From jeff at bioinformatics.org Fri Jun 1 19:53:03 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:18 2006 Subject: [Pipet Users] Re: Piper development References: <200106012213.SAA16114@www.bioinformatics.org> Message-ID: <3B182ADF.AED671A0@bioinformatics.org> cognite@zianet.com wrote: > > o What is the state of Piper development? Looking at the cvs from > www.bioinformatics.org/piper > it looks like few changes have been posted since a server was moved some > months ago (3,5,6,9,10,11 months ago most changes) and the three projects > began to be integrated (gMessaging, Loci, Overflow). Is that not working, > or something? The state of the CVS module doesn't reflect the state of Piper very well. As you said, Piper is a collaboration between 3 projects, and each tends to be developed somewhat independently. Overflow is not in the CVS module at all, and it is perhaps the most actively developed. gMessaging has undergone some major changes recently, but thay haven't been committed to CVS. Loci is the only one whose activity is reflected by CVS, but that's because one major contributor moved elsewhere and the other one (Yours Truly) is busier evangelizing than coding :-) > o Python is shown as the language of the Piper Build-time subsystem > (along with CORBA communications), as opposed to C++ for its Run-time > subsystem in the diagram of slide 10 of the Feb. 2001 slideset of > J.W.Bizzaro posted on the site. > www.bioinformatics.org/piper/dpci,emtatopmbpse2000/slide_10.html > > But in the cvs, I see only one python file (a super-simple __init__.py). You have to look a bit deeper. All of the UIL and DL are Python -- lots of it. > It looks like the role of the python may be for GUI-to-process > ("User Interfaces Layer") as well as something called "Definitions Layer". > Why would python not be used for the Brokering layer of the Run-time > subsystem? The UIL and DL were originally "Loci" and written entirely in Python. The BL was originally "gMessaging" and written entirely in C (now C++). The PL was and still is "Overflow" and written entirely in C++. The different languages are artifacts of the collaboration, but since they are "connected" via CORBA, and the whole system is modular, having more than one language isn't an issue -- except library dependencies, but we managed to reduce it to 2 languages Python and C++. > -- The other informationflow? diagram in the > www.bioinformatics.org/piper/design subpage is far more complex; the bottom > 2 rows don't seem to correspond directly to the slide. Perhaps you could > explain it a bit more? The former was written more recently by Jarl van Katwijk, and it's mainly about his part: brokering. The slides were written by myself a year ago, and it gives a rough idea as to how Piper is modularized. > Thanks! Best wishes. The idea of overlaying inputs from various URLs onto > a user screen set up with XML, with commands using variable parameter values > underneath, built with process diagrams having enterable value slots, looks > like certainly a coming thing. Yes, we've seen hints of it around, and Piper is an attempt to make a Free Software implementation with some other very unique ideas. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Mon Jun 4 21:12:34 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] [Fwd: Trouble installing piper] Message-ID: <3B1C3202.E13A9F0F@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "Bryant Lau" Subject: Trouble installing piper Date: Mon, 04 Jun 2001 22:08:37 -0000 Size: 1582 Url: http://bioinformatics.org/pipermail/pipet-users/attachments/20010605/5358adbe/attachment.mht From jeff at bioinformatics.org Mon Jun 4 21:24:11 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] Re: Trouble installing piper References: Message-ID: <3B1C34BB.3B106736@bioinformatics.org> Hi Bryant. RH 7.0 uses glibc 2.2 and gcc 2.96. I recall that Overflow will compile and install with both, but Piper won't install with them. Please tell us what version of Piper you're using, and send us the error message. We may have seen it before, but we'd like to get it fixed soon. There are no binaries or RPMS, but they should be on their way. Cheers. Jeff Bryant Lau wrote: > > I'm a student at the