From jeff at bioinformatics.org Fri Jun 1 19:35:34 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:50 2006 Subject: [Pipet Devel] [Fwd: Piper development] Message-ID: <3B1826C6.C1912292@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: cognite@zianet.com Subject: Piper development Date: Fri, 1 Jun 2001 18:13:41 -0400 Size: 2712 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010601/10ddbdbd/attachment.mht From jeff at bioinformatics.org Sat Jun 2 17:17:06 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:50 2006 Subject: [Pipet Devel] Re: Piper development References: <200106022101.RAA01715@www.bioinformatics.org> Message-ID: <3B1957D2.DA253580@bioinformatics.org> cognite@zianet.com wrote: > > Thank you for a very nice and informative reply. > > Guess you "evangelized" me; I'm going back to do some more looking at Piper > and its components! You're very welcome. Let us know if you have any more questions. We should be updating CVS shortly and coming out with our 0.X "Gates of Dawn" series. We'd also like to promote the system as a standard where other projects can include Piper (e.g., some of the free desktops) and swap out components. There is already some synergy with a couple projects: Narval and BlueBox and interest from companies like Juno Online and Open Channel Software. 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 Wed Jun 6 17:33:53 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:50 2006 Subject: [Pipet Devel] [Fwd: Compiled Tree for Piper] Message-ID: <3B1EA1C1.715DD017@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "Bryant Lau" Subject: Compiled Tree for Piper Date: Wed, 06 Jun 2001 19:53:06 -0000 Size: 3586 Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/20010606/9d866965/attachment.mht From jeff at bioinformatics.org Wed Jun 6 17:38:30 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:50 2006 Subject: [Pipet Devel] Re: Compiled Tree for Piper References: Message-ID: <3B1EA2D6.71E1AE1@bioinformatics.org> Bryant Lau wrote: > > I've followed your instructions, using rh6.2 instead, and I still haven't > been able to install a working version of Piper. I was able to get a > (mildly hacked) version compiled, but after installing, there were problems > with the Python scripts, so it didn't work. I would like to install Piper > to see how it looks like, so I was wondering if you would have a compiled > tree of piper that you could send me, so I can see what it looks like?. Did you use the CVS version, as Brad suggested? Please paste the error message that you got this time. Regarding a compiled version, we don't have one ready, but if you're having a problem with Python, it won't help anyway. 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 Wed Jun 6 22:44:14 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:50 2006 Subject: [Pipet Devel] JEAN-MARC Message-ID: <3B1EEA7E.3CF3DFA1@bioinformatics.org> Brad suggested that there may have been a change in Overflow that broke our wrapper. The error message that Bryant sent seems to indicate that. What do you think? --------------------------------- 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 23:55:54 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] JEAN-MARC References: <3B1EEA7E.3CF3DFA1@bioinformatics.org> Message-ID: <3B1EFB4A.ADD20B05@gel.usherb.ca> > Brad suggested that there may have been a change in Overflow that broke our > wrapper. The error message that Bryant sent seems to indicate that. What do > you think? 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 jeff at bioinformatics.org Thu Jun 7 00:19:39 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] JEAN-MARC References: <3B1EEA7E.3CF3DFA1@bioinformatics.org> <3B1EFB4A.ADD20B05@gel.usherb.ca> Message-ID: <3B1F00DB.40B34D72@bioinformatics.org> Hi Jean-Marc! Jean-Marc Valin wrote: > > BTW, the CVS version has a couple fixes for some build problems (autoconf, ...) > if anybody had a problem. Thanks for the fix. > 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. Maybe I suggested not using it for Python code, and I did say that I am unfamiliar with it. But, yes, it is probably best to stick with it. I need to read up on it. Do you have any suggestions for documentation on autoconf/make? 