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From: SourceForge.net <no...@so...> - 2007-08-04 18:08:01
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Feature Requests item #1741291, was opened at 2007-06-21 22:48 Message generated for change (Comment added) made by fbergmann You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486724&aid=1741291&group_id=58157 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Installation Group: None >Status: Pending >Resolution: Postponed >Priority: 2 Private: No Submitted By: Sandeep Srinivasa (sss8ue) >Assigned to: Frank Bergmann (fbergmann) Summary: could we have a mercurial repository Initial Comment: Hi, to hack through the source, it helps to have a revision history. Is it possible to have a mercurial repository, so that it is very easy for any developer to have an entire revision history. I see that the code in the CVS right now does not have a lot of revisions. FYI, it is very trivial to convert from CVS to mercurial (and also to host on sourceforge - http://www.selenic.com/mercurial/wiki/index.cgi/MercurialOnSourceforge) thanks ---------------------------------------------------------------------- >Comment By: Frank Bergmann (fbergmann) Date: 2007-08-04 11:07 Message: Logged In: YES user_id=1059684 Originator: NO truth be told, these days most work is done around SBW modules (http://jdesigner.sf.net) rather than on the framework below. As for mercurial, honestly, i haven't come across it before ... i'll keep it in mind for later, thank you best Frank ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486724&aid=1741291&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2007-06-22 05:48:32
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Feature Requests item #1741291, was opened at 2007-06-22 11:18 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486724&aid=1741291&group_id=58157 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Installation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Sandeep Srinivasa (sss8ue) Assigned to: Nobody/Anonymous (nobody) Summary: could we have a mercurial repository Initial Comment: Hi, to hack through the source, it helps to have a revision history. Is it possible to have a mercurial repository, so that it is very easy for any developer to have an entire revision history. I see that the code in the CVS right now does not have a lot of revisions. FYI, it is very trivial to convert from CVS to mercurial (and also to host on sourceforge - http://www.selenic.com/mercurial/wiki/index.cgi/MercurialOnSourceforge) thanks ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486724&aid=1741291&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2007-06-18 05:42:25
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Bugs item #1738879, was opened at 2007-06-17 22:42 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=1738879&group_id=58157 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: SBW core Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Frank Bergmann (fbergmann) Assigned to: Frank Bergmann (fbergmann) Summary: SBW Java Core - OSX ... Initial Comment: see: https://sourceforge.net/forum/message.php?msg_id=4358642 probably outdated SBWCore-debug.jar ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=1738879&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2004-06-27 17:15:38
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Bugs item #980767, was opened at 2004-06-27 10:15 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=980767&group_id=58157 Category: None Group: None Status: Open Resolution: None Priority: 5 Submitted By: Peter D Wilson (dflora) Assigned to: Nobody/Anonymous (nobody) Summary: Mouse Access Violation on Win2K Initial Comment: After opening various model files, passing the mouse across the graphic display generates an access violation. On other occassions it generates an Invalid Typecast error. Work around.. don't interact withn the diagram, however then one can't access properties via the diagram. Peter D Wilson ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=980767&group_id=58157 |
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From: Michael H. <mh...@ca...> - 2003-08-12 20:54:09
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Just a quick update on recent actions: As some of you no doubt already noticed, I've been restructuring the CVS repository for SBW on SourceForge. The last of the moves should be finished tonight. There are two goals in these moves: (1) moving out SBML-only items into the SBML project, and (2) cleaning up the directory structure a little bit to hopefully make it more logical for other people. The new structure will have two modules in the project, the 'sbw' module (same as now) and the 'project' module (most of what's in sbw/project currently). The manuals for SBW are now living in sbw/docs/src instead of project/docs/sbw/, and a bunch of things are gone from project/docs and moved to the SBML project. I've had the moves done on the CVS server itself by the SF admins, because that's the only way in CVS to maintain the files' revision histories when moving directories. The unfortunate side-effect of this is that when you do your next cvs update on your local sandboxes, it's going to complain about nonexistent directories and other things. The easiest thing to do is simply check out the whole SBW 'sbw' and 'project' modules in a new location, and if you have any changes not checked in, copy the individual files over into the new locations and then check them in. Sorry for the extra work, but this will make things better in the long run. MH |
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From: SourceForge.net <no...@so...> - 2003-08-12 02:08:27