University of Toronto, and I was interested in > installing piper. However, I'm having trouble compiling it, even after > installing all the packages and libraries. Do you have a compiled version > for linux (rh 7.0) that you could send me? Right now, I just want to be > able to run it, and see what the program is like. -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Tue Jun 5 10:12:00 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] [Fwd: Trouble installing piper] Message-ID: <3B1CE8B0.3E52B617@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "Bryant Lau" Subject: Re: Trouble installing piper Date: Tue, 05 Jun 2001 13:57:08 -0000 Size: 3374 Url: http://bioinformatics.org/pipermail/pipet-users/attachments/20010605/b6bae4ad/attachment.mht From chapmanb at arches.uga.edu Tue Jun 5 13:19:23 2001 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] Re: [Fwd: Trouble installing piper] In-Reply-To: <3B1CE8B0.3E52B617@bioinformatics.org> References: <3B1CE8B0.3E52B617@bioinformatics.org> Message-ID: <15133.5275.371015.248627@taxus.athen1.ga.home.com> Bryant: > Hmm, ok.. I downloaded of piper off the internet (I think version 0.0.1), > and I think I've managed to install all the necessary libraries. I then did > the "configure", then I was able to do the "make" with no problem. When I > try doing a "make install" this is the error message I get. > > gmake[3]: *** No rule to make target `POA_piper/__init__.py', needed by > `install-piperPYTHON'. Stop. The problem here is that 0.0.1 is really old. There was a change in the standard python mapping, so that the POA directories generated by the omniidl IDL compiler changed from 'POA_blah' to 'blah__POA'. This means that the autoconf installer is looking for created directories by the wrong name. Thing are correct in CVS, so the best bet is to upgrade to something more recent. If 0.0.1 is really that old (I can't remember when it was put together, too much drinking I guess :-), than there have been a lot of changes and it would be worthwhile to upgrade, anyways. Hope this helps, Brad From blau5 at hotmail.com Wed Jun 6 18:54:40 2001 From: blau5 at hotmail.com (Bryant Lau) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] (no subject) Message-ID: Hi, I switched to the cvs copy of piper now (on rh6.2), but when I do the autogen.sh, these warnings come up: ./configure: GNOME_INIT: command not found . . ./configure: GNOME_COMPILE_WARNINGS: command not found . . ./configure: GNOME_INIT: command not found It is able to complete though, however the makefile is screwed up in dl/vflow/interfaces. I think the problem is that there are 2 "vflowmodule0 7 31 10 20001 6 28 10 6 4 3 2 1 0SO)" where there should be vflowmodule$(SO) I fix that, but when I next compile, I get this error message (where I am now stuck): gmake[5]: Entering directory `/root/newtmp/piper/src/dl/vflow/interfaces' c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I/usr/include/gnome-xml -I/usr/include/python1.5 -I/usr/lib/python1.5/config -fPIC -g -O2 -I/usr/local/include -g -O2 -c mod_vflow_wrap.c mod_vflow_wrap.c: In function `struct PyObject * _wrap_UIDocument_scanDL(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:959: no method `UIDocument::scanDL' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINetwork_getType(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1101: no matching function for call to `UINetwork::getType ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINetwork_getNodes(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1342: no matching function for call to `UINetwork::getNodes ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINetwork_getLinks(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1368: no matching function for call to `UINetwork::getLinks ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINetwork_getTerminals(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1394: no matching function for call to `UINetwork::getTerminals ()' /usr/include/UINetwork.h:88: candidates are: UINetwork::getTerminals(UINetTerminal::NetTermType) mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINode_getType(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1583: no matching function for call