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 Thu Jun 7 00:31:48 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] /products/gbuild Message-ID: <3B1F03B4.F9A371BF@bioinformatics.org> http://www.cryon.com/gbuild/ Jeff From jeff at bioinformatics.org Mon Jun 11 01:14:38 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] overflow install problem Message-ID: <3B2453BE.3773CFB5@bioinformatics.org> I tried compiling from CVS tonight. I don't quite understand this error..... Jeff ------------------------------ Making install in src make[2]: Entering directory `/usr/src/Overflow/Overflow-20010610-inst/NNet/src' /bin/sh ../libtool --mode=compile c++ -DLINUX=1 -DHAVE_FLOAT_H=1 -DHAVE_HASH_MAP=1 -DHAVE_LIBM=1 -D_REENTRANT=1 -I. -I. -I../include -I../../data-flow/include [l_INCLUDEDIR -g -O2 -c FFLayer.cc c++ -DLINUX=1 -DHAVE_FLOAT_H=1 -DHAVE_HASH_MAP=1 -DHAVE_LIBM=1 -D_REENTRANT=1 -I. -I. -I../include -I../../data-flow/include "[l_INCLUDEDIR" -g -O2 -Wp,-MD,.deps/FFLayer.pp -c FFLayer.cc -fPIC -DPIC -o FFLayer.lo c++: cannot specify -o with -c or -S and multiple compilations make[2]: *** [FFLayer.lo] Error 1 make[2]: Leaving directory `/usr/src/Overflow/Overflow-20010610-inst/NNet/src' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/usr/src/Overflow/Overflow-20010610-inst/NNet' make: *** [install-recursive] Error 1 From valj01 at gel.usherb.ca Mon Jun 11 07:53:34 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] overflow install problem References: <3B2453BE.3773CFB5@bioinformatics.org> Message-ID: <3B24B13E.49614568@gel.usherb.ca> > I tried compiling from CVS tonight. I don't quite understand this error..... > Jeff > > ------------------------------ > Making install in src > make[2]: Entering directory > `/usr/src/Overflow/Overflow-20010610-inst/NNet/src' > /bin/sh ../libtool --mode=compile c++ -DLINUX=1 -DHAVE_FLOAT_H=1 > -DHAVE_HASH_MAP=1 -DHAVE_LIBM=1 -D_REENTRANT=1 -I. -I. -I../include > -I../../data-flow/include [l_INCLUDEDIR -g -O2 -c FFLayer.cc > c++ -DLINUX=1 -DHAVE_FLOAT_H=1 -DHAVE_HASH_MAP=1 -DHAVE_LIBM=1 -D_REENTRANT=1 > -I. -I. -I../include -I../../data-flow/include "[l_INCLUDEDIR" -g -O2 > -Wp,-MD,.deps/FFLayer.pp -c FFLayer.cc -fPIC -DPIC -o FFLayer.lo > c++: cannot specify -o with -c or -S and multiple compilations > make[2]: *** [FFLayer.lo] Error 1 > make[2]: Leaving directory `/usr/src/Overflow/Overflow-20010610-inst/NNet/src' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory `/usr/src/Overflow/Overflow-20010610-inst/NNet' > make: *** [install-recursive] Error 1 I think the problem is with the "[l_INCLUDEDIR" that shouldn't be there. That's probably an autoconf test that failed and resulted in a variable not being set. That test is probably : gnome-config --cflags xml What do you get when you run that command? Maybe it's just that gnome-config is not in your path... or that you don't have libxml installed. I thought I had fixed this build problem but it seems that I haven't. Jean-Marc -- Jean-Marc Valin Universite de Sherbrooke - Genie Electrique valj01@gel.usherb.ca From jeff at bioinformatics.org Tue Jun 12 04:17:31 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] overflow install problem References: <3B2453BE.3773CFB5@bioinformatics.org> <3B24B13E.49614568@gel.usherb.ca> Message-ID: <3B25D01B.A77F6708@bioinformatics.org> Jean-Marc Valin wrote: > > gnome-config --cflags xml > > What do you get when you run that command? root@dexter:Overflow-20010610-inst> gnome-config --cflags xml -I/usr/include/gnome-xml 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 valj01 at gel.usherb.ca Tue Jun 12 07:37:11 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] overflow install problem References: <3B2453BE.3773CFB5@bioinformatics.org> <3B24B13E.49614568@gel.usherb.ca> <3B25D01B.A77F6708@bioinformatics.org> Message-ID: <3B25FEE7.B6F8972B@gel.usherb.ca> > root@dexter:Overflow-20010610-inst> gnome-config --cflags xml > -I/usr/include/gnome-xml Then I don't understand what's going on. Could you send me both your