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Hi Alan,

Thanks very much for all your help, though. It's nice to know that the sdk
is visible in my java environment, even if the particular model call seems
to not be working. As you say, hopefully Andrew or someone with similar
knowledge will be able to help me in this next bit.

thanks,
Allyson

On 9 June 2011 14:44, Alan Garny <alan.garny at dpag.ox.ac.uk> wrote:

> Hi Allyson,
>
>
>
> Sorry, but I can?t help you further. My current knowledge of the SDK is
> limited to the fact that I know it exists. I am going to use it, but I have
> yet to make a move in that direction. I would expect Andrew Miller to be the
> best person to help you with your issue, so hopefully he will soon get back
> to you.
>
>
>
> Alan
>
>
>
> *From:* cellml-tools-developers-bounces at cellml.org [mailto:
> cellml-tools-developers-bounces at cellml.org] *On Behalf Of *Allyson Lister
> *Sent:* 09 June 2011 14:35
>
> *To:* A list for the developers of CellML tools
> *Subject:* Re: [cellml-dev] installing the cellmlapi
>
>
>
> Hi Alan,
>
> Thanks for the tip - it's a lot easier to use the sdk!
>
> I copied the SimpleJavaExample from the getting started page you linked to
> below. It does load the cellml libraries, but fails on the following line:
>
> Model m = dml.loadFromURL("
> http://www.cellml.org/models/beeler_reuter_1977_version04/download";);
>
> with the following exception:
>
> Exception in thread "main" java.lang.RuntimeException: Native code threw
> exception
> at pjm2pcm.cellml_api.DOMModelLoader.loadFromURL(Native Method)
> at
> uk.ac.cisban.saint.SimpleJavaExample.doExample(SimpleJavaExample.java:16)
> at uk.ac.cisban.saint.SimpleJavaExample.main(SimpleJavaExample.java:8)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at com.intellij.rt.execution.application.AppMain.main(AppMain.java:115)
>
> Do you know what could be going wrong? I am indeed connected to the
> internet, and visiting the model url from a browser does result in me being
> prompted to download a model.
>
> Thanks again,
> Allyson
>
> On 9 June 2011 13:18, Alan Garny <alan.garny at dpag.ox.ac.uk> wrote:
>
> Hi Allyson,
>
>
>
> From what I can tell, the link to which you refer (
> http://cellml-api.sourceforge.net/ubuntu_9_04.html) is based on something
> that I personally wrote several years ago when trying to get the CellML API
> to compile on Ubuntu. So, could it be that it is now out of date??
>
>
>
> Otherwise, rather than trying to build the CellML API from its source code,
> would it be worth your time trying to use the binaries that have officially
> been released last week? For more information:
> http://www.cellml.org/about/news/cellmlapi19 and
> http://www.cellml.org/tools/api/docs/getting-started-with-the-cellml-api.
>
>
>
> Alan
>
>
>
> *From:* cellml-tools-developers-bounces at cellml.org [mailto:
> cellml-tools-developers-bounces at cellml.org] *On Behalf Of *Allyson Lister
> *Sent:* 09 June 2011 12:55
> *To:* A list for the developers of CellML tools
> *Subject:* [cellml-dev] installing the cellmlapi
>
>
>
> Hi all,
>
> I'm just back in the game after maternity leave, and am trying to install
> (with java enabled) the cellml api on my ubuntu 11.04 machine. Up until the
> last step, the instructions for 9.04 are working just fine:
>
> http://cellml-api.sourceforge.net/ubuntu_9_04.html
>
> Which version of the cellml api is pulled from mercurial using the command
> on this page? Is there a document that contains the version number? The
> README doesn't seem to have it... Perhaps there's a mercurial command?
> Sorry, I don't use mercurial all that much.
>
> So, here are the commands from the ubuntu installation instructions page
> which I used successfully:
> hg clone
> http://cellml-api.hg.sourceforge.net:8000/hgroot/cellml-api/cellml-api
> aclocal && autoconf && automake
> ./configure --enable-context=no --enable-annotools --enable-cuses
> --enable-cevas --enable-malaes --enable-ccgs --enable-cis --enable-vacss
> --enable-rdf --enable-celeds --enable-examples=yes --enable-java
> CPPFLAGS="-I/usr/lib/jvm/java-6-sun/include
> -I/usr/lib/jvm/java-6-sun/include/linux"
> make check
>
> However, when I run "sudo make install", I get the following error. I'm
> including a few lines of output prior to the error, to provide context:
>
> ----------------------------------------------------------------------
> Libraries have been installed in:
> /usr/local/lib
>
> If you ever happen to want to link against installed libraries
> in a given directory, LIBDIR, you must either use libtool, and
> specify the full pathname of the library, or use the `-LLIBDIR'
> flag during linking and do at least one of the following:
> - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
> during execution
> - add LIBDIR to the `LD_RUN_PATH' environment variable
