From jeff at bioinformatics.org  Wed Jan  3 07:28:59 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:05 2006
Subject: [Pipet Users] Forbes.com: Everywhere Network
Message-ID: <3A531B0B.C68A6349@bioinformatics.org>

``In a lab at the University of California at Berkeley, computer scientist
John Kubiatowicz is designing a networking scheme that, in ten years, just
might take over your life. The idea, dubbed OceanStore, is an architecture for
the next next-generation Internet. It is aimed at solving one of the Net's
looming big problems:how to reliably and securely retrieve data from anywhere
in the world, on any computing device.''

http://www.forbes.com/futuretech/forbes/2001/0108/242.html

It's a little like FreeNet.

Jeff


From jeff at bioinformatics.org  Fri Jan  5 09:13:59 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:05 2006
Subject: [Pipet Users] Slashdot | GTK+ without X!
Message-ID: <3A55D6A7.542349CE@bioinformatics.org>

It looks like we will be able to run Pied/Piper (the Gtk/Gnome UI for Piper)
without X:

  http://slashdot.org/article.pl?sid=01/01/05/018228&mode=flat

What use is this?  Perhaps Pied/Piper can be used as a desktop on
dedicated/embedded systems?

Cheers.
Jeff


From jeff at bioinformatics.org  Sat Jan  6 07:26:42 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:05 2006
Subject: [Pipet Users] from Alex Lancaster
Message-ID: <3A570F02.9563FD50@bioinformatics.org>

Below is part of a message I got yesterday...

-------------------------------
I was looking at getting involved with Piper, since I like the idea of
pipes for GUIs and multiplexing for CLI...  We do a lot of population
genetic data analysis that involves running various analysis programs
on data, and "piping" it off into different programs, merging results
etc, and also getting into <buzzword>"data mining"</buzzword>.  Due to
time constraints I've been hacking up some godawful shell and awk, but
in the medium-to-long term, Piper, Python and such has to be the way
to go.  So I could act as a beta-tester/bug fixer/guinea pig project
for Piper.  I've been playing around a bit with hacking on GNOME
programs, so I like the idea that you're using GNOME/CORBA as a
foundation.

Another project you maybe interested in, and is, at least
conceptually, related to Piper, is IMT:

 http://sourceforge.net/projects/imt

It's a simulation framework in XML that is designed to be a high-level
glue that can bind different simulation frameworks together.  In
essence to provide an abstraction for mixing different layers such as
"R", "Grass" (open source GIS), "GALib" (open source genetic algorithm
library) and "Swarm" (open source discrete event/agent based modelling
toolkit, which is the project I used to be employed to work on before
I went back to grad school).  It's a little different in that it was
inspired more by simulation/modelling issues than bioinformatic/data
analysis, but both IMT and Piper seem, in a broad sense to complement
each other (or at least interoperate).  I haven't worked on IMT, but I
know all the people involved and my former Swarm colleague is working
on the Swarm/IMT integration right on.

Anyway, I mention all of this to give you an idea of my background and
interests.  The holy grail in all this is interoperability and
seamlesness (as much as possible) between data and models in different
knowledge domains, and most genomics/bioinformatics companies doing
any kind of software seem hell-bent to reinvent as many wheels as
possible and create a few Tower's of Babel in the process... 

So that's why the existence of the Open Lab, especially in the gold
rush stampede mentality that so many companies and universities
(sadly) seem to have for genomics these days, is such a vital thing.


From jarl at casema.net  Fri Jan 12 19:31:50 2001
From: jarl at casema.net (jarl van katwijk)
Date: Fri Feb 10 19:39:06 2006
Subject: [Pipet Users] DL to PL connection structure of the BL
Message-ID: <3A5FA1F6.1D4A84EC@casema.net>

Hi Piper People,

As promised I made an overview of the structure of the BL nodes that connect the
DL to the PL. This configuration is realised during boot-up of the BL, and will
always be there. Making it configurable or optional can be done, but seems to of
no interest to Piper ;)

Note that all the parts between the DL and PL on the drawing are
one-and-the-same process, the BL. The sensors, visuals and collectors are
dynamic loadable modules, that's why I did draw them seperate from the pipeline.

Also take notice of the way the communication between the DL and PL is setup.
Communications back and forth go through the pipeline, so they are authorized,
scheduled, etc. Also is it in the nature that the DL and PL do not need to be
one the same machine. Neither do the possible other instances.


When there're no complains, no mistakes or unclear stuff, can you put this on
the piper site Jeff? Thnx ;)

jarl
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From karlmax at oberland.net  Mon Jan 22 16:11:23 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:06 2006
Subject: [Pipet Users] Piper & Overflow problem
Message-ID: <200101222111.VAA00949@schreyer.oberland.net>

Hi list,

some time ago I downloaded Piper and all the stuff needed to
make it run. After some hassles ( and after installing gcc
2.95.2 ) I got everything to compile and install. When I start
piper, I get the following output in the xterm I start it from:

deMoivre:~# piper
Starting definition layer...
Starting pied...
deMoivre:~# 
Gdk-WARNING **: locale not supported by C library
/dev/dsp: No such device
Getting document...
Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Connecting with the bl...
Environmental variable VSH_DL2BL_IOR not found.
Using default ior file location.
IOR file for Brokering Layer not found.
Connection with BL not established.
Loading crash info...
Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
error: net LoadFile already existed
error: net SaveAs already existed
error: net LP already existed
error: net HP already existed
error: net LPC_DECOMP already existed
Document:ShowNetwork

I get a window, but whatever I try, I get no symbols to put some
arrangement together with.

Checking the indicated files for the undefined symbols shows
indeed that said symbols are undefined.

The same applies if I start up FreeSpeech / Overflow: I get a
window, but I don't get symbols to draw networks with. I guess
for the same reason.....

What mistake did I make or what do I still need ?

