Re: [cellml-discussion] CellML2Dot
Okay thanks, I'm going to put this on the backburner for a few days and get fixing some more models. More later. James David Nickerson wrote: > PS - as you go through this if you can think of anything that would make > the process easier for you can you please file them under the tracker at > http://sourceforge.net/projects/cellml, thanks! > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML2Dot
PS - as you go through this if you can think of anything that would make the process easier for you can you please file them under the tracker at http://sourceforge.net/projects/cellml, thanks! ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML2Dot
> I ran cmake -i (wizard mode) and it gave the following output: > > "[EMAIL PROTECTED]:~/usr/CellML2Dot$ cmake -i > Would you like to see advanced options? [No]:no > Please wait while cmake processes CMakeLists.txt files > > CMake Error: Error in cmake code at > /people/jlaw060/usr/CellML2Dot/FindCellML.cmake:67: > MESSAGE Could not find CellML this very descriptive message is saying that it can't find the CellML API library and include files. If you look in the BUILD file it gives an example of how to make a debug and/or release (optimised) version of CellML2Dot - you need to set the CMAKE_INCLUDE_PATH and CMAKE_LIBRARY_PATH to point to where you have the CellML API installed. Alternatively, you can use the wizard to manually enter CELLML_INCLUDE_DIR and CELLML_LIBRARY. > Current CMake stack: > /people/jlaw060/usr/CellML2Dot/CMakeLists.txt;/usr/share/CMake/Modules/CMakeCInformation.cmake;/usr/share/CMake/Modules/CMakeCXXInformation.cmake;/people/jlaw060/usr/CellML2Dot/FindCellML.cmake > > > Variable Name: CELLML_INCLUDE_DIR > Description: Path to a file. > Current Value: CELLML_INCLUDE_DIR-NOTFOUND > New Value (Enter to keep current value): > > Variable Name: CELLML_LIBRARY > Description: Path to a library. > Current Value: CELLML_LIBRARY-NOTFOUND > New Value (Enter to keep current value): > > Variable Name: CMAKE_BACKWARDS_COMPATIBILITY > Description: For backwards compatibility, what version of CMake commands > and syntax should this version of CMake allow. > Current Value: 2.4 > New Value (Enter to keep current value): > > Variable Name: CMAKE_BUILD_TYPE > Description: Choose the type of build, options are: None(CMAKE_CXX_FLAGS > or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel. > Current Value: > New Value (Enter to keep current value): > > Variable Name: CMAKE_INSTALL_PREFIX > Description: Install path prefix, prepended onto install directories. > Current Value: /usr/local > New Value (Enter to keep current value): > > Variable Name: EXECUTABLE_OUTPUT_PATH > Description: Single output directory for building all executables. > Current Value: > New Value (Enter to keep current value): > > Variable Name: LIBRARY_OUTPUT_PATH > Description: Single output directory for building all libraries. > Current Value: > New Value (Enter to keep current value): > > Please wait while cmake processes CMakeLists.txt files > " > > David Nickerson wrote: >> Hi James, >> >> James Lawson wrote: >>> Hi Andre, >>> >>> In the workshop you showed us a slide of a program you'd made for >>> debugging models that showed all the connections etc. Is this that >>> program? I tried to get the source off subversion but it didn't work. Do >>> you have any tips on getting this tool to work? >> do you mean that you were unable to get the source out of the >> SourceForge subversion server or that you were unable to build it? I >> just checked the command on the cellml.sourceforge.net page (svn >> checkout >> https://cellml.svn.sourceforge.net/svnroot/cellml/CellML2Dot/trunk >> CellML2Dot) and it worked fine for me. >> >> If its building thats causing grief, then its probably one of the many >> dependencies that is missing. Hopefully the cmake process will tell you >> what it can't find, otherwise I really need to get around to writing >> some documentation >> >> oh, and yes, that is that program :) >> >> >> Andre. >> ___ >> cellml-discussion mailing list >> cellml-discussion@cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion > > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML2Dot