to `UINode::getType ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINode_getInputs(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1640: no matching function for call to `UINode::getInputs ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINode_getOutputs(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1666: no matching function for call to `UINode::getOutputs ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINode_getParameters(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1692: no matching function for call to `UINode::getParameters ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINode_getDescription(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1706: no matching function for call to `UINode::getDescription ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINode_setPos(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1747: no matching function for call to `UINode::setPos (double &, double &)' mod_vflow_wrap.c: In function `struct PyObject * _wrap_ParameterText_description_get(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1879: `class ParameterText' has no member named `description' mod_vflow_wrap.c: In function `struct PyObject * _wrap_ParameterText_description_set(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1898: `class ParameterText' has no member named `description' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINodeParameters_addParameterText(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1965: no matching function for call to `UINodeParameters::addParameterText (string &, string &, string &, string &)' /usr/include/UINodeParameters.h:47: candidates are: UINodeParameters::addParameterText(string, string, string) mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINodeParameters_removeParameterText(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1983: no matching function for call to `UINodeParameters::removeParameterText (string &)' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINodeParameters_get_textParams(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1998: no matching function for call to `UINodeParameters::get_textParams ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_new_UITerminal(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:2030: no matching function for call to `UITerminal::UITerminal (ItemInfo *&, UINode *&, bool &, double &, double &)' /usr/include/UITerminal.h:82: candidates are: UITerminal::UITerminal(const UITerminal &) /usr/include/UITerminal.h:36: UITerminal::UITerminal(string, UINode *, bool, double, double) mod_vflow_wrap.c: In function `struct PyObject * _wrap_UITerminal_getType(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:2078: no matching function for call to `UITerminal::getType ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UITerminal_getDescription(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:2096: no matching function for call to `UITerminal::getDescription ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UITerminal_isInputTerminal(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:2114: no matching function for call to `UITerminal::isInputTerminal ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UITerminal_getConnections(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:2128: no matching function for call to `UITerminal::getConnections ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UILink_getFromTerminal(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:2273: no matching function for call to `UILink::getFromTerminal ()' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UILink_getToTerminal(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:2287: no matching function for call to `UILink::getToTerminal ()' gmake[5]: *** [mod_vflow_wrap.o] Error 1 I have installed both Overflow and gms (from the cvs). I also have omniORB and omniORBpy and the other libraries installed. Can anyone help me with this? Thanks, Bryant Lau _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From blau5 at hotmail.com Wed Jun 6 19:10:24 2001 From: blau5 at hotmail.com (Bryant Lau) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better Message-ID: Okay, after configuring with the --with-overflow flag, the make problem seems a little better. This is now my error message at that part: gmake[5]: Entering directory `/root/newtmp/piper/src/dl/vflow/interfaces' c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I/usr/include/gnome-xml -I/usr/include/python1.5 -I/usr/lib/python1.5/config -fPIC -g -O2 -I/opt/overflow/include -g -O2 -c mod_vflow_wrap.c mod_vflow_wrap.c: In function `struct PyObject * _wrap_UIDocument_scanDL(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:959: no method `UIDocument::scanDL' mod_vflow_wrap.c: In function `struct PyObject * _wrap_UINetwork_newLink(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:1258: no matching function for call to `UINetwork::newLink (UITerminal *&, UITerminal *&)' /opt/overflow/include/UINetwork.h:139: candidates are: UINetwork::newLink(UITerminal *, UITerminal *, char *) gmake[5]: *** [mod_vflow_wrap.o] Error 1 gmake[5]: Leaving directory `/root/newtmp/piper/src/dl/vflow/interfaces' I still had to go through the same warning messages and fixing the Makefile as before though. Thanks, Bryant Lau _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From jeff at bioinformatics.org Wed Jun 6 22:44:21 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: Message-ID: <3B1EEA85.A43B2EEB@bioinformatics.org> Hi Bryant. It looks like there may have been a change in Overflow that broke the wrapper in Piper. We're checking it out now, and we'll get right back to you. Jeff Bryant Lau wrote: > > Okay, after configuring with the --with-overflow flag, the make problem > seems a little better. This is now my error message at that part: > > gmake[5]: Entering directory `/root/newtmp/piper/src/dl/vflow/interfaces' > c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I/usr/include/gnome-xml > -I/usr/include/python1.5 -I/usr/lib/python1.5/config -fPIC -g -O2 > -I/opt/overflow/include -g -O2 -c mod_vflow_wrap.c > mod_vflow_wrap.c: In function `struct PyObject * > _wrap_UIDocument_scanDL(struct PyObject *, struct PyObject *)': > mod_vflow_wrap.c:959: no method `UIDocument::scanDL' > mod_vflow_wrap.c: In function `struct PyObject * > _wrap_UINetwork_newLink(struct PyObject *, struct PyObject *)': > mod_vflow_wrap.c:1258: no matching function for call to `UINetwork::newLink > (UITerminal *&, UITerminal *&)' > /opt/overflow/include/UINetwork.h:139: candidates are: > UINetwork::newLink(UITerminal *, UITerminal *, char *) > gmake[5]: *** [mod_vflow_wrap.o] Error 1 > gmake[5]: Leaving directory `/root/newtmp/piper/src/dl/vflow/interfaces' -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From valj01 at gel.usherb.ca Wed Jun 6 23:58:12 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: <3B1EEA85.A43B2EEB@bioinformatics.org> Message-ID: <3B1EFBD4.59B6349C@gel.usherb.ca> > Hi Bryant. It looks like there may have been a change in Overflow that broke > the wrapper in Piper. We're checking it out now, and we'll get right back to > you. Jeff (re-post to the list) Oops... Fixed in CVS. If all you want is the patch, it's a one-liner: data-flow/include/UINetwork.h - virtual UILink *newLink (UITerminal *_from, UITerminal *_to, char *str); + virtual UILink *newLink (UITerminal *_from, UITerminal *_to, char *str=NULL); BTW, the CVS version has a couple fixes for some build problems (autoconf, ...) if anybody had a problem. Also Jeff while I'm on the subject, a while ago you suggested not to use autoconf/automake for Piper. I wanted that I really feel we *should* use those tools. While it's a bit hard getting started with it, it's about the only way to have some software portable, believe me. Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From blau5 at hotmail.com Thu Jun 7 11:24:36 2001 From: blau5 at hotmail.com (Bryant Lau) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better Message-ID: Hi, I got that fixed.. but now I have another error, saying no method 'UIDocument::scanDL'.. I tried looking for a scanDL method in overflow, but I couldn't find any. Could anyone help me with this? Here's the error message: c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I/usr/include/gnome-xml -I/usr/include/python1.5 -I/usr/lib/python1.5/config -fPIC -g -O2 -I/opt/overflow/include -g -O2 -c mod_vflow_wrap.c mod_vflow_wrap.c: In function `struct PyObject * _wrap_UIDocument_scanDL(struct PyObject *, struct PyObject *)': mod_vflow_wrap.c:959: no method `UIDocument::scanDL' gmake[5]: *** [mod_vflow_wrap.o] Error 1 Thanks, Bryant Lau >From: Jean-Marc Valin >Reply-To: pipet-users@bioinformatics.org >To: pipet-users@bioinformatics.org >Subject: Re: [Pipet Users] the make problem is a bit better >Date: Wed, 06 Jun 2001 23:58:12 -0400 > > > Hi Bryant. It looks like there may have been a change in Overflow that >broke > > the wrapper in Piper. We're checking it out now, and we'll get right >back to > > you. Jeff >(re-post to the list) > >Oops... Fixed in CVS. If all you want is the patch, it's a one-liner: > >data-flow/include/UINetwork.h >- virtual UILink *newLink (UITerminal *_from, UITerminal *_to, char >*str); >+ virtual UILink *newLink (UITerminal *_from, UITerminal *_to, char >*str=NULL); > >BTW, the CVS version has a couple fixes for some build problems (autoconf, >...) >if anybody had a problem. Also Jeff while I'm on the subject, a while ago >you >suggested not to use autoconf/automake for Piper. I wanted that I really >feel we >*should* use those tools. While it's a bit hard getting started with it, >it's >about the only way to have some software portable, believe me. > > Jean-Marc > >-- >Jean-Marc Valin >Universite de Sherbrooke - Genie Electrique >valj01@gel.usherb.ca > >_______________________________________________ >pipet-users maillist - pipet-users@bioinformatics.org >http://bioinformatics.org/mailman/listinfo/pipet-users > _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From jmvalin at locusdialogue.com Thu Jun 7 11:51:12 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: Message-ID: <3B1FA2EF.71373375@locusdialogue.com> > I got that fixed.. but now I have another error, saying no method > 'UIDocument::scanDL'.. I tried looking for a scanDL method in overflow, but > I couldn't find any. Could anyone help me with this? OK, my fault again ;-( I forgot that this change breaks source compatibility with Piper. In the Piper source, UIDocument::scanDL() should be replaced by scanDL(), which is found in "path.h". Jean-Marc From blau5 at hotmail.com Thu Jun 7 12:38:21 2001 From: blau5 at hotmail.com (Bryant Lau) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better Message-ID: Ok, that works too... but now, when it gets to bl/plugins, it does the same thing. I replaced the UIDocument::scanDL with scanDL as before, but now I'm getting this message: plugin_sensor_PL_main.c:86: warning: implicit declaration of function `int scanDL(...)' /bin/sh ../libtool --mode=link c++ -g -ggdb -D__x86__ -Wall -o PL BL2PLSK.o plugin_sensor_PL_main.o -L/usr/lib -lgthread -lglib -lpthread -lomniORB3 -lomnithread -ltcpwrapGK -L/usr/local/lib -L/opt/overflow/lib -lflow -lxml -lz c++ -g -ggdb -D__x86__ -Wall -o PL BL2PLSK.o plugin_sensor_PL_main.o -L/usr/lib -lgthread -lglib -lpthread -lomniORB3 -lomnithread -ltcpwrapGK -L/usr/local/lib -L/opt/overflow/lib -lflow -lxml -lz plugin_sensor_PL_main.o: In function `BL2PL_i::upload(char const *)': /root/newtmp/piper/src/bl/plugins/plugin_sensor_PL_main.c:86: undefined reference to `scanDL' I tried #include "path.h" but it doesn't help the problem... Could someone help me with this? Thanks, Bryant Lau >From: Jean-Marc Valin >Reply-To: pipet-users@bioinformatics.org >To: pipet-users@bioinformatics.org, blau5@hotmail.com >Subject: Re: [Pipet Users] the make problem is a bit better >Date: Thu, 07 Jun 2001 11:51:12 -0400 > > > I got that fixed.. but now I have another error, saying no method > > 'UIDocument::scanDL'.. I tried looking for a scanDL method in overflow, >but > > I couldn't find any. Could anyone help me with this? > >OK, my fault again ;-( I forgot that this change breaks source >compatibility with Piper. In the Piper source, UIDocument::scanDL() >should be replaced by scanDL(), which is found in "path.h". > > Jean-Marc > >_______________________________________________ >pipet-users maillist - pipet-users@bioinformatics.org >http://bioinformatics.org/mailman/listinfo/pipet-users > _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From jmvalin at locusdialogue.com Thu Jun 7 13:37:58 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: Message-ID: <3B1FBBF6.CCAAB449@locusdialogue.com> > Ok, that works too... but now, when it gets to bl/plugins, it does the same > thing. I replaced the UIDocument::scanDL with scanDL as before, but now > I'm getting this message: > > plugin_sensor_PL_main.c:86: warning: implicit declaration of function `int > scanDL(...)' > /bin/sh ../libtool --mode=link c++ -g -ggdb -D__x86__ -Wall -o PL > BL2PLSK.o plugin_sensor_PL_main.o -L/usr/lib -lgthread -lglib -lpthread > -lomniORB3 -lomnithread -ltcpwrapGK -L/usr/local/lib -L/opt/overflow/lib > -lflow -lxml -lz > c++ -g -ggdb -D__x86__ -Wall -o PL BL2PLSK.o plugin_sensor_PL_main.o > -L/usr/lib -lgthread -lglib -lpthread -lomniORB3 -lomnithread -ltcpwrapGK > -L/usr/local/lib -L/opt/overflow/lib -lflow -lxml -lz > plugin_sensor_PL_main.o: In function `BL2PL_i::upload(char const *)': > /root/newtmp/piper/src/bl/plugins/plugin_sensor_PL_main.c:86: undefined > reference to `scanDL' > > I tried #include "path.h" but it doesn't help the problem... Could someone > help me with this? OK, now it's a different problem. It's not the compilation but the link. It cannot find scanDL function in the -lflow library. I think it has something to do with C vs C++. plugin_sensor_PL_main.c is a C file. First, I don't even understand how it could have worked before, if plugin_sensor_PL_main.c was using a C++ function (UIDocument::scanDL()). Also, I thought the BL had been converted to C++. So there are two options now: the first is to convert plugin_sensor_PL_main.c to a C++ file. The other (which I'll apply anyway) is to change (int data-flow/include/path.h): vector envList(char *envName); void scanDL(bool debug=false); to extern "C" { vector envList(char *envName); void scanDL(bool debug=false); } Anyway, I think this is a BL issue more than a PL (Overflow) issue. Jarl? Jean-Marc P.S. Could you run: nm /opt/overflow/lib/libflow.so | grep scanDL and send me the results From blau5 at hotmail.com Fri Jun 8 16:06:31 2001 From: blau5 at hotmail.com (Bryant Lau) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better Message-ID: I finally got it all compiled! But now, after the make install, when I run it, I get this weird message: Traceback (innermost last): File "runpiper.py", line 14, in ? from piperconfig import * ImportError: No module named piperconfig When I add the directory of the "piperconfig.py" to the PYTHONPATH environment variable, then it gets past that stage, but I get another error message: rm: cannot remove `/root/piper_info/ior/*': No such file or directory Starting processing layer... Starting brokering layer... Starting definition layer... Starting pied... sh: PL: command not found Loading plugin /usr/local/lib/libplugin_sensor_irc.so... Message: Initialising IRC sensor, make sure the default config (gms sourcecode ./plugins/plugin_sensor_irc.h) is reachable using DEFAULTS for irc_config Traceback (innermost last): File "./startdl.py", line 9, in ? from modules.dlmain import DlMain ImportError: No module named modules.dlmain Traceback (innermost last): File "startpied.py", line 16, in ? import modules.piper.UIL2DL ImportError: No module named modules.piper.UIL2DL Am I doing anything wrong here? Bryant >From: Jean-Marc Valin >To: Bryant Lau >CC: jmvalin@locusdialog.com >Subject: Re: [Pipet Users] the make problem is a bit better >Date: Thu, 07 Jun 2001 16:35:12 -0400 > > > I tried changing the path.h file, but I still get the same error. >Here's > > the error message again, just in case I'm missing anything. > > > > Thanks, > > Bryant > > > > P.S. here's the results of the "nm /opt/overflow/lib/libflow.so | grep > > scanDL": > > > > [root@devlab12 src]# nm /opt/overflow/lib/libflow.so | grep scanDL > > 00128a68 T scanDL__Fb > >Maybe you forgot to recompile Overflow with this modification? The nm >command should give you something like: > >0012d928 T scanDL > >(the __Fb suffix is added by the C++ compiler because of function >overloading) > >Note that the previous patch I sent is not totally correct. The lines I >added should be in a #ifdef __cplusplus: > >#ifdef __cplusplus >extern "C" { >#endif >vector envList(char *envName); >void scanDL(bool debug=false); >#ifdef __cplusplus >} >#endif > >There's