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Bugs item #699096, was opened at 2003-03-06 16:43 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=699096&group_id=58157 Category: SBW core Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: BrokerShutdown is no longer needed Initial Comment: The BrokerShutdown module is not actually needed, since one can run the SBWBroker.jar with the --shutdown option to accomplish the same thing. It might be best to remove this module to avoid confusing people. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-08-11 18:59 Message: Logged In: YES user_id=343670 Removed from the latest version in CVS. Moved it to src/sbw/tests ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=699096&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-08-09 04:06:10
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Bugs item #690457, was opened at 2003-02-20 19:12 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=690457&group_id=58157 Category: SBW core Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: java-module-actions.mk should not do same actions as core Initial Comment: The actions of java-module-actions.mk for the javadoc portion are basically the same as for the SBW core, but they shouldn't be. They should reflect the fact that a module is being javadoc'ed rather than an SBW core library. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-08-08 21:06 Message: Logged In: YES user_id=343670 This iwsn't worth it. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=690457&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-08-09 04:04:48
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Bugs item #627259, was opened at 2002-10-22 21:00 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=627259&group_id=58157 Category: SBW documentation Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Michael Hucka (mhucka) >Assigned to: Michael Hucka (mhucka) Summary: intro.pdf out of date Initial Comment: Ben Kovitz reported that the docs/user/intro.pdf document is out of date and describes things that are no longer true of SBW. Intro.pdf needs to be updated. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-08-08 21:04 Message: Logged In: YES user_id=343670 I've updated the document finally. The latest version is in CVS. It will be included in the next release. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=627259&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-08-06 02:08:00
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Bugs item #690458, was opened at 2003-02-20 19:13 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=690458&group_id=58157 Category: SBW core Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Michael Hucka (mhucka) Assigned to: Nobody/Anonymous (nobody) Summary: Python library should remove .tmp files Initial Comment: The python library does not properly clean up its .tmp files in all cases. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-08-05 19:08 Message: Logged In: YES user_id=343670 Ben Kovitz implemented the necessary changes recently. This still needs to be tested, especially on windows. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=690458&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-08-05 22:36:41
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Bugs item #627258, was opened at 2002-10-22 20:59 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=627258&group_id=58157 Category: SBW documentation Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: Font problems in PDF docs under Windows Initial Comment: Ben Kovitz reported that some of the PDF documents (notably docs/user/modules.pdf) exhibit font problems under Acrobat on even the most recent Windows OS. It appears that maybe the Courier font were not included in the document when the PDF was generated, leading to bad font substitutions at the client end. The fix is to rexamine the generation of the PDF files and make sure proper font subsetting is done. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-08-05 15:36 Message: Logged In: YES user_id=343670 This should be fixed now and the new versions of the PDFs shouldn't have this problem. I changed the cek*.cls style files to avoid using the font that was causing the problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=627258&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-08-05 19:03:41
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Bugs item #783683, was opened at 2003-08-05 15:03 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=783683&group_id=58157 Category: None Group: None Status: Open Resolution: None Priority: 5 Submitted By: Jeremy Zucker (topramen) Assigned to: Nobody/Anonymous (nobody) Summary: BSOD upon sbw-1.0.5-win-full install Initial Comment: Hello there, I tried to install SBW-1.0.5-win-full on my vanilla windows 2000 pro laptop. I previously installed Java 1.4.2 successfully. When I tried to install SBW, I got the Blue Screen of Death just as it finished installing, and then it rebooted. The message flashed by pretty quickly, but it said something like: "Memory dump" When the desktop came up, Systems Biology Workbench was not installed on the system... When I repeated the install, I got BSOD again with the same error message, but this time, the Systems Biology Workbench did install when the desktop came up. Anyone else encountered weirdness like this before? I am on a Dell Latitude 610c. I can try repeating the install to get the complete BSOD message, but at this point, SBW works, so I'll let it go for now. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=783683&group_id=58157 |
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From: Eula C. <dza...@ya...> - 2003-06-07 12:17:13
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From: Darius H. <573...@ao...> - 2003-05-29 17:37:23
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From: Mike H. <mh...@ca...> - 2003-04-20 07:01:20