data-flow/src/Makefile and your NNet/src/Makefile so I can investigate. BTW, please try a fresh build before. Jean-Marc From jeff at bioinformatics.org Tue Jun 12 08:04:55 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] overflow install problem References: <3B2453BE.3773CFB5@bioinformatics.org> <3B24B13E.49614568@gel.usherb.ca> <3B25D01B.A77F6708@bioinformatics.org> <3B25FEE7.B6F8972B@gel.usherb.ca> Message-ID: <3B260567.35766BDF@bioinformatics.org> Jean-Marc Valin wrote: > > Then I don't understand what's going on. Could you send me both your > data-flow/src/Makefile and your NNet/src/Makefile so I can investigate. > > BTW, please try a fresh build before. ? Do you want me to re-download and rebuild before sending you the makefiles? 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 valj01 at gel.usherb.ca Tue Jun 12 08:35:28 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] overflow install problem References: <3B2453BE.3773CFB5@bioinformatics.org> <3B24B13E.49614568@gel.usherb.ca> <3B25D01B.A77F6708@bioinformatics.org> <3B25FEE7.B6F8972B@gel.usherb.ca> <3B260567.35766BDF@bioinformatics.org> Message-ID: <3B260C90.C5868199@gel.usherb.ca> > ? Do you want me to re-download and rebuild before sending you the makefiles? Get the CVS version or at least 0.4.3. And make sure to have a fresh build. Jean-Marc From jeff at bioinformatics.org Tue Jun 12 08:45:40 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] overflow install problem References: <3B2453BE.3773CFB5@bioinformatics.org> <3B24B13E.49614568@gel.usherb.ca> <3B25D01B.A77F6708@bioinformatics.org> <3B25FEE7.B6F8972B@gel.usherb.ca> <3B260567.35766BDF@bioinformatics.org> <3B260C90.C5868199@gel.usherb.ca> Message-ID: <3B260EF4.ADC6826@bioinformatics.org> Jean-Marc Valin wrote: > > Get the CVS version or at least 0.4.3. And make sure to have a fresh build. These are from a fresh build (up until the install error) of CVS source on June 10 (newer than 0.4.3). Jeff -------------- next part -------------- -------------- next part -------------- From jeff at bioinformatics.org Wed Jun 13 05:57:52 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors Message-ID: <3B273920.81953DC0@bioinformatics.org> I still can't install Overflow completely, but most of it seemed to get installed before the error, so I tried compiling Piper against it. It did compile, but when I run it, I get an error that it cannot find libflow-0.5.so. Okay, so if Overflow didn't install completely, then I should not expect this file to be there. BUT IT IS THERE. I even added the path to $PATH, but I still get this error. ldconfig doesn't show the lib, and ldd also says that it is not found. Don't know what to do. Also, Jarl, I still get that "DL2BL IOR file not found" error. Doesn't anyone else get it? The IOR file ISN'T being written. What part is responsible for it? Can we have a message output that it is written or can't be? Jeff ------------------------------------------------- Starting processing layer... Starting brokering layer... PL: error while loading shared libraries: libflow-0.5.so: cannot load shared object file: No such file or directory BL: error while loading shared libraries: libflow-0.5.so: cannot load shared object file: No such file or directory Starting definition layer... Starting pied... Default location of the DL2BL IOR file: /home/jeff/piper_info/ior/dl2bl.ior Wrote IOR file /home/jeff/piper_info/ior/uil2dl.ior Getting document... error: net LoadFile already existed error: net SaveAs already existed error: net SpectrumProbe already existed error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed error: net dB already existed error: net undB already existed Connecting with the bl... DL2BL IOR file not found. Connection with BL not established. Loading crash info... error: net LoadFile already existed error: net SaveAs already existed error: net SpectrumProbe already existed error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed error: net dB already existed error: net undB already existed error: net LoadFile already existed error: net SaveAs already existed error: net SpectrumProbe already existed error: net LP already existed error: net HP already existed error: net LPC_DECOMP already existed error: net dB already existed error: net undB already existed omniORB: Caught an unexpected Python exception during up-call. Traceback (innermost last): File "/opt/piper/dl/modules/uicommunication.py", line 341, in loadCrashInfo self.loadDocument(self.crash_file) File "/opt/piper/dl/modules/uicommunication.py", line 364, in loadDocument self.user.temp_locus.load_from_file(file, self) File "/opt/piper/dl/modules/compositelocus.py", line 510, in load_from_file raise IOError("File to load did not have a MAIN network defined.") IOError: File to load did not have a MAIN network defined. Aborted ----------------------------------------------- From valj01 at gel.usherb.ca Wed Jun 13 08:06:19 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> Message-ID: <3B27573B.8AA3B69D@gel.usherb.ca> > I still can't install Overflow completely, but most of it seemed to get > installed before the error, so I tried compiling Piper against it. It did > compile, but when I run it, I get an error that it cannot find > libflow-0.5.so. Okay, so if Overflow didn't install completely, then I should > not expect this file to be there. BUT IT IS THERE. I even added the path to > $PATH, but I still get this error. ldconfig doesn't show the lib, and ldd > also says that it is not found. Don't know what to do. I didn't see anything wrong with the Makefile... The problem you had was with the "[l_INCLUDEDIR" on the g++ command line (probably in the "DEFS" Makefile variable) This looks OK in the Makefiles you sent. As for the run-time errors, it's because Overflow finds some .n files twice. It's just a minor warning (everything else should work). Did you define VFLOW_PATH? If so, don't define it. Overflow now knows how to find its toolboxes. If you noved the Overflow install directory, just set VFLOW_HOME to the new base directory (eg /opt/overflow). As for findint libflow, it you ran "make install", it should be found... but you can always set the LD_LIBRARY_PATH (not PATH). Jean-Marc From jeff at bioinformatics.org Wed Jun 13 08:30:50 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> Message-ID: <3B275CFA.933CB17E@bioinformatics.org> Jean-Marc Valin wrote: > > I didn't see anything wrong with the Makefile... The problem you had was with > the "[l_INCLUDEDIR" on the g++ command line (probably in the "DEFS" Makefile > variable) This looks OK in the Makefiles you sent. I don't get it. It should be substituting the defined path at that point. Any idea why not? > As for the run-time errors, it's because Overflow finds some .n files twice. > It's just a minor warning (everything else should work). Did you define > VFLOW_PATH? If so, don't define it. Overflow now knows how to find its > toolboxes. If you noved the Overflow install directory, just set VFLOW_HOME to > the new base directory (eg /opt/overflow). > > As for findint libflow, it you ran "make install", it should be found... but you > can always set the LD_LIBRARY_PATH (not PATH). VFLOW_PATH= no effect VFLOW_HOME=/opt/overflow no effect LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/overflow/lib fixed! Hmm. Strange, it used to work without setting LD_LIB. 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 valj01 at gel.usherb.ca Wed Jun 13 08:39:54 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> Message-ID: <3B275F1A.D9C82523@gel.usherb.ca> > > I didn't see anything wrong with the Makefile... The problem you had was with > > the "[l_INCLUDEDIR" on the g++ command line (probably in the "DEFS" Makefile > > variable) This looks OK in the Makefiles you sent. > > I don't get it. It should be substituting the defined path at that point. > Any idea why not? The only other time I saw that was because libxml wasn't installed and gnome-config returned an error, which means that the variable isn't substitued correctly. The error you have is probably similar. > > > As for the run-time errors, it's because Overflow finds some .n files twice. > > It's just a minor warning (everything else should work). Did you define > > VFLOW_PATH? If so, don't define