still another reason why it may not work. If that's the case, >remove the "=false" in the scanDL prototype and add the argument >explicitly in the Piper code. Hope it works this time. It's been a while >since the last time I had feedback on a recent version of Overflow in >Piper. Sorry for the inconvenience! > > Jean-Marc _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From jeff at bioinformatics.org Fri Jun 8 17:32:25 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: Message-ID: <3B214469.9011F8B4@bioinformatics.org> Bryant Lau wrote: > > Traceback (innermost last): > File "runpiper.py", line 14, in ? > from piperconfig import * > ImportError: No module named piperconfig > > When I add the directory of the "piperconfig.py" to the PYTHONPATH > environment variable, There's a line in runpiper.py to include the config directory: # hack to include the configuration file in the PYTHONPATH sys.path.insert(0, os.path.join(os.curdir, 'config')) What version of Python are you using? > ImportError: No module named modules.dlmain > ImportError: No module named modules.piper.UIL2DL These are there. Are you running Piper from the installed location or from the package location? What path did you choose to install Piper in? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Fri Jun 8 17:34:31 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: Message-ID: <3B2144E6.F1B19296@bioinformatics.org> Bryant Lau wrote: > > I finally got it all compiled! Bryant, can you send us the diff on the files that you had to modify? Thanks! Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jarl at xs4all.nl Sat Jun 9 00:20:20 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: <3B1FBBF6.CCAAB449@locusdialogue.com> Message-ID: <3B21A404.30767E7E@xs4all.nl> > Anyway, I think this is a BL issue more than a PL (Overflow) issue. > Jarl? I've been compiling, but not yet finished, let you people know more tomorrow. jarl From jarl at xs4all.nl Sun Jun 10 23:22:02 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] the make problem is a bit better References: Message-ID: <3B24395A.255580F0@xs4all.nl> Bryant Lau wrote: > > I finally got it all compiled! But now, after the make install, when I run > it, I get this weird message: > > Traceback (innermost last): > File "runpiper.py", line 14, in ? > from piperconfig import * > ImportError: No module named piperconfig > > When I add the directory of the "piperconfig.py" to the PYTHONPATH > environment variable, then it gets past that stage, but I get another error > message: > > rm: cannot remove `/root/piper_info/ior/*': No such file or directory > Starting processing layer... > Starting brokering layer... > Starting definition layer... > Starting pied... > sh: PL: command not found > Loading plugin /usr/local/lib/libplugin_sensor_irc.so... Message: > Initialising IRC sensor, make sure the default config (gms sourcecode > ./plugins/plugin_sensor_irc.h) is reachable > using DEFAULTS for irc_config > Traceback (innermost last): > File "./startdl.py", line 9, in ? > from modules.dlmain import DlMain > ImportError: No module named modules.dlmain > Traceback (innermost last): > File "startpied.py", line 16, in ? > import modules.piper.UIL2DL > ImportError: No module named modules.piper.UIL2DL > > Am I doing anything wrong here? The binairy 'PL' should be in your path, I'll have a look at this too and try to fix it. I'm installing to /usr/local/bin, so it's working for me, but as you probably have placed Piper somewhere else try expanding your $PATH. BTW I'm updating the Piper cvs code so it can compile to Overflow again. Bad Jean Marc! ;-) nah, anyways, somebody should at least test a new release of one of the components. As I have been having a break from Piper for a few months I didn't had an eye on consistency for a while and the state Bryant found Piper is pretty sad... jarl From jarl at xs4all.nl Mon Jun 11 00:06:35 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] CVS status References: <3B24395A.255580F0@xs4all.nl> Message-ID: <3B2443CB.CB41F074@xs4all.nl> Hi all, Fixed code in cvs, it now compiles against latest overflow again. A quick test running Piper shows not everything is OK already, the DL\UI have problems. The PL and BL are runnning, but no loading all plugins, will look at this later on. Can somebody (Jeff;)) have a look at this DL\UI issue? I will do too, but not sure I'm the man to do Python coding.. jarl From jeff at bioinformatics.org Sun Jun 10 18:20:37 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] CVS status References: <3B24395A.255580F0@xs4all.nl> <3B2443CB.CB41F074@xs4all.nl> Message-ID: <3B23F2B5.E9E8B202@bioinformatics.org> Jarl van Katwijk wrote: > > Fixed code in cvs, it now compiles against latest overflow again. Which versions of gcc & glibc did you use? Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jarl at xs4all.nl Mon Jun 11 00:27:08 2001 From: jarl at xs4all.nl (Jarl van Katwijk) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] CVS status References: <3B24395A.255580F0@xs4all.nl> <3B2443CB.CB41F074@xs4all.nl> <3B23F2B5.E9E8B202@bioinformatics.org> Message-ID: <3B24489C.FCC4F3B5@xs4all.nl> > > Fixed code in cvs, it now compiles against latest overflow again. > > Which versions of gcc & glibc did you use? gcc --version : 2.95.3 glibc : libc-2.2.1 From jean-marc.valin at hermes.usherb.ca Sun Jun 10 21:33:21 2001 From: jean-marc.valin at hermes.usherb.ca (jean-marc.valin@hermes.usherb.ca) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] CVS status In-Reply-To: <3B23F2B5.E9E8B202@bioinformatics.org> References: <3B24395A.255580F0@xs4all.nl> <3B2443CB.CB41F074@xs4all.nl> <3B23F2B5.E9E8B202@bioinformatics.org> Message-ID: <992223201.3b241fe16b228@imp.usherb.ca> > Jarl van Katwijk wrote: > > > > Fixed code in cvs, it now compiles against latest overflow again. > > Which versions of gcc & glibc did you use? Did I say that Overflow now works correctly with gcc 2.95, gcc 2.96RH (for non-completely-buggy versions), and gcc3-pre. As for egcs 1.1.2, I'm not really sure. I had a report of one person having problems with it, but I don't know whether it's the compiler or the setup. Also, I'll soon release a 0.5.0 version that will have the recent changes allowing to compile Piper. Jean-Marc From blau5 at hotmail.com Mon Jun 11 15:58:58 2001 From: blau5 at hotmail.com (Bryant Lau) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] have compiled piper, but can't run it... Message-ID: I tried putting the PL's path (for me it was in /cpiper/bin) in the PATH, but it doesn't work... It still gives this message: Traceback (innermost last): File "runpiper.py", line 14, in ? from piperconfig import * ImportError: No module named piperconfig Does anyone know if I'm supposed to have any paths in the environment variable PYTHONPATH? Thanks, Bryant Lau _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From jeff at bioinformatics.org Wed Jun 13 06:06:53 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] have compiled piper, but can't run it... References: Message-ID: <3B273B3D.DDD4B744@bioinformatics.org> Bryant Lau wrote: > > Traceback (innermost last): > File "runpiper.py", line 14, in ? > from piperconfig import * > ImportError: No module named piperconfig Hey Bryant. This has nothing to do with the PL. Please tell us (1) the directory from which you are running Piper, and (2) the command that you are using. Basically, I want to know if you have the main piper script installed in /usr/bin/piper. Cheers. Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Fri Jun 15 01:40:17 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] couple relevant links Message-ID: <3B299FC1.4A2BAE02@bioinformatics.org> gnucash 1.6 and the dependency nightmare http://www.lwn.net/ Python 2.0.1c1 - GPL-compatible release candidate http://mail.python.org/pipermail/python-list/2001-June/048419.html (from Slashdot) Jeff -- J.W. Bizzaro jeff@bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Tue Jun 19 08:29:51 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:39:19 2006 Subject: [Pipet Users] adventure-based UIs Message-ID: <3B2F45BF.4A1217A@bioinformatics.org> Slashdot posted another example of a user interface based on an adventure game, like Zork: http://uwsg.iu.edu/hypermail/linux/kernel/0106.2/0098.html This is the plan for our console interface. Do you see how this could work in a network of nodes? I'd like to get the source for the interpreter. Jeff