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Dear SBW enthusiasts, SBW version 1.0.5 is now available for downloading from http://www.sbw-sbml.org. Most of the changes in this incremental release are minor bug fixes, but there is one new module that should be interesting to everyone: a spiffy new SBW Browser module written by Ben Kovitz. This module provides the ability to browse the SBW environment on a local host, inspect the modules and services available (much as Herbert Sauro's SBW Inspector for Windows does), and generate interface descriptions in different formats. It is portable to all architectures that SBW supports or will support in the future. Please try it out and let Ben know your comments. We are planning several feature enhancements to the SBW Browser in the near future. sys...@ca... |
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From: SourceForge.net <no...@so...> - 2003-04-19 00:38:34
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Bugs item #668879, was opened at 2003-01-15 19:10 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=668879&group_id=58157 Category: SBW standard modules Group: v1.0 >Status: Closed >Resolution: Wont Fix Priority: 4 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: Deprecation warnings in SimDriver under JDK 1.4 Initial Comment: When compiling the debugging version of the SimDriver module, the following deprecation warnings are reported: "/usr/local/java/jdk1.4.1_01/bin/javac" -g -deprecation -classpath "../../../sbw/lib/Java/SBWCore-debug.jar:../../../imported/grace/grace.jar:../../../imported/gnu-regexp/gnu-regexp.jar:../../../imported/cup/java-cup-runtime.jar:../../../imported/junit/junit.jar" edu/caltech/sbw/analyses/*.java edu/caltech/sbw/components/*.java edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:585: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated startTimeField.setNextFocusableComponent(endTimeField); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:586: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated endTimeField.setNextFocusableComponent(numberOfPointsField); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:587: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated numberOfPointsField.setNextFocusableComponent(outputVariablesList); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:588: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated outputVariablesList.setNextFocusableComponent(hiddenVariablesList); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:589: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated hiddenVariablesList.setNextFocusableComponent(outputVariablesButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:590: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated outputVariablesButton.setNextFocusableComponent(hideVariablesButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:591: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated startButton.setNextFocusableComponent(stopButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:592: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated stopButton.setNextFocusableComponent(pauseButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:593: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated pauseButton.setNextFocusableComponent(restartButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:597: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated restartButton.setNextFocusableComponent(SteadyStateButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:601: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated SteadyStateButton.setNextFocusableComponent(MCAButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:606: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated restartButton.setNextFocusableComponent(MCAButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:609: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated optionsButton.setNextFocusableComponent(closeButton); ^ edu/caltech/sbw/analyses/TimeBasedAnalysisFrame.java:610: warning: setNextFocusableComponent(java.awt.Component) in javax.swing.JComponent has been deprecated closeButton.setNextFocusableComponent(startTimeField); ^ 14 warnings ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-04-18 17:38 Message: Logged In: YES user_id=343670 The SimDriver is being rewritten anyway, so this isn't worth fixing in the implementation. I fixed the makefile so that it didn't compile with -deprecation turned on, thus quieting the messages. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=668879&group_id=58157 |
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From: Michael H. <mh...@ca...> - 2003-04-18 17:55:05
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>>>>> On 18 Apr 2003, Herbert Sauro <Her...@kg...> wrote:
Herbert_Sauro> Caltech have for some reason changed my
Herbert_Sauro> static ip address on my cvs
Herbert_Sauro> repository. Does anyone know how to change
Herbert_Sauro> all the root files in the cvs directories
Herbert_Sauro> for my projects? At the moment I'm having
Herbert_Sauro> to edit them by hand (I don't have a domain
Herbert_Sauro> name) to the new ip address?
By root files, you mean the files 'Root' in each of the CVS
directories? The ones that contain lines like
:ext:mh...@cv...:/cvsroot/sbw
?
The only way I know to do this is using a combination of
unix shell commands. But first, it's not clear to me why
you have the >IP address< in there. Can you not obtain a
host name for the server? Symbolic names will of course
insulate you from changes to IP addresses. (Or is this your
machine at home?)
Anyway, here's a set of csh commands that ought to do it.
Start this from the top-most directory of your repository:
foreach f (`find . -name Root`)
sed -e 's/OLDIPADDRESS/NEWIPADDRESS/g' < $f > $f.new
/bin/mv $f.new $f
end
This is csh syntax and won't work in bash (which is probably
your default shell, so watch out).
