object file: No such file or directory.
> > > >
> > > > That file IS there in that folder, if, again, I understand this correctly....
> > > >
> > > >
> > > > As I said, I'm new to Ubuntu etc so perhaps I went wrong with some aspects of teh installation (I've been rushing as I'm on a tight deadline to get this up and running!). Have I made a mistake installing the Matlab psychtoolbox to the usr/share folder? If I made a mistake in the PTB install somewhere, how can I roll back everything I've attempted and start again?
> > > >
> > > > thans for any help on this! I'm really looking forward to ditching Win fully!
> > > >
> > >
> >
>
6
Just FYI, NeuroDebian meanwhile also provides a Psychtoolbox package for Matlab

http://neuro.debian.net/pkgs/matlab-psychtoolbox-3.html

Here's the philosophical part:

http://neuro.debian.net/proj_matlab.html

They haven't really pubicized this variant yet.

Theoretically this would sort out the dependency issues, if it weren't for Mathworks to include some duplicated system libraries in the Matlab tree that overrides the system libraries.

Psychtoolbox is compiled against the *newer* default system libraries and fails to load with Matlab's *older* libraries. Matlab on the other hand usually works fine with the system libraries, so the solution was to remove those old versions from Matlab's tree.

Onfortunately Mathworks failed to follow a change in library paths for multi-architecture setups, so it's still necessary to create a shortcut to the old location:

sudo ln -s /lib64/x86_64-linux-gnu/libc-2.1?.so /lib64/libc.so.6

Now why PTB wants to compile that java program now, I'm not sure?

But it's asking for javac, the java compiler, and that is in openjdk-6-jdk. Try and install that as well.

--Tobias
7
Now it seems like it's attempting to compile those Java commands but says it does not have permission to modify the relevant command files in the OCTAVE folder, which is true, those are root.

BUT: it sounds like what might be best if I totally purge and remove the current stuff related to PTB I have on this machine - including the octave and matlab-lined versions and install your version instead. However, being a Linux newbie I have no real idea how to successfully - i.e., totally - remove packages so I can start afresh. Any pointers would be appreciated!

--- In psychtoolbox@yahoogroups.com, "T Wolf" <ptb.mail.reflector@...> wrote:
>
> Just FYI, NeuroDebian meanwhile also provides a Psychtoolbox package for Matlab
>
> http://neuro.debian.net/pkgs/matlab-psychtoolbox-3.html
>
> Here's the philosophical part:
>
> http://neuro.debian.net/proj_matlab.html
>
> They haven't really pubicized this variant yet.
>
> Theoretically this would sort out the dependency issues, if it weren't for Mathworks to include some duplicated system libraries in the Matlab tree that overrides the system libraries.
>
> Psychtoolbox is compiled against the *newer* default system libraries and fails to load with Matlab's *older* libraries. Matlab on the other hand usually works fine with the system libraries, so the solution was to remove those old versions from Matlab's tree.
>
> Onfortunately Mathworks failed to follow a change in library paths for multi-architecture setups, so it's still necessary to create a shortcut to the old location:
>
> sudo ln -s /lib64/x86_64-linux-gnu/libc-2.1?.so /lib64/libc.so.6
>
> Now why PTB wants to compile that java program now, I'm not sure?
>
> But it's asking for javac, the java compiler, and that is in openjdk-6-jdk. Try and install that as well.
>
> --Tobias
>
8
so I completely removed and purged all psychtoolbox-3 items - including teh Octave one - and reinstalled the version Tobias pointed to, and reinstalled the Java sdk, and, after opening up permissions to the PTB folder it has recompiled the java commands and is working :-)

Now my only issue is how on earth to get a decent on-screen font to work under the Linux implement of drawformattedtext... I'll try that after a beer ;-) thanks for the help!

--- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@...> wrote:
>
> Now it seems like it's attempting to compile those Java commands but says it does not have permission to modify the relevant command files in the OCTAVE folder, which is true, those are root.
>
> BUT: it sounds like what might be best if I totally purge and remove the current stuff related to PTB I have on this machine - including the octave and matlab-lined versions and install your version instead. However, being a Linux newbie I have no real idea how to successfully - i.e., totally - remove packages so I can start afresh. Any pointers would be appreciated!
>
> --- In psychtoolbox@yahoogroups.com, "T Wolf" <ptb.mail.reflector@> wrote:
> >
> > Just FYI, NeuroDebian meanwhile also provides a Psychtoolbox package for Matlab
> >
> > http://neuro.debian.net/pkgs/matlab-psychtoolbox-3.html
> >
> > Here's the philosophical part:
> >
> > http://neuro.debian.net/proj_matlab.html
> >
> > They haven't really pubicized this variant yet.
> >
> > Theoretically this would sort out the dependency issues, if it weren't for Mathworks to include some duplicated system libraries in the Matlab tree that overrides the system libraries.
> >
> > Psychtoolbox is compiled against the *newer* default system libraries and fails to load with Matlab's *older* libraries. Matlab on the other hand usually works fine with the system libraries, so the solution was to remove those old versions from Matlab's tree.
> >
> > Onfortunately Mathworks failed to follow a change in library paths for multi-architecture setups, so it's still necessary to create a shortcut to the old location:
> >
> > sudo ln -s /lib64/x86_64-linux-gnu/libc-2.1?.so /lib64/libc.so.6
> >
> > Now why PTB wants to compile that java program now, I'm not sure?
> >
> > But it's asking for javac, the java compiler, and that is in openjdk-6-jdk. Try and install that as well.
> >
> > --Tobias
> >
>
9
Ok, i think there is a packaging error in the NeuroDebian packages which explain your trouble and probably also ugly looking fonts.

The ND packages don't contain a precompiled GetCharJava.class as they should, only the GetCharJava.java source file, therefore the need to recompile from source via javac.

Also the matlab-psychtoolbox-3 package seems to miss many crucial dependencies, so installing it alone won't install all the required support libraries or the text rendering plugins for high quality text. This will need to be fixed in the next ND release.

Can you install octave-psychtoolbox-3 as well? or for that matter everything with a psychtoolbox in its name? That should pull in all missing support libraries and the text rendering plugins.

Probably none of us ever noticed, as the development machines always have so many variants of ptb installed that we'd get a missing file just from one of the other installed ptb's.

-mario

--- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@...> wrote:
>
> so I completely removed and purged all psychtoolbox-3 items - including teh Octave one - and reinstalled the version Tobias pointed to, and reinstalled the Java sdk, and, after opening up permissions to the PTB folder it has recompiled the java commands and is working :-)
>
> Now my only issue is how on earth to get a decent on-screen font to work under the Linux implement of drawformattedtext... I'll try that after a beer ;-) thanks for the help!
>
> --- In psychtoolbox@yahoogroups.com, "jim.parkinson" <jimparkinson@> wrote:
> >
> > Now it seems like it's attempting to compile those Java commands but says it does not have permission to modify the relevant command files in the OCTAVE folder, which is true, those are root.
> >
> > BUT: it sounds like what might be best if I totally purge and remove the current stuff related to PTB I have on this machine - including the octave and matlab-lined versions and install your version instead. However, being a Linux newbie I have no real idea how to successfully - i.e., totally - remove packages so I can start afresh. Any pointers would be appreciated!
> >
> > --- In psychtoolbox@yahoogroups.com, "T Wolf" <ptb.mail.reflector@> wrote:
> > >
> > > Just FYI, NeuroDebian meanwhile also provides a Psychtoolbox package for Matlab
> > >
> > > http://neuro.debian.net/pkgs/matlab-psychtoolbox-3.html
> > >
> > > Here's the philosophical part:
> > >
> > > http://neuro.debian.net/proj_matlab.html
> > >
> > > They haven't really pubicized this variant yet.
> > >
> > > Theoretically this would sort out the dependency issues, if it weren't for Mathworks to include some duplicated system libraries in the Matlab tree that overrides the system libraries.
> > >
> > > Psychtoolbox is compiled against the *newer* default system libraries and fails to load with Matlab's *older* libraries. Matlab on the other hand usually works fine with the system libraries, so the solution was to remove those old versions from Matlab's tree.
> > >
> > > Onfortunately Mathworks failed to follow a change in library paths for multi-architecture setups, so it's still necessary to create a shortcut to the old location:
> > >
> > > sudo ln -s /lib64/x86_64-linux-gnu/libc-2.1?.so /lib64/libc.so.6
> > >
> > > Now why PTB wants to compile that java program now, I'm not sure?
> > >
> > > But it's asking for javac, the java compiler, and that is in openjdk-6-jdk. Try and install that as well.
> > >
> > > --Tobias
> > >
> >
>