it. Overflow now knows how to find its > > toolboxes. If you noved the Overflow install directory, just set VFLOW_HOME to > > the new base directory (eg /opt/overflow). > > > > As for findint libflow, it you ran "make install", it should be found... but you > > can always set the LD_LIBRARY_PATH (not PATH). > > VFLOW_PATH= no effect > VFLOW_HOME=/opt/overflow no effect > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/overflow/lib fixed! The LD_LIBRARY_PATH fixed the "error: net SaveAs already existed" type errors? or just the "libflow not found" error? Jean-Marc From jeff at bioinformatics.org Wed Jun 13 08:47:22 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> Message-ID: <3B2760DA.37D7C4FA@bioinformatics.org> Jean-Marc Valin wrote: > > The only other time I saw that was because libxml wasn't installed and > gnome-config returned an error, which means that the variable isn't substitued > correctly. The error you have is probably similar. This is what I have: libxml-devel-1.8.7-0_helix_1 libxml-1.8.7-0_helix_1 libxml10-1.0.0-2 jeff@dexter:jeff> ldconfig -p | grep 'xml' libxmltok.so.0 (libc6) => /usr/lib/libxmltok.so.0 libxmltok.so (libc6) => /usr/lib/libxmltok.so libxmlparse.so.0 (libc6) => /usr/lib/libxmlparse.so.0 libxmlparse.so (libc6) => /usr/lib/libxmlparse.so libxml.so.1 (libc6) => /usr/lib/libxml.so.1 libxml.so.0 (libc6) => /usr/lib/libxml.so.0 libxml.so (libc6) => /usr/lib/libxml.so libwwwxml.so.0 (libc6) => /usr/lib/libwwwxml.so.0 libwwwxml.so (libc6) => /usr/lib/libwwwxml.so > The LD_LIBRARY_PATH fixed the "error: net SaveAs already existed" type errors? > or just the "libflow not found" error? Just the libflow not found. 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 jmvalin at locusdialogue.com Wed Jun 13 09:03:48 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> <3B2760DA.37D7C4FA@bioinformatics.org> Message-ID: <3B2764B4.860800A9@locusdialogue.com> Are you still having problems compiling? If so, could you try to find where the error happens (eg. find where in which makefile an incorrect argument is)? Jean-Marc From jeff at bioinformatics.org Wed Jun 13 19:50:09 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> <3B2760DA.37D7C4FA@bioinformatics.org> <3B2764B4.860800A9@locusdialogue.com> Message-ID: <3B27FC31.4065B119@bioinformatics.org> Jean-Marc Valin wrote: > > Are you still having problems compiling? If so, could you try to find > where the error happens (eg. find where in which makefile an incorrect > argument is)? I did a search through the source, and interestingly, this line shows up in each makefile everywhere: GNOME_XML_INCLUDE = -I/usr/include/gnome-xml EXCEPT for all makefiles in the NNet tree: GNOME_XML_INCLUDE = [l_INCLUDEDIR Perhaps the NNet directory is not configured properly. 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 Wed Jun 13 20:59:00 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> <3B2760DA.37D7C4FA@bioinformatics.org> <3B2764B4.860800A9@locusdialogue.com> <3B27FC31.4065B119@bioinformatics.org> Message-ID: <3B280C54.72A068E7@bioinformatics.org> "J.W. Bizzaro" wrote: > > GNOME_XML_INCLUDE = [l_INCLUDEDIR The same is true for the GNOME_XML_LIB variable, and only in the NNet directory. 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 Wed Jun 13 21:05:03 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> <3B2760DA.37D7C4FA@bioinformatics.org> <3B2764B4.860800A9@locusdialogue.com> <3B27FC31.4065B119@bioinformatics.org> Message-ID: <3B280DBF.DA66380A@bioinformatics.org> I changed them by hand in the NNet tree, and Overflow installs correctly. 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 Wed Jun 13 21:16:03 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] piper name Message-ID: <3B281053.E9477D9F@bioinformatics.org> Jarl, How's the attempt to get the other Piper to change its name on Freshmeat? He's had it there for 2 months, and I think that it is hurting our promotion effort. Maybe we should ask Gary to send him a message. 