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From jeff at bioinformatics.org  Mon Jan 22 17:52:00 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:06 2006
Subject: [Pipet Users] Piper & Overflow problem
References: <200101222111.VAA00949@schreyer.oberland.net>
Message-ID: <3A6CB990.3A6508F8@bioinformatics.org>

Hi Karl-Max.  Thanks for (trying to) try Piper ;-)

Karl-Max Wagner wrote:
> 
> Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi

The audio_blocks library does belong to Overflow/Piper (the PL), and it is
pretty obvious that there is a dependency problem (perhaps a needed library). 
I can't be of much more help than that, unfortunately, since that is
Jean-Marc's domain, but I wanted to be sure that someone got back to you right
away.

We'll wait patiently for Jean-Marc's reply.

Cheers.
Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From jeff at bioinformatics.org  Mon Jan 22 17:58:23 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:06 2006
Subject: [Pipet Users] Piper & Overflow problem
References: <200101222111.VAA00949@schreyer.oberland.net>
Message-ID: <3A6CBB0F.1BF6B03C@bioinformatics.org>

Karl-Max Wagner wrote:
> 
> deMoivre:~#
> Gdk-WARNING **: locale not supported by C library
> /dev/dsp: No such device

Actually, I'm now scratching my head over this.

What OS are you using?

What versions of Gtk and Gnome are you using?

Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From karlmax at oberland.net  Mon Jan 22 19:36:55 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:06 2006
Subject: [Pipet Users] Piper & Overflow problem
In-Reply-To: <3A6CB990.3A6508F8@bioinformatics.org> from "J.W. Bizzaro" at Jan 22, 2001 10:52:00 PM
Message-ID: <200101230036.AAA01362@schreyer.oberland.net>

> > Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> 
> The audio_blocks library does belong to Overflow/Piper (the PL), and it is
> pretty obvious that there is a dependency problem (perhaps a needed library). 

Right. I just have no idea what to check to find out. I just
know that the complaint with the undefined symbol is true: nm
applied to that file says that this function is actually
undefined. So the code for it did not get compiled in for some
reason. If I knew more about that function I might be able to
track down what causes this.

> I can't be of much more help than that, unfortunately, since that is
> Jean-Marc's domain, but I wanted to be sure that someone got back to you right

That's OK, no problem :-).

> We'll wait patiently for Jean-Marc's reply.

Yes. Sure.

Thanks for your quick response.

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From karlmax at oberland.net  Mon Jan 22 19:30:54 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:06 2006
Subject: [Pipet Users] Piper & Overflow problem
In-Reply-To: <3A6CBB0F.1BF6B03C@bioinformatics.org> from "J.W. Bizzaro" at Jan 22, 2001 10:58:23 PM
Message-ID: <200101230030.AAA01345@schreyer.oberland.net>

> > deMoivre:~#
> > Gdk-WARNING **: locale not supported by C library

That is probably OK, because I didn't set any locale and no time
zone.

> > /dev/dsp: No such device

This is OK, too, as there is no sound card in this machine.
However, that is not the point: I have no need for the sound
routines anyway. Or is it the problem that due to this some
stuff wasn't compiled into Overflow and this is causing havoc
now ? Just guessing......

What I worry a lot more about is that an apparently important
function in all the modules is undefined.
 
I am running Slackware 7.0 here. Python is version 1.5. Gtk is
version 1.2.6. If you need more info, just tell me what.

Maybe I should tell you what I want to do with piper: I am
developing a system for softradio design, which takes a block
diagram of a system, makes a mthematical model of it, runs it
against a path simulation, and finally synthesizes DSP code from
a library of functions to be loaded into prefabricated softradio
testboxes. The whole stuff is to be released under GNU/GPL as
soon as I have a working prototype. After that the design can be
tested in real life. Not that unlike what FreeSpeech does. The
idea of piper suits my needs very well because a data flow
oriented GUI frontend is pretty much what is needed for my
application.

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From jeff at bioinformatics.org  Mon Jan 22 20:02:40 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:06 2006
Subject: [Pipet Users] Piper & Overflow problem
References: <200101230030.AAA01345@schreyer.oberland.net>
Message-ID: <3A6CD830.107BB06@bioinformatics.org>

Karl-Max Wagner wrote:
> 
> Maybe I should tell you what I want to do with piper: I am
> developing a system for softradio design, which takes a block
> diagram of a system, makes a mthematical model of it, runs it
> against a path simulation, and finally synthesizes DSP code from
> a library of functions to be loaded into prefabricated softradio
> testboxes. The whole stuff is to be released under GNU/GPL as
> soon as I have a working prototype. After that the design can be
> tested in real life. Not that unlike what FreeSpeech does. The
> idea of piper suits my needs very well because a data flow
> oriented GUI frontend is pretty much what is needed for my
> application.

Cool.  Then, perhaps you *MIGHT* be interested in helping with the development
of Overflow/Piper.  Of course, I'm sure you'd like to see it working first
;-)  If you are interested, contact me directly about getting an account, CVS
access, etc. on our server.

In any case, it sounds like you and Jean-Marc have a lot to talk about. 
Personally, I'm from the "Loci" end of Piper, and my interests lie in
distributed data processing for scientific research.  But, I think our
mixed-bag of backgrounds will be an asset in the long run.

Cheers.
Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From karlmax at oberland.net  Tue Jan 23 07:36:54 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper & Overflow problem
In-Reply-To: <3A6CD830.107BB06@bioinformatics.org> from "J.W. Bizzaro" at Jan 23, 2001 01:02:40 AM
Message-ID: <200101231236.MAA00515@schreyer.oberland.net>

> > tested in real life. Not that unlike what FreeSpeech does. The
> > idea of piper suits my needs very well because a data flow
> > oriented GUI frontend is pretty much what is needed for my
> > application.
> 
> Cool.  Then, perhaps you *MIGHT* be interested in helping with the development

Well, as I am also considering to make a backend ( "backend in
the lingo of my project means the stuff for making the software
for the target architecture ) for PC's with a soundcard, it
makes sense to add a directory to Overflow with my radio
modules.