MH
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From: Herbert S. <Her...@kg...> - 2003-04-18 17:33:53
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Caltech have for some reason changed my static ip address on my cvs repository. Does anyone know how to change all the root files in the cvs directories for my projects? At the moment I'm having to edit them by hand (I don't have a domain name) to the new ip address? Herbert ---------------------------------------------------------- There are only three kinds of people in this world; those that can count, and those that can't. If God meant us to use unicode, He would have put 16 bits in a byte.= Marcus Urban. Dr Herbert M Sauro Keck Graduate Institute 535 Watson Drive Claremont CA, 91711 Tel: USA 1-909-607-0377 Email : hs...@kg... <mailto:hs...@kg...> Web: www.sys-bio.org <http://www.sys-bio.org> |
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From: SourceForge.net <no...@so...> - 2003-04-18 04:37:31
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Bugs item #689767, was opened at 2003-02-19 18:19 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=689767&group_id=58157 Category: SBW core Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: Python data passing is broken Initial Comment: As discovered by Herbert: The python library interface is broken in 1.0.3. Attempting to pass arguments to methods seems to fail. It may or may not be limited to array arguments. Test case: Either write a small test module to accept an array, eg 2D array or use the current version of Jarnac, it contains a small matrix service for computing eigenvalues. Try the following from Python: import Numeric m = Numeric.array(([1.2, 3.4], [5.6, 8.9])) Jarnac.mat.getEigenValues (m) Should get something like this, actuall values depend on input matrix. array([[ 6.0425695, -0.3425695], [ 0. , 0. ]]) >>> But sbwpython in 1.0.3 returns an error. It works fine in 1.0.2. Tested under windows. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-04-17 21:37 Message: Logged In: YES user_id=343670 Seems to be fixed now. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=689767&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-04-17 05:13:21
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Bugs item #698643, was opened at 2003-03-06 03:25 Message generated for change (Settings changed) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=698643&group_id=58157 Category: SBW standard modules >Group: v1.0 Status: Open Resolution: None >Priority: 9 Submitted By: Henning Schmidt (henning71) >Assigned to: Michael Hucka (mhucka) Summary: NOM service not found Initial Comment: I run Windows 2000. And installed SBW using the newest release available just now (6/3/2003). Whenever I start a program (JDesigner or Jarnac or ...) they print out the message "Warning: Failed to create NOM object: NOM service not found". What is it what I did wrong during installation? Search on the web did not show any results solving the problem. Thanks, /Henning ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=698643&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-04-17 05:08:23
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Bugs item #650942, was opened at 2002-12-09 08:15 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=650942&group_id=58157 Category: SBW standard modules Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Balbir Thomas (balbirthomas) Assigned to: Michael Hucka (mhucka) Summary: SBML to Matlab ODE translation error Initial Comment: Dear Sir I recently installed SBW (version 1.0.2) along with Jarnac (version 2.0 beta build #15 ) and JDesigner (version 1.7 ) . While I am able to make and simulate models in JDesigner but trying to convert the SBML models into a Matlab ODE throws and error. The complete error message is attached in file errors.txt. This occurs for even the sample models such as oscil.xml provide with the JDesigner installation. Further trying to validate oscil.xml with SBMLvalidator gives the following error : Error in validating SBML file: [oscli.xml] Reason: Element content is invalid according to the DTD/Schema. Expecting: {http://www.sbml.org/sbml/level1}model. at char 17 of line 4 Text of file <annotations> Please note I do have the file sbml.xsd in the required location : file:/C:/Program Files/ERATO/modules/sbml.xsd I have written to Prof Sauro and he suggested that this is probably a problem with the SBW installation so I am submitting this as a bug here. I would be grateful if you could let me know how I may fix this. sincerely B Thomas ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-04-16 22:08 Message: Logged In: YES user_id=343670 This was caused by the same problem as bug #713619. The validator assumed that the pathname to the schema file did not contain spaces, and installations into \Program Files\ERATO screwed things up. ---------------------------------------------------------------------- Comment By: Chris Wassman (cwassman) Date: 2003-02-25 16:11 Message: Logged In: YES user_id=193359 Possibly related issue. I found that the sbml.xsd file in: sbw-1.0.3/src/modules/MatlabTranslator does not work with the SBMLValidator. In order to get the validator to work you must use the sbml.xsd file found in the modules/Validator/src directory. Anyhow the error I