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 valj01 at gel.usherb.ca Wed Jun 13 22:00:55 2001 From: valj01 at gel.usherb.ca (Jean-Marc Valin) Date: Fri Feb 10 19:20:51 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> <3B2760DA.37D7C4FA@bioinformatics.org> <3B2764B4.860800A9@locusdialogue.com> <3B27FC31.4065B119@bioinformatics.org> <3B280DBF.DA66380A@bioinformatics.org> Message-ID: <3B281AD7.8173967B@gel.usherb.ca> > I changed them by hand in the NNet tree, and Overflow installs correctly. You got me on that one... could you send me the configure script from NNet and the one from HMM (which I assume is OK). Also, are you getting that on a fresh checkout? If so, there must be something special about you installation. What's really strange is that the configure.in's are almost identical. Jean-Marc From jeff at bioinformatics.org Thu Jun 14 05:54:43 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:52 2006 Subject: [Pipet Devel] domains Message-ID: <3B2889E3.87188E61@bioinformatics.org> Pipers, I registered 2 domains for Piper: pipernet.org pipernet.net (piper.* are taken), to be used largely for Piper itself and for network standards -- "Piper Network Consortium" or whatever. 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 Thu Jun 14 06:19:27 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:52 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> <3B2760DA.37D7C4FA@bioinformatics.org> <3B2764B4.860800A9@locusdialogue.com> <3B27FC31.4065B119@bioinformatics.org> <3B280DBF.DA66380A@bioinformatics.org> <3B281AD7.8173967B@gel.usherb.ca> Message-ID: <3B288FAF.E6F596D3@bioinformatics.org> Jean-Marc Valin wrote: > > You got me on that one... could you send me the configure script from NNet and > the one from HMM (which I assume is OK). Also, are you getting that on a fresh > checkout? If so, there must be something special about you installation. What's > really strange is that the configure.in's are almost identical. -------------- next part -------------- From jeff at bioinformatics.org Thu Jun 14 06:28:45 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:52 2006 Subject: [Pipet Devel] runtime errors References: <3B273920.81953DC0@bioinformatics.org> <3B27573B.8AA3B69D@gel.usherb.ca> <3B275CFA.933CB17E@bioinformatics.org> <3B275F1A.D9C82523@gel.usherb.ca> <3B2760DA.37D7C4FA@bioinformatics.org> <3B2764B4.860800A9@locusdialogue.com> <3B27FC31.4065B119@bioinformatics.org> <3B280DBF.DA66380A@bioinformatics.org> <3B281AD7.8173967B@gel.usherb.ca> Message-ID: <3B2891DD.486C1A99@bioinformatics.org> Jean-Marc Valin wrote: > > Also, are you getting that on a fresh checkout? It was a fresh checkout/first build on June 10. I should try it again sometime, but I did get it installed by hand and working. 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 18 09:27:09 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:52 2006 Subject: [Pipet Devel] GCC 3.0 - GNU Project - Free Software Foundation (FSF) Message-ID: <3B2E01AD.AC7AB857@bioinformatics.org> http://gcc.gnu.org/gcc-3.0/gcc-3.0.html Jeff From jmvalin at locusdialogue.com Mon Jun 18 11:03:27 2001 From: jmvalin at locusdialogue.com (Jean-Marc Valin) Date: Fri Feb 10 19:20:52 2006 Subject: [Pipet Devel] GCC 3.0 - GNU Project - Free Software Foundation (FSF) References: <3B2E01AD.AC7AB857@bioinformatics.org> Message-ID: <3B2E183F.A3D654CA@locusdialogue.com> > http://gcc.gnu.org/gcc-3.0/gcc-3.0.html Last time I checked, Overflow was gcc3-ready. I'm going to re-check now that the real thing is released. Jean-Marc From jeff at bioinformatics.org Fri Jun 22 12:09:51 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri Feb 10 19:20:52 2006 Subject: [Pipet Devel] name Message-ID: <3B336DCF.697B25EF@bioinformatics.org> Greetings, Pipers! The person who registered the name Piper at SourceForge has kindly agreed to let us use it instead. We'll have the name and a link to our website, plus we can post news there, which will garner us more attention than at most other places. I'll let you know when it is ready. Also, what is happening with the project at Freshmeat? Jarl, are you still here? I'm thinking that we could also announce "PiperNet" (our standards project) at Freshmeat. Thoughts/comments? 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 --