> of Overflow/Piper.  Of course, I'm sure you'd like to see it working first
> ;-)  If you are interested, contact me directly about getting an account, CVS
> access, etc. on our server.

Thanks a lot. For the moment, however, I am busy with my
frontend stuff, so there is no immediate need. However, I'll
study the internal interfaces of Overflow/Piper because it makes
a lot of sense to me to make my stuff compatible to it.

If you wish I can send you the OHP's of two presentations I did
in Japan about it ( I have to mention here that this is a
cooperation project with Prof. Ikuo Oka of the Department of
Computer Networking of Osaka City University in Japan ).

It goes somewhat beyond the scope of this mailing list to
discuss a different project in detail.

> In any case, it sounds like you and Jean-Marc have a lot to talk about. 

Yes, that's for sure.

> Personally, I'm from the "Loci" end of Piper, and my interests lie in
> distributed data processing for scientific research.  But, I think our

Actually, I found the "Loci" idea fascinating. It meant that I
could run simulations distributed over a network. That was a
wholly new aspect of things.

> mixed-bag of backgrounds will be an asset in the long run.

This was another thing I liked: I thought when such diverse
projects merge they sure thought a lot about interfaces,
modularity and reusability of components of the entire project
and so it could allow me to plug functionality into my stuff.

Funny enough - the ingredient projects of piper apparently
started sometime in spring 2000 - it was about the same time
when I got serious about my stuff.

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From valj01 at gel.usherb.ca  Tue Jan 23 20:46:27 2001
From: valj01 at gel.usherb.ca (Jean-Marc Valin)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper & Overflow problem
References: <200101222111.VAA00949@schreyer.oberland.net>
Message-ID: <3A6E33F3.795A8644@gel.usherb.ca>

I see two possible cause for your problems here (maybe both). I apologize,
because they're both semi/not documented...

1) It is strongly suggested *not* to install with /usr or /usr/local as the
$prefix. From version to version, things change and you end up with old junk
that causes conflicts. Instead, install with a prefix set to an overflow-only
directlry.

2) There's a VFLOW_PATH environment variable which you have to set. It's a
colon-separated path that must include the $prefix/lib directory, as well as all
the $prefix/toolbox/... directories. Also, remember to put your $prefix/lib
directory in your LD_LIBRARY_PATH. All that's a bit ugly and making it cleaner
is on the TODO list.

I hope this helps... otherwise, try starting vflow and tell me what the errors
are. If there's anything else, feel free to contact me.

	Jean-Marc

-- 
Jean-Marc Valin
Universite de Sherbrooke - Genie Electrique
valj01@gel.usherb.ca


From karlmax at oberland.net  Fri Jan 26 15:19:02 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] FreeSpeech Test results
In-Reply-To: <3A6E33F3.795A8644@gel.usherb.ca> from "Jean-Marc Valin" at Jan 23, 2001 08:46:27 PM
Message-ID: <200101262019.UAA00740@schreyer.oberland.net>

> 1) It is strongly suggested *not* to install with /usr or /usr/local as the
> $prefix. From version to version, things change and you end up with old junk
> that causes conflicts. Instead, install with a prefix set to an overflow-only
> directlry.

OK. I changed the ac_default_prefix in configure to
/usr/local/FreeSpeech. Unfortunately, some libraries were
installed under /usr/local/lib. OK, not much of a problem.

> 2) There's a VFLOW_PATH environment variable which you have to set. It's a
> colon-separated path that must include the $prefix/lib directory, as well as all
> the $prefix/toolbox/... directories. Also, remember to put your $prefix/lib
> directory in your LD_LIBRARY_PATH. All that's a bit ugly and making it cleaner
> is on the TODO list.

OK. I did this. Actually, I made a script setting all that to
the right values and wow ! now when I press the right mouse key
I get a lot of menues and can select all sorts of stuff and make
diagrams and the like. Very nice. I didn't whether everything
works now, but at least it looks a lot better.

> I hope this helps... otherwise, try starting vflow and tell me what the errors
> are. If there's anything else, feel free to contact me.

Well, FreeSpeech definitely works now. 

Funny enough, piper works now, too. I haven't the foggiest idea
why. At least I can invoke funny symbols with lines to a pair of
red disks with a black rim.

Sorry if I sound stupid: but some instructions in how to use
this toy would be welcome ;-).

If I press the middle mouse key, two little Martians ( or
whatever they are ) and when I release it they sink into
oblivion. Inside all the symbol boxes there are two little
martians as well. Somehow I fail figuring it out :-(.

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From jeff at bioinformatics.org  Fri Jan 26 15:48:06 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] FreeSpeech Test results
References: <200101262019.UAA00740@schreyer.oberland.net>
Message-ID: <3A71E286.EDBD0AF8@bioinformatics.org>

Karl-Max Wagner wrote:
> 
> If I press the middle mouse key, two little Martians ( or
> whatever they are ) and when I release it they sink into
> oblivion. Inside all the symbol boxes there are two little
> martians as well. Somehow I fail figuring it out :-(.

8^D That really is unintentional.  I had the "Martians" (two people) icon
appear by default for all nodes (each node can have its own icon), but I
changed it so that there are none by default (they have to be specified). 
Apparently I forgot to change the DnD code too!  They are cute though :-)

I'll add that to my bug list.

Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From karlmax at oberland.net  Fri Jan 26 15:53:25 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
Message-ID: <200101262053.UAA00817@schreyer.oberland.net>

Hi list,

I know wrote all the stuff piper complains about into a file.
Here is it:

Gdk-WARNING **: locale not supported by C library
/dev/dsp: No such device
Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Connecting with the bl...
Environmental variable VSH_DL2BL_IOR not found.
Using default ior file location.
IOR file for Brokering Layer not found.
Connection with BL not established.
Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
error: net LoadFile already existed
error: net SaveAs already existed
error: net LP already existed
error: net HP already existed
error: net LPC_DECOMP already existed
Getting document...
Loading crash info...
Document:ShowNetwork
Network:showLocus
........

Question: What is this environmental variable VSH_DL2BL_IOR all
about ?

What is going wrong at IOR file for Brokering Layer not found ? 

undefined symbol: connectToNode__4NodeUiP4NodeUi : I checked
that using nm: They are undefined. However, vflow seems to work.
What is all that about ?

Piper seems to have a good memory: each time I start it up my
old scribblings are there still.

Actually I have no idea whether I just can ignore all that
because this is not completed yet or whether there is still
something wrong and has to be ironed out. Hope that helps.

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From chapmanb at arches.uga.edu  Fri Jan 26 17:00:46 2001
From: chapmanb at arches.uga.edu (Brad Chapman)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
In-Reply-To: <200101262053.UAA00817@schreyer.oberland.net>
References: <200101262053.UAA00817@schreyer.oberland.net>
Message-ID: <14961.62350.184139.89589@taxus.athen1.ga.home.com>

Hi Karl-Max;

> I know wrote all the stuff piper complains about into a file.
> Here is it:
[all of the errors piper generates]

Believe it or not, there are all expected -- at least, I get most of them
:-). Piper is still under heavy development, so some of this is
debugging output and some of this is errors that haven't been fixed
yet. You are doing excellent to have it all running. Congrats!

I'll handle the parts that I know about.

> Question: What is this environmental variable VSH_DL2BL_IOR all
> about ?

This is my debugging output. I'll actually remove this right now and
commit it so it doesn't complain about that any more. This is
something old that I was doing that never really worked out
well. Don't worry about this, the message'll be gone in CVS in a second.

> Piper seems to have a good memory: each time I start it up my
> old scribblings are there still.

I hope you like it -- that took a lot of coding :-). If you shut down
via the pop-up menu (session->quit) this is considered a "normal"
shutdown and you should get a blank screen when you start up. If you
shut down via the (X) in the upper left corner, then this is
considered a crash (well, just a simulated crash, for testing
purposes), and piper remembers what you were working on so you don't
have to re-do it all.
 
> Actually I have no idea whether I just can ignore all that
> because this is not completed yet or whether there is still
> something wrong and has to be ironed out. Hope that helps.

I think you're doing really well. Happy to hear you are trying it out!

Brad



From karlmax at oberland.net  Fri Jan 26 16:14:36 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] FreeSpeech Test results
In-Reply-To: <3A71E286.EDBD0AF8@bioinformatics.org> from "J.W. Bizzaro" at Jan 26, 2001 08:48:06 PM
Message-ID: <200101262114.VAA00894@schreyer.oberland.net>

> 8^D That really is unintentional.  I had the "Martians" (two people) icon
> appear by default for all nodes (each node can have its own icon), but I
> changed it so that there are none by default (they have to be specified). 
> Apparently I forgot to change the DnD code too!  They are cute though :-)
> 
> I'll add that to my bug list.

I am using piper-20000926 right now because I could download it
easily from the piper page. Should I check out a newer version
from cvs ?

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From karlmax at oberland.net  Fri Jan 26 17:47:16 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
In-Reply-To: <14961.62350.184139.89589@taxus.athen1.ga.home.com> from "Brad Chapman" at Jan 26, 2001 05:00:46 PM
Message-ID: <200101262247.WAA01068@schreyer.oberland.net>

> Believe it or not, there are all expected -- at least, I get most of them
> :-). Piper is still under heavy development, so some of this is
> debugging output and some of this is errors that haven't been fixed

Aha. Good. Sort of suspected that. However, wasn't quite sure
and thought it might be better to report that in case I bumped
into something.

> I think you're doing really well. Happy to hear you are trying it out!

Piper is getting more punishment in the future for sure as I
intend to use it in my own project.

And here already the big question: FreeSpeech / Overflow has a
GUI and Piper has one. I guess that the FreeSpeech / Overflow
GUI is gonna be scrapped sometime in the future, right ? So it
would be a bad idea to look into the interfaces to the
components, I guess - I'd better stick to piper. Is there
already something like an interface description to hook my stuff
in ?

My intention is to use the application interface ( or whatever
it is called ) in order to be piper compatible. Is that already
sort of fixed or - due to development - sort of a moving target
?

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From jeff at bioinformatics.org  Fri Jan 26 18:11:21 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] FreeSpeech Test results
References: <200101262114.VAA00894@schreyer.oberland.net>
Message-ID: <3A720419.5C9C1C79@bioinformatics.org>

Karl-Max Wagner wrote:
> 
> I am using piper-20000926 right now because I could download it
> easily from the piper page. Should I check out a newer version
> from cvs ?

Yeah, that's pretty old.  The web page points to it as a recent snapshot (I
need to correct that), but I have snapshots made every day now,
automagically.  They are kept in

    ftp://bioinformatics.org/pub/piper/CVS

You can also do an anonymous CVS checkout via this command:

    cvs -d:pserver:anonymous@bioinformatics.org:/cvsroot checkout piper

If you're compiling the Sept 2000 Piper with a recent version of Overflow,
that *MIGHT* explain some of the error messages.  Just a guess.

Cheers.
Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From karlmax at oberland.net  Fri Jan 26 18:12:34 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] FreeSpeech Test results
In-Reply-To: <3A720419.5C9C1C79@bioinformatics.org> from "J.W. Bizzaro" at Jan 26, 2001 11:11:21 PM
Message-ID: <200101262312.XAA01178@schreyer.oberland.net>

> > I am using piper-20000926 right now because I could download it

Sorry, I meant piper-20001112.