get when I used the wrong sbml.xsd [from linux command prompt] looks like this: [Validation failed] Error parsing SBML [Error] matlabtest.xml:3:68: General Schema Error: Schema in file:/tmp/sbw-1.0.3/src/modules/Validator/src/sbml.xsd has a different target namespace from the one specified in the instance document :http://www.sbml.org/sbml/level1. which looks quite similar to this issue. I suggest you ensure you have the correct sbml.xsd file. Cheers, Chris ---------------------------------------------------------------------- Comment By: Michael Hucka (mhucka) Date: 2003-01-02 19:01 Message: Logged In: YES user_id=343670 After some private email exchanges, we determined that this problem actually arose because SBW had been installed into C:\Program FIles\... Apparently there is a pathname parsing problem somewhere in the sbml-matlab translator that causes it to fail to work properly when SBW's installation directory path has a space in it. (or perhaps the dependency is on being installed in C:\ERATO). I'm going to file this as a bug. ---------------------------------------------------------------------- Comment By: Michael Hucka (mhucka) Date: 2002-12-20 12:50 Message: Logged In: YES user_id=343670 We have not been able to reproduce this. It may be an installation problem, but other installations seem to work properly, so it is difficult to know what may be going on here. Can you try one thing for us? Could you uninstall SBW (make sure to stop the broker first before doing this) and then install SBW in C:/ERATO (or any pathname that does not have a space in it the way that C:/Program Files/... does). This is the only thing that I can think of that might be involved here. The code is designed to work with any pathname, but it's possible there's still a bug somewhere involving this. By the way, what version of Java do you have installed? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=650942&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-04-17 04:59:04
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Bugs item #713619, was opened at 2003-04-01 16:13 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=713619&group_id=58157 Category: SBW core Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: Installation path must not have spaces Initial Comment: apparently there's some dependency somewhere (possibly in the installer, possibly in the scripts for SBW) that causes installations on Windows to fail if the chosen installation directory has spaces in the name (like "Program Files"). This was fixed at one time, and seems to have crept back. We need to track down the problem code and fix it. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-04-16 21:59 Message: Logged In: YES user_id=343670 There were multiple problems. The createbrokerstart.bat script had an error in pathname quoting that caused it to create a file called "C:\Program" on Windows if you installed into something like C:\Program Files\ERATO. A worse problem existed in the SBML validator module. It constructed a pathname for the XML Schema file that it handed to Xerces, but the pathname contained spaces and screwed things up. It is not valid to have a URL/URI with spaces in the name, so this needed a different fix. I've decided to start putting the SBML schema file into C:\Windows on Windows. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=713619&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-04-16 03:49:27
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Bugs item #722252, was opened at 2003-04-15 20:10 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=722252&group_id=58157 Category: SBW standard modules Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: Gibson doesn't build on Red Hat 8.0 Initial Comment: g++ -Wall -O2 -DLINUX -D_GNU_SOURCE -I../../sbw/lib/CPP -c SecondOrderReaction.cpp -o Release/SecondOrderReaction.o SecondOrderReaction.cpp: In member function `virtual float SecondOrderReaction::NextTime(CellState*)': SecondOrderReaction.cpp:40: choosing `double pow(double, double)' over `float std::pow(float, float)' SecondOrderReaction.cpp:40: because worst conversion for the former is better than worst conversion for the latter SecondOrderReaction.cpp:40: choosing `double pow(double, double)' over `float std::pow(float, int)' SecondOrderReaction.cpp:40: because worst conversion for the former is better than worst conversion for the latter make[3]: *** [Release/SecondOrderReaction.o] Error 1 make[3]: Leaving directory `/home/mhucka/sbw-1.0.3/src/modules/Gibson' make[2]: *** [default] Error 2 make[2]: Leaving directory `/home/mhucka/sbw-1.0.3/src/modules/Gibson' ---------------------------------------------------------------------- Comment By: Michael Hucka (mhucka) Date: 2003-04-15 21:06 Message: Logged In: YES user_id=343670 This should be fixed by changes recently checked into CVS. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=722252&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-04-16 02:53:45