Okay, Andrew helped me sort the subversion issue out, it was hitting the firewall. Perhaps if I can figure out how to install it then we might be able to help other Linux novice types. I ran cmake -i (wizard mode) and it gave the following output: "[EMAIL PROTECTED]:~/usr/CellML2Dot$ cmake -i Would you like to see advanced options? [No]:no Please wait while cmake processes CMakeLists.txt files CMake Error: Error in cmake code at /people/jlaw060/usr/CellML2Dot/FindCellML.cmake:67: MESSAGE Could not find CellML Current CMake stack: /people/jlaw060/usr/CellML2Dot/CMakeLists.txt;/usr/share/CMake/Modules/CMakeCInformation.cmake;/usr/share/CMake/Modules/CMakeCXXInformation.cmake;/people/jlaw060/usr/CellML2Dot/FindCellML.cmake Variable Name: CELLML_INCLUDE_DIR Description: Path to a file. Current Value: CELLML_INCLUDE_DIR-NOTFOUND New Value (Enter to keep current value): Variable Name: CELLML_LIBRARY Description: Path to a library. Current Value: CELLML_LIBRARY-NOTFOUND New Value (Enter to keep current value): Variable Name: CMAKE_BACKWARDS_COMPATIBILITY Description: For backwards compatibility, what version of CMake commands and syntax should this version of CMake allow. Current Value: 2.4 New Value (Enter to keep current value): Variable Name: CMAKE_BUILD_TYPE Description: Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel. Current Value: New Value (Enter to keep current value): Variable Name: CMAKE_INSTALL_PREFIX Description: Install path prefix, prepended onto install directories. Current Value: /usr/local New Value (Enter to keep current value): Variable Name: EXECUTABLE_OUTPUT_PATH Description: Single output directory for building all executables. Current Value: New Value (Enter to keep current value): Variable Name: LIBRARY_OUTPUT_PATH Description: Single output directory for building all libraries. Current Value: New Value (Enter to keep current value): Please wait while cmake processes CMakeLists.txt files " David Nickerson wrote: > Hi James, > > James Lawson wrote: >> Hi Andre, >> >> In the workshop you showed us a slide of a program you'd made for >> debugging models that showed all the connections etc. Is this that >> program? I tried to get the source off subversion but it didn't work. Do >> you have any tips on getting this tool to work? > > do you mean that you were unable to get the source out of the > SourceForge subversion server or that you were unable to build it? I > just checked the command on the cellml.sourceforge.net page (svn > checkout > https://cellml.svn.sourceforge.net/svnroot/cellml/CellML2Dot/trunk > CellML2Dot) and it worked fine for me. > > If its building thats causing grief, then its probably one of the many > dependencies that is missing. Hopefully the cmake process will tell you > what it can't find, otherwise I really need to get around to writing > some documentation > > oh, and yes, that is that program :) > > > Andre. > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML2Dot
>>> In the workshop you showed us a slide of a program you'd made for >>> debugging models that showed all the connections etc. Is this that >>> program? I tried to get the source off subversion but it didn't work. Do >>> you have any tips on getting this tool to work? >> do you mean that you were unable to get the source out of the >> SourceForge subversion server or that you were unable to build it? I >> just checked the command on the cellml.sourceforge.net page (svn >> checkout >> https://cellml.svn.sourceforge.net/svnroot/cellml/CellML2Dot/trunk >> CellML2Dot) and it worked fine for me. >> > > That's what I ran in my console. Perhaps I don't have the permission or > something. It said it couldn't connect to the server. Here's what I got: > > "[EMAIL PROTECTED]:~$ svn checkout > https://cellml.svn.sourceforge.net/svnroot/cellml/CellML2Dot/trunkCellML2Dot > svn: PROPFIND request failed on '/svnroot/cellml/CellML2Dot/trunkCellML2Dot' > svn: PROPFIND of '/svnroot/cellml/CellML2Dot/trunkCellML2Dot': could not > connect to server (https://cellml.svn.sourceforge.net) > [EMAIL PROTECTED]:~$" ok - I think that because you are behind the University firewall you cannot access the subversion server directly, although using https you should be able to get access through the institue's proxy server but I'm not sure how to set that up... >> If its building thats causing grief, then its probably one of the many >> dependencies that is missing. Hopefully the cmake process will tell you >> what it can't find, otherwise I really need to get around to writing >> some documentation > > Uhh.. I'm not really super familiar with Linux.. What is cmake and how > might I use it? hmyou might have a bit of trouble building CellML2Dot as there is very little documentation ;-) cmake is a new style configuration and build system which seems to be gaining popularity over older more traditional multiplatform build systems. If you manage to check out the source code there is a bit of documentation telling you how to build CellML2Dot, but you'll probably find that it keeps telling you all the bits you are missing and you'll have to install them. Come to think of it, I think the CellML API is the only non-standard software required so it might not be that bad. > Great, it looked really useful. I've been looking for a way to visualise > connections better than PCEnv. Perhaps, actually, it could be integrated > into PCEnv, as an extension or something, or at least the concept. Thanks. Andre. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML2Dot