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From jeff at bioinformatics.org  Fri Jan 26 20:26:55 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
References: <200101262053.UAA00817@schreyer.oberland.net> <14961.62350.184139.89589@taxus.athen1.ga.home.com>
Message-ID: <3A7223DF.A8546EF4@bioinformatics.org>

Brad Chapman wrote:
> 
> Believe it or not, there are all expected -- at least, I get most of them
> :-). Piper is still under heavy development, so some of this is
> debugging output and some of this is errors that haven't been fixed
> yet.

That's right, you'll get a lot of messages, but nearly all will be for
debugging.  On the Pied/Piper GUI end, every time you do something, you get
some sort of feedback.  When I feel that most of my bugs are gone, and most of
my features are added, Pied/Piper will be silent.

> I think you're doing really well. Happy to hear you are trying it out!

And we need some more people to try it out!!! :-)

Karl-Max Wagner wrote:
> 
> Sorry if I sound stupid: but some instructions in how to use
> this toy would be welcome ;-).

Jean-Marc, Jarl, and I do need to write something soon.  My question for Jarl
is if there is a simple demo of the BL communicating across a network.  Give
me some basic instructions, and I can spiffy it up a bit.

> And here already the big question: FreeSpeech / Overflow has a
> GUI and Piper has one.

Right.

> I guess that the FreeSpeech / Overflow
> GUI is gonna be scrapped sometime in the future, right ?

That is our intention :-)  Brad and I want to make Pied/Piper nice enough so
that Jean-Marc will prefer it to his own GUI.

> So it
> would be a bad idea to look into the interfaces to the
> components, I guess - I'd better stick to piper. Is there
> already something like an interface description to hook my stuff
> in ?

It wouldn't be a bad idea to look into Overflow's component UI's, because
Pied/Piper actually uses the same UI libraries and generates the same (almost)
XML network descriptions.

As for hooking a program to Piper, it would be done through Overflow, the PL
(although it can be done through GMS, the BL, but we're going to try and use
Overflow as the interface).

Overflow can do command-line generation and connect us to proggies that way. 
You can also make C++ components to be used directly in Overflow.  Jean-Marc,
do you have any instructions for Karl-Max on how to do this?

The other way to "add a UI to Piper" would be to create a separate one
altogether.  UI's in the UIL communicate with the rest of Piper via CORBA. 
So, it is possible to bypass Pied/Piper altogether.

This is basically how communication works:

    [UIL --> DL] --> [BL --> PL]
     Build-Time        Run-Time

> My intention is to use the application interface ( or whatever
> it is called ) in order to be piper compatible. Is that already
> sort of fixed or - due to development - sort of a moving target
> ?

It should be open for changes still, since we WANT to interface Piper with
other programs.  That's sort of the whole purpose to Piper ;-)  It probably is
more a moving target than anything, but collaborations with other projects
will help us to nail it down a bit better.

I'd like some comments from Jean-Marc on this, please.

What I would personally prefer is a way to interface programs with Piper using
Pied/Piper alone.  IOW, use "connect the dots" to build your interface, rather
than program and compile.  The best way to do this, though, would be to have a
collection of very small components for the API.

Cheers.
Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From jarl at casema.net  Sat Jan 27 20:01:30 2001
From: jarl at casema.net (jarl van katwijk)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
References: <200101262053.UAA00817@schreyer.oberland.net>
Message-ID: <3A736F6A.2090604@casema.net>

Hi Karl-Max,

I'm the guy responsible for the BL of Piper, and many of it's bugs. I'm 
sorry I was silent until now, I switched isp and had a hard time getting 
ADSL running. Now that it does I'll spam this list again as usual ;)

About your Piper log:

> 
> Gdk-WARNING **: locale not supported by C library
> /dev/dsp: No such device
> Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> Connecting with the bl...
> Environmental variable VSH_DL2BL_IOR not found.
> Using default ior file location.
> IOR file for Brokering Layer not found.
> Connection with BL not established.

This surtainly is a problem. The BL should be running and the connection 
must be enstablised else you wont be able to commit networks from the 
GUI to the processing layer. The BL stands for Brokering Layer, it's 
handles communication, resources and security.

I'm wondering if you have the BL compiled at al, do you have a binairy 
"BL" somewhere on your filesystem? If not, I whould be very interested 
in you BL compilation log (in ./piper/bl, do a make over there and mail 
me the errors if so.)

> 
> Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi

> Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
> error: net LoadFile already existed
> error: net SaveAs already existed
> error: net LP already existed
> error: net HP already existed
> error: net LPC_DECOMP already existed
> Getting document...
> Loading crash info...
> Document:ShowNetwork
> Network:showLocus
> .........
> 
> undefined symbol: connectToNode__4NodeUiP4NodeUi : I checked
> that using nm: They are undefined. However, vflow seems to work.
> What is all that about ?

These are normal, the Overflow libs is just called to initialise 2 times 
I think. Nothing to worry, it's just not as nice as Piper 1.0 will be ;)

bye,
jarl



From karlmax at oberland.net  Sun Jan 28 20:25:03 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
In-Reply-To: <3A7223DF.A8546EF4@bioinformatics.org> from "J.W. Bizzaro" at Jan 27, 2001 01:26:55 AM
Message-ID: <200101290125.BAA00866@schreyer.oberland.net>

> It wouldn't be a bad idea to look into Overflow's component UI's, because
> Pied/Piper actually uses the same UI libraries and generates the same (almost)
> XML network descriptions.

OK. If you could dump some hints into the Wiki it wouldn't harm.

> As for hooking a program to Piper, it would be done through Overflow, the PL
> (although it can be done through GMS, the BL, but we're going to try and use
> Overflow as the interface).
> 
> Overflow can do command-line generation and connect us to proggies that way. 