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Bugs item #722252, was opened at 2003-04-15 20:10 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=722252&group_id=58157 Category: SBW standard modules Group: v1.0 Status: Open Resolution: None Priority: 9 Submitted By: Michael Hucka (mhucka) Assigned to: Michael Hucka (mhucka) Summary: Gibson doesn't build on Red Hat 8.0 Initial Comment: g++ -Wall -O2 -DLINUX -D_GNU_SOURCE -I../../sbw/lib/CPP -c SecondOrderReaction.cpp -o Release/SecondOrderReaction.o SecondOrderReaction.cpp: In member function `virtual float SecondOrderReaction::NextTime(CellState*)': SecondOrderReaction.cpp:40: choosing `double pow(double, double)' over `float std::pow(float, float)' SecondOrderReaction.cpp:40: because worst conversion for the former is better than worst conversion for the latter SecondOrderReaction.cpp:40: choosing `double pow(double, double)' over `float std::pow(float, int)' SecondOrderReaction.cpp:40: because worst conversion for the former is better than worst conversion for the latter make[3]: *** [Release/SecondOrderReaction.o] Error 1 make[3]: Leaving directory `/home/mhucka/sbw-1.0.3/src/modules/Gibson' make[2]: *** [default] Error 2 make[2]: Leaving directory `/home/mhucka/sbw-1.0.3/src/modules/Gibson' ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=722252&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-04-16 02:52:14
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Bugs item #678225, was opened at 2003-01-31 09:09 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=678225&group_id=58157 Category: None >Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Andrew Finney (afinney) >Assigned to: Michael Hucka (mhucka) >Summary: Java Client Lib. Excep. when no "." in module id name Initial Comment: discovered by stephen ramsey as follows: I have written a sample SBW module and client program to access the module through the SBW "Broker". However, I'm noticing something strange when I attempt to run the "module". When I instantiate a ModuleImpl class with the following arguments, -------------------------------------------------------------------------- // NOTE-- no package name specified here public class MainRobustRand { public static void main(String []pArgs) { try { // some code omitted my modImpl = new ModuleImpl("math"); // this throws a run-time exception // some code omitted } } } -------------------------------------------------------------------------- I get the following run-time exception: -------------------------------------------------------------------------- Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1 at java.lang.String.substring(String.java:1480) at edu.caltech.sbw.ModuleImpl.modulePackageName (ModuleImpl.java:907) at edu.caltech.sbw.ModuleImpl.<init> (ModuleImpl.java:354) at MainRobustRand.main(MainRobustRand.java:9) -------------------------------------------------------------------------- Following the stack backtrace, this exception seems to come from the fact that in your implementation of the ModuleImpl class, you have the following code: -------------------------------------------------------------------------- private String modulePackageName() { StackTrace trace = new StackTrace(2 + Config.getStackDepthOffset()); String className = trace.getClassname(); return className.substring(0, className.lastIndexOf('.')); } -------------------------------------------------------------------------- Now, if className does not contain a period character, then the return value of "lastIndexOf" will be the integer "-1", which will cause the "substring" method to throw an exception ---------------------------------------------------------------------- Comment By: Michael Hucka (mhucka) Date: 2003-04-15 20:09 Message: Logged In: YES user_id=343670 This should be fixed by changes recently checked into CVS. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=678225&group_id=58157 |
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From: SourceForge.net <no...@so...> - 2003-04-12 01:28:40
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Bugs item #708296, was opened at 2003-03-23 01:25 Message generated for change (Comment added) made by mhucka You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=708296&group_id=58157 Category: SBW core >Group: v1.0 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Joerg R. Weimar (weimar) Assigned to: Michael Hucka (mhucka) Summary: Fix for Linux installation problem Initial Comment: The linux installlation of sbw1.0.3 had the follwing problem: in many cases starting a service failed with the message that no main class was found in the maanifest. The problem comes form th efact that some jars have teir own META-INF/MANIFEST file, and jar does not delete these to create a new one. FIX: insert the follwing lines at line 316 of sbw-1.0.3/src/scripts/sbw-make-jar and remake all jar files. # Added by Jörg R. Weimar (jw...@jw...): # delete META-INF/MANIFEST files from the other packages we unpacked. /bin/rm -rf META-INF # Create the jar file. ---------------------------------------------------------------------- >Comment By: Michael Hucka (mhucka) Date: 2003-04-11 18:45 Message: Logged In: YES user_id=343670 I've tried to find a specific instance where this happens, and none of the jar files that I've seen seem to include old manifest files. However, I don't see anything wrong with doing this cleanup step and obviously it must affect your (J. Weimar's) installation, so let's put this in. It's in the version checked into CVS and will be in the next release. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=486721&aid=708296&group_id=58157 |