David Nickerson wrote: > Hi James, > > James Lawson wrote: >> Hi Andre, >> >> In the workshop you showed us a slide of a program you'd made for >> debugging models that showed all the connections etc. Is this that >> program? I tried to get the source off subversion but it didn't work. Do >> you have any tips on getting this tool to work? > > do you mean that you were unable to get the source out of the > SourceForge subversion server or that you were unable to build it? I > just checked the command on the cellml.sourceforge.net page (svn > checkout > https://cellml.svn.sourceforge.net/svnroot/cellml/CellML2Dot/trunk > CellML2Dot) and it worked fine for me. > That's what I ran in my console. Perhaps I don't have the permission or something. It said it couldn't connect to the server. Here's what I got: "[EMAIL PROTECTED]:~$ svn checkout https://cellml.svn.sourceforge.net/svnroot/cellml/CellML2Dot/trunkCellML2Dot svn: PROPFIND request failed on '/svnroot/cellml/CellML2Dot/trunkCellML2Dot' svn: PROPFIND of '/svnroot/cellml/CellML2Dot/trunkCellML2Dot': could not connect to server (https://cellml.svn.sourceforge.net) [EMAIL PROTECTED]:~$" > If its building thats causing grief, then its probably one of the many > dependencies that is missing. Hopefully the cmake process will tell you > what it can't find, otherwise I really need to get around to writing > some documentation Uhh.. I'm not really super familiar with Linux.. What is cmake and how might I use it? > > oh, and yes, that is that program :) > Great, it looked really useful. I've been looking for a way to visualise connections better than PCEnv. Perhaps, actually, it could be integrated into PCEnv, as an extension or something, or at least the concept. Thanks, James > > Andre. > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML2Dot
Hi James, James Lawson wrote: > Hi Andre, > > In the workshop you showed us a slide of a program you'd made for > debugging models that showed all the connections etc. Is this that > program? I tried to get the source off subversion but it didn't work. Do > you have any tips on getting this tool to work? do you mean that you were unable to get the source out of the SourceForge subversion server or that you were unable to build it? I just checked the command on the cellml.sourceforge.net page (svn checkout https://cellml.svn.sourceforge.net/svnroot/cellml/CellML2Dot/trunk CellML2Dot) and it worked fine for me. If its building thats causing grief, then its probably one of the many dependencies that is missing. Hopefully the cmake process will tell you what it can't find, otherwise I really need to get around to writing some documentation oh, and yes, that is that program :) Andre. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] CellML2Dot
Hi Andre, In the workshop you showed us a slide of a program you'd made for debugging models that showed all the connections etc. Is this that program? I tried to get the source off subversion but it didn't work. Do you have any tips on getting this tool to work? Thanks, James ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Draft graphing metadata specification updated
Regarding the example at: http://www.cellml.org/news_items/draft-graphing-metadata-specification-updated I'm quite new to RDF. I haven't had success producing the RDF-graph for this example, but I would be interested in seeing it. Perhaps posting a snapshot of the RDF-graph would be helpful, to others too. Also, is there a description of what the symbols used in the data-model (http://www.cellml.org/specifications/metadata/graphs/graph_data_rdf_graph-02.png) mean, or is it an informal diagram? ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML tracker
> >> > > I don't know of any per-issue subscription feature in PCNG, and a web > > search didn't seem to find anything about this. > > > > Perhaps you have details about this? > > hI guess I was getting a bit confused about the subscription > ability with plone on, for example, wiki pages. I'd thought someone once > told me that could be used on other items as well (such as tracker > issues) but I can't find anything at the moment Poi has it. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