Where is that stuff defined ?

> You can also make C++ components to be used directly in Overflow.  Jean-Marc,
> do you have any instructions for Karl-Max on how to do this?

I intend to use octave ( mathematical language ) for my frontend
and build the backend stuff using perl or python programs 
(which of the two is still tbd ).
 
>     [UIL --> DL] --> [BL --> PL]
>      Build-Time        Run-Time
> 
> > My intention is to use the application interface ( or whatever
> > it is called ) in order to be piper compatible. Is that already
> > sort of fixed or - due to development - sort of a moving target
> > ?
> 
> It should be open for changes still, since we WANT to interface Piper with
> other programs.  That's sort of the whole purpose to Piper ;-)  It probably is
> more a moving target than anything, but collaborations with other projects
> will help us to nail it down a bit better.

Well, I am totally open in that. At the moment I can specify the
interface the way I want. So taking over the piper interface
isn't such a bad idea to begin with.

> What I would personally prefer is a way to interface programs with Piper using
> Pied/Piper alone.  IOW, use "connect the dots" to build your interface, rather
> than program and compile.  The best way to do this, though, would be to have a
> collection of very small components for the API.

This is more or less what I intend: I would like to get a
definition of what is connected with what to generate an octave
program with it and later on to generate actual DSP code for the
softradio box.

If I click on the building block symbols I get some locus etc.
pull down menu. Is it also planned that I can click on the
symbol and then can get a ( configurable ) menu for getting data
of that object resp. getting a ( defineable ) form for entering
properties ? This is very welcome in lots of operations, e.g.
FFT to define which length the vectors to be used have (at least
I need it for reasons of generating the final DSP code -
contrary to Overflow I always have to work cross-platform and
for the final code speed is everything. Even the fastest DSP's
are always too slow in radio).
 
=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From karlmax at oberland.net  Sun Jan 28 20:06:20 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
In-Reply-To: <3A736F6A.2090604@casema.net> from "jarl van katwijk" at Jan 28, 2001 02:01:30 AM
Message-ID: <200101290106.BAA00845@schreyer.oberland.net>

> I'm the guy responsible for the BL of Piper, and many of it's bugs. I'm 
> sorry I was silent until now, I switched isp and had a hard time getting 
> ADSL running. Now that it does I'll spam this list again as usual ;)

Sounds familiar. Having ADSL here for a little over two months
now....

> GUI to the processing layer. The BL stands for Brokering Layer, it's 
> handles communication, resources and security.

I know. However, not a helluva lot more :-(((.

> I'm wondering if you have the BL compiled at al, do you have a binairy 
> "BL" somewhere on your filesystem? If not, I whould be very interested 
> in you BL compilation log (in ./piper/bl, do a make over there and mail 
> me the errors if so.)

A quick check showed that everything in there was in a virgin
state. When compiling, there were errors about some omniORB
stuff not found: the omniORB install process is kinda
incomplete, so I did some mass linking into /usr/local/include
and /usr/local/lib to fix this ( btw. if anybody has some tips
of what of omniORB is to be installed manually where I'd
appreciate this ;-)). After that the compile and install ran
just fine.

Testing now yielded the following:

Gdk-WARNING **: locale not supported by C library
/dev/dsp: No such device
Toolbox load error: /usr/local/lib/audio_blocks.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/vq.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/hmm.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Toolbox load error: /usr/local/lib/nnet.tlb: undefined symbol: connectToNode__4NodeUiP4NodeUi
Getting document...
Loading crash info...
no crash info
Adding a Network...
Document:ShowNetwork
<!--mouse click at 136.0 55.0 -->
Network:showLocus
<!--clicked on NOT -->
<!--was workspace now NOT -->
<!--mouse click at 138.0 156.0 -->

......more status stuff......happily clicking together some
nonsense......

.......last mouseclicks are for confirming shutdown......

<!--mouse click at 86.0 120.0 -->
<!--mouse click at 170.0 153.0 -->
Connecting with the bl...
Environmental variable VSH_DL2BL_IOR not found.
Using default ior file location.
IOR file for Brokering Layer not found.
Connection with BL not established.
shutting down dl...

Well, the complaints here are obviously in the course of the
shutdown process because the BL get pulled from under the system
and the rest of the system starts wailing. AFAIU this is
perfectly normal. Seems as if the BL now works.

BTW, tried to compile piper-20010126 which failed. I got the
following:

gmake[4]: Entering directory /root/piper/dl/vflow'
Making all in interfaces
gmake[5]: Entering directory /root/piper/dl/vflow/interfaces'
gmake[5]: *** No rule to make target flowmodule.so', needed by 
ll-am'.  Stop.
gmake[5]: Leaving directory /root/piper/dl/vflow/interfaces'
gmake[4]: *** [all-recursive] Error 1

What I did now was to compare the makefiles between my old piper
version and the new one in the directory
piper/dl/vflow/interfaces. The result is interesting:

--- ./piper_old/dl/vflow/interfaces/Makefile	Sun Jan  7 00:12:39 2001
+++ ./piper/dl/vflow/interfaces/Makefile	Sat Jan 27 18:57:50 2001
@@ -203,8 +203,8 @@
 
 maintainer-clean-libtool:
 
-vflowmodule$(SO): $(vflowmodule__SO__OBJECTS) $(vflowmodule__SO__DEPENDENCIES)
-	@rm -f vflowmodule$(SO)
+vflowmodule0 11 10 6 4 3 2 1 0SO): $(vflowmodule__SO__OBJECTS) $(vflowmodule__SO__DEPENDENCIES)
+	@rm -f vflowmodule0 11 10 6 4 3 2 1 0SO)
 	$(vflowmodule__SO__LINK) $(vflowmodule__SO__LDFLAGS) $(vflowmodule__SO__OBJECTS) $(vflowmodule__SO__LDADD) $(LIBS)
 
 tags: TAGS

Actually, in the new vflowmodule line there is an opening
bracket missing. The same in the @rm line. No wonder that make
gets confused.