> during linking
> - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
> - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>
> See any operating system documentation about shared libraries for
> more information, such as the ld(1) and ld.so(8) manual pages.
> ----------------------------------------------------------------------
> test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
> /bin/bash ./libtool --mode=install /usr/bin/install -c CellML2C
> CellML2Python CellML2Matlab CustomGen testCeLEDS ValidateCellML RunCellML
> '/usr/local/bin'
> libtool: install: /usr/bin/install -c .libs/CellML2C
> /usr/local/bin/CellML2C
> libtool: install: /usr/bin/install -c .libs/CellML2Python
> /usr/local/bin/CellML2Python
> libtool: install: /usr/bin/install -c .libs/CellML2Matlab
> /usr/local/bin/CellML2Matlab
> libtool: install: /usr/bin/install -c .libs/CustomGen
> /usr/local/bin/CustomGen
> libtool: install: /usr/bin/install -c .libs/testCeLEDS
> /usr/local/bin/testCeLEDS
> libtool: install: /usr/bin/install -c .libs/ValidateCellML
> /usr/local/bin/ValidateCellML
> libtool: install: /usr/bin/install -c .libs/RunCellML
> /usr/local/bin/RunCellML
> test -z "/usr/local/share/cellmlapi" || /bin/mkdir -p
> "/usr/local/share/cellmlapi"
> /usr/bin/install -c -m 644 ./cellml.jar '/usr/local/share/cellmlapi'
> test -z "/usr/local/include" || /bin/mkdir -p "/usr/local/include"
> /usr/bin/install -c -m 644 ./interfaces/IfaceDOM_APISPEC.hxx
> ./interfaces/IfaceDOM_events.hxx ./interfaces/Ifacexpcom.hxx
> ./interfaces/IfaceMathML_content_APISPEC.hxx
> ./interfaces/IfaceCellML_APISPEC.hxx ./interfaces/IfaceRDF_APISPEC.hxx
> ./interfaces/IfaceCellML_events.hxx sources/cellml/CellMLBootstrap.hpp
> cda_config.h sources/cda_compiler_support.h
> sources/cellml-api-cxx-support.hpp ./interfaces/IfaceRDF_APISPEC.hxx
> ./interfaces/IfaceAnnoTools.hxx ./AnnoTools/sources/AnnoToolsBootstrap.hpp
> ./interfaces/IfaceCUSES.hxx ./CUSES/sources/CUSESBootstrap.hpp
> ./interfaces/IfaceCeVAS.hxx ./CeVAS/sources/CeVASBootstrap.hpp
> ./interfaces/IfaceMaLaES.hxx ./MaLaES/sources/MaLaESBootstrap.hpp
> ./interfaces/IfaceCCGS.hxx ./CCGS/sources/CCGSBootstrap.hpp
> ./interfaces/IfaceCeLEDS.hxx ./CeLEDS/sources/CeLEDSBootstrap.hpp
> ./interfaces/IfaceCeLEDSExporter.hxx
> ./CeLEDSExporter/sources/CeLEDSExporterBootstrap.hpp
> ./interfaces/IfaceVACSS.hxx ./VACSS/sources/VACSSBootstrap.hpp
> ./interfaces/IfaceCIS.hxx ./CIS/sources/CISBootstrap.hpp
> '/usr/local/include'
> /usr/bin/install: will not overwrite just-created
> `/usr/local/include/IfaceRDF_APISPEC.hxx' with
> `./interfaces/IfaceRDF_APISPEC.hxx'
> make[2]: *** [install-includeHEADERS] Error 1
> make[2]: Leaving directory `/home/allyson/Programs/cellml-api'
> make[1]: *** [install-am] Error 2
> make[1]: Leaving directory `/home/allyson/Programs/cellml-api'
> make: *** [install] Error 2
>
> It does seem an odd error - why is it trying to overwrite a file with what
> appears to be the same file? I tried make uninstall and then make install
> again, but the same error occurs.
>
> Thanks for your help!
>
> Allyson
>
> --
> Allyson Lister
>
> Please note the new email address of allyson.lister at newcastle.ac.uk,
> although the old email address will still work.
>
> Newcastle University, http://www.ncl.ac.uk
> http://themindwobbles.wordpress.com
>
>
> _______________________________________________
> cellml-tools-developers mailing list
> cellml-tools-developers at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-tools-developers
>
>
>
>
> --
> Allyson Lister
>
> Please note the new email address of allyson.lister at newcastle.ac.uk,
> although the old email address will still work.
>
> Newcastle University, http://www.ncl.ac.uk
> http://themindwobbles.wordpress.com
>
>
> _______________________________________________
> cellml-tools-developers mailing list
> cellml-tools-developers at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-tools-developers
>
>


--
Allyson Lister

Please note the new email address of allyson.lister at newcastle.ac.uk,
although the old email address will still work.

Newcastle University, http://www.ncl.ac.uk
http://themindwobbles.wordpress.com
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• [cellml-dev] installing the cellmlapi, Allyson Lister, 06/09/2011
  • [cellml-dev] installing the cellmlapi, Alan Garny, 06/10/2011
    • [cellml-dev] installing the cellmlapi, Allyson Lister, 06/10/2011
      • [cellml-dev] installing the cellmlapi, Alan Garny, 06/10/2011
        • [cellml-dev] installing the cellmlapi, Allyson Lister, 06/10/2011
          • [cellml-dev] installing the cellmlapi, Randall Britten, 06/10/2011
          • Message not available
            • [cellml-dev] installing the cellmlapi, Allyson Lister, 06/13/2011

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