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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 So, could it be that it is now out of date??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
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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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