I also failed to get Overflow-20010126 working. It says:

Probe.o: In function arameterSet::ParameterSet(ParameterSet const &)':
/usr/local/include/NodeFactory.h(.gnu.linkonce.d.__vt_5Probe+0x34): undefined reference to ode::setDebugMode(void)'
/usr/local/include/NodeFactory.h(.gnu.linkonce.d.__vt_5Probe+0x40): undefined reference to ode::resetDebugMode(void)'
TextProbe.o: In function odeFactory<TextProbe>::Create(basic_string<char, string_char_traits<char>, __default_alloc_template<true, 0> > const &, ParameterSet const &)':
/root/Overflow/Overflow/vflow/src/TextProbe.cc(.gnu.linkonce.d.__vt_9TextProbe+0x34): undefined reference to ode::setDebugMode(void)'
/root/Overflow/Overflow/vflow/src/TextProbe.cc(.gnu.linkonce.d.__vt_9TextProbe+0x40): undefined reference to ode::resetDebugMode(void)'
PlotProbe.o: In function Vector_alloc_base<float, allocator<float>, true> type_info function':
/root/Overflow/Overflow/vflow/src/PlotProbe.cc(.gnu.linkonce.d.__vt_9PlotProbe+0x34): undefined reference to ode::setDebugMode(void)'
/root/Overflow/Overflow/vflow/src/PlotProbe.cc(.gnu.linkonce.d.__vt_9PlotProbe+0x40): undefined reference to ode::resetDebugMode(void)'
SpectrumProbe.o: In function Vector_alloc_base<float, allocator<float>, true> type_info function':
/root/Overflow/Overflow/vflow/src/SpectrumProbe.cc:8: undefined reference to ode::setDebugMode(void)'
/root/Overflow/Overflow/vflow/src/SpectrumProbe.cc:8: undefined reference to ode::resetDebugMode(void)'
collect2: ld returned 1 exit status
make[3]: *** [vflow] Error 1
make[3]: Leaving directory /root/Overflow/Overflow/vflow/src'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory /root/Overflow/Overflow/vflow'
make[1]: *** [all-recursive-am] Error 2
make[1]: Leaving directory /root/Overflow/Overflow/vflow'
make: *** [all-recursive] Error 1

No idea what's wrong here.......

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From jeff at bioinformatics.org  Sun Jan 28 22:31:35 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
References: <200101290125.BAA00866@schreyer.oberland.net>
Message-ID: <3A74E417.CBDEF0FE@bioinformatics.org>

Karl-Max Wagner wrote:
> 
[stuff that Jean-Marc can answer best]
>
> > It should be open for changes still, since we WANT to interface Piper with
> > other programs.  That's sort of the whole purpose to Piper ;-)  It probably is
> > more a moving target than anything, but collaborations with other projects
> > will help us to nail it down a bit better.
> 
> Well, I am totally open in that. At the moment I can specify the
> interface the way I want. So taking over the piper interface
> isn't such a bad idea to begin with.

What do you mean by "taking over the piper interface"?  "Interface" has a
number of meanings to us.

[stuff for Jean-Marc again]

> If I click on the building block symbols I get some locus etc.
> pull down menu. Is it also planned that I can click on the
> symbol and then can get a ( configurable ) menu for getting data
> of that object resp. getting a ( defineable ) form for entering
> properties ?

Have you tried double-clicking over a node (blue box)?  That drops down a
"windowlet" (small window) which contains widgets for changeable parameters. 
These widgets/parameters can be pre-specified in XML.

Cheers.
Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From jeff at bioinformatics.org  Sun Jan 28 22:36:24 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:07 2006
Subject: [Pipet Users] Piper startup logging...
References: <200101290106.BAA00845@schreyer.oberland.net>
Message-ID: <3A74E538.87F65DE1@bioinformatics.org>

Karl-Max Wagner wrote:
> 
> A quick check showed that everything in there was in a virgin
> state. When compiling, there were errors about some omniORB
> stuff not found: the omniORB install process is kinda
> incomplete, so I did some mass linking into /usr/local/include
> and /usr/local/lib to fix this ( btw. if anybody has some tips
> of what of omniORB is to be installed manually where I'd
> appreciate this ;-)).

On my system, I kept the omniORB install directory in place and then (re)set
the environment variables in my .bashrc:

export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/opt/omniORB_300/lib/i586_linux_2.0_glibc2.1
export PATH=$PATH:/usr/opt/omniORB_300/bin/i586_linux_2.0_glibc2.1
export
PYTHONPATH=$PYTHONPATH:/usr/opt/omniORB_300/lib/python:/usr/opt/omniORB_300/lib/i586_linux_2.0_glibc2.1

You can see by this, though, that the contents of lib/<os> and bin/<os> can be
dumped into your corresponding system directories.  omniORB doesn't seem to do
that on install, however.

Cheers.
Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From jeff at bioinformatics.org  Sun Jan 28 22:41:24 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:08 2006
Subject: [Pipet Users] Piper startup logging...
References: <200101290125.BAA00866@schreyer.oberland.net> <3A74E417.CBDEF0FE@bioinformatics.org>
Message-ID: <3A74E664.B3392DB3@bioinformatics.org>

"J.W. Bizzaro" wrote:
> 
> What do you mean by "taking over the piper interface"?  "Interface" has a
> number of meanings to us.

I guess you're talking about the Piper --> External App interface.  Are you
saying that you want to work on (program) the Piper end of that interface?

Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From jeff at bioinformatics.org  Tue Jan 30 01:43:46 2001
From: jeff at bioinformatics.org (J.W. Bizzaro)
Date: Fri Feb 10 19:39:08 2006
Subject: [Pipet Users] DL to PL connection structure of the BL
References: <3A5FA1F6.1D4A84EC@casema.net>
Message-ID: <3A7662A2.17EE1DBB@bioinformatics.org>

jarl van katwijk wrote:
> 
> As promised I made an overview of the structure of the BL nodes that connect the
> DL to the PL.

This document is now online:

  http://www.bioinformatics.org/piper/design.html

Jeff
-- 
J.W. Bizzaro                                           jeff@bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein
--


From karlmax at oberland.net  Tue Jan 30 17:55:40 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:08 2006
Subject: [Pipet Users] DL to PL connection structure of the BL
In-Reply-To: <3A7662A2.17EE1DBB@bioinformatics.org> from "J.W. Bizzaro" at Jan 30, 2001 06:43:46 AM
Message-ID: <200101302255.WAA01074@schreyer.oberland.net>

>   http://www.bioinformatics.org/piper/design.html

What might be good in there would be to add the communications
mechanism between the different blocks: DL and BL talk together
over CORBA and XML, and the BL talk to the PL in fact by
plugging library functions together and running them.

In case somebody wants to plug his/her stuff into that IMHO the
best interface is to connect to the DL via CORBA and write one's
own BL ( which seems to be a good idea anyway ) as well as the
PL ( which is obvious, of course ).

Another way is to add library functions to Overflow, however,
AFAIU this requires using C++ - so far there is apparently no
way to interface other languages. Am I right on that ?

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================


From jarl at xs4all.nl  Tue Jan 30 19:47:07 2001
From: jarl at xs4all.nl (jarl van katwijk)
Date: Fri Feb 10 19:39:08 2006
Subject: [Pipet Users] DL to PL connection structure of the BL
References: <200101302255.WAA01074@schreyer.oberland.net>
Message-ID: <3A77608B.758BD278@xs4all.nl>

> What might be good in there would be to add the communications
> mechanism between the different blocks: DL and BL talk together
> over CORBA and XML,

see ./piper/idl/DL2BL.idl ;)
Not a perfect idl, but something we can work with.

And about xml: the dl outputs xml formatted data. Nice to see such a similair
view on the design :)

> and the BL talk to the PL in fact by
> plugging library functions together and running them.

see ./piper/idl/BL2PL.idl

>
> In case somebody wants to plug his/her stuff into that IMHO the
> best interface is to connect to the DL via CORBA and write one's
> own BL ( which seems to be a good idea anyway ) as well as the
> PL ( which is obvious, of course ).

Yer, sure. All layers of Piper are more-of-less seperate packages of code. They
share that they all are compliant to Piper. To a Piper layer to be precise.
We also gave bogus layers a though, something involving authetication keys orso
will eventually be in place.

jarl



From valj01 at gel.usherb.ca  Tue Jan 30 23:40:55 2001
From: valj01 at gel.usherb.ca (Jean-Marc Valin)
Date: Fri Feb 10 19:39:08 2006
Subject: [Pipet Users] FreeSpeech Test results
References: <200101262019.UAA00740@schreyer.oberland.net>
Message-ID: <3A779757.CABD82B3@gel.usherb.ca>

My mail server blocked for a couple days, so I got all the messages in batch, in
the wrong order... Are you still having problems with Overflow or is everything
fine now? BTW, did I say you should track and remove any Overflow library that
was previously installed elsewhere (like /usr/lib or /usr/local/lib)? If there's
still a problem, tell me and I'll try to help.

	Jean-Marc

P.S. Another thing you need to make sure of: The Overflow ABI changes
frequently, so make sure that the Piper version you have is linked to the exact
same version of Overflow that's installed. Otherwise, it's almost guarantied not
to work.

-- 
Jean-Marc Valin
Universite de Sherbrooke - Genie Electrique
valj01@gel.usherb.ca


From karlmax at oberland.net  Wed Jan 31 08:47:52 2001
From: karlmax at oberland.net (Karl-Max Wagner)
Date: Fri Feb 10 19:39:08 2006
Subject: [Pipet Users] DL to PL connection structure of the BL
In-Reply-To: <3A77608B.758BD278@xs4all.nl> from "jarl van katwijk" at Jan 31, 2001 01:47:07 AM
Message-ID: <200101311347.NAA00306@schreyer.oberland.net>

> > What might be good in there would be to add the communications
> > mechanism between the different blocks: DL and BL talk together
> > over CORBA and XML,
> 
> see ./piper/idl/DL2BL.idl ;)
> Not a perfect idl, but something we can work with.
> 
> And about xml: the dl outputs xml formatted data. Nice to see such a similair
> view on the design :)

No, what I wanted to say is that it would be good in the block
diagram to note that the communications in this place uses
CORBA. It's just adding a few words and OTOH saves a lot of time
poking through the code.

> > and the BL talk to the PL in fact by
> > plugging library functions together and running them.
> 
> see ./piper/idl/BL2PL.idl

So that means BL and PL also communicate using CORBA, right ? If
so, it would come in handy if that were noted in the diagram as
well - particularly because that is new. In older docs it was
written that BL and PL communicate over direct library calls.

=======================================================================
        "It was hell. They knew it.          Karl-Max Wagner
          But they called it                 karlmax@oberland.net
            W-I-N-D-O-Z-E"                   ham radio: DB8CO
            *********Member of No Code International*********
            ***********Visit http://www.nocode.org***********
            ********Membership Number NCI-2563-DB8CO*********
    _
   / /  (_)__  __ ____  __
  / /__/ / _ \/ // /\ \/ /  . . . t h e   c h o i c e   o f   a
 /____/_/_//_/\_,_/ /_/\_\             G N U   g e n e r a t i o n . .

"Et ceterum censeo ut Microsoftem delendum esse" (Cato, adapted)
"Quo usque tandem abutere nostra patientia ?" (Cicero, original)
=======================================================================