- From: a.l.lister at newcastle.ac.uk (Allyson Lister)
- Subject: [cellml-dev] installing the cellmlapi
- Date: Mon, 13 Jun 2011 09:39:30 +0100
Hi Randall,
Thanks for the idea, but I'm not in a proxy system here at home, where I am
doing the testing. You're right that Newcastle University does have a proxy,
but in this particular instance, that isn't the problem.
Thanks,
Allyson
On 9 June 2011 22:39, Randall Britten <r.britten at auckland.ac.nz> wrote:
>
Hi Allyson
>
>
>
>
Just a wild guess, perhaps your browser is configured to use a proxy, but
>
it is not a system wide configuration to use the proxy, or if it is system
>
wide, perhaps Java for some reason is not heeding the configuration.
>
>
>
>
Regards,
>
>
Randall
>
>
>
>
*From:* cellml-tools-developers-bounces at cellml.org [mailto:
>
cellml-tools-developers-bounces at cellml.org] *On Behalf Of *Allyson Lister
>
*Sent:* Friday, 10 June 2011 1:52 a.m.
>
>
*To:* A list for the developers of CellML tools
>
*Subject:* Re: [cellml-dev] installing the cellmlapi
>
>
>
>
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
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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:
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>
Hi Allyson,
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>
>
>
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
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yet to make a move in that direction. I would expect Andrew Miller to be the
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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
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exception
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at pjm2pcm.cellml_api.DOMModelLoader.loadFromURL(Native Method)
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at
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uk.ac.cisban.saint.SimpleJavaExample.doExample(SimpleJavaExample.java:16)
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at uk.ac.cisban.saint.SimpleJavaExample.main(SimpleJavaExample.java:8)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at
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sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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at
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sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
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at java.lang.reflect.Method.invoke(Method.java:597)
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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
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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
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that I personally wrote several years ago when trying to get the CellML API
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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,
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would it be worth your time trying to use the binaries that have officially
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been released last week? For more information:
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http://www.cellml.org/about/news/cellmlapi19 and
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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
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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
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which I used successfully:
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hg clone
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http://cellml-api.hg.sourceforge.net:8000/hgroot/cellml-api/cellml-api
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aclocal && autoconf && automake
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./configure --enable-context=no --enable-annotools --enable-cuses
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--enable-cevas --enable-malaes --enable-ccgs --enable-cis --enable-vacss
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--enable-rdf --enable-celeds --enable-examples=yes --enable-java
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CPPFLAGS="-I/usr/lib/jvm/java-6-sun/include
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-I/usr/lib/jvm/java-6-sun/include/linux"
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make check
>
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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:
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/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:
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- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
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during execution
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- add LIBDIR to the `LD_RUN_PATH' environment variable
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during linking
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- 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
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CellML2Python CellML2Matlab CustomGen testCeLEDS ValidateCellML RunCellML
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'/usr/local/bin'
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libtool: install: /usr/bin/install -c .libs/CellML2C
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/usr/local/bin/CellML2C
>
libtool: install: /usr/bin/install -c .libs/CellML2Python
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/usr/local/bin/CellML2Python
>
libtool: install: /usr/bin/install -c .libs/CellML2Matlab
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/usr/local/bin/CellML2Matlab
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libtool: install: /usr/bin/install -c .libs/CustomGen
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/usr/local/bin/CustomGen
>
libtool: install: /usr/bin/install -c .libs/testCeLEDS
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/usr/local/bin/testCeLEDS
>
libtool: install: /usr/bin/install -c .libs/ValidateCellML
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/usr/local/bin/ValidateCellML
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libtool: install: /usr/bin/install -c .libs/RunCellML
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/usr/local/bin/RunCellML
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test -z "/usr/local/share/cellmlapi" || /bin/mkdir -p
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"/usr/local/share/cellmlapi"
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/usr/bin/install -c -m 644 ./cellml.jar '/usr/local/share/cellmlapi'
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test -z "/usr/local/include" || /bin/mkdir -p "/usr/local/include"
>
/usr/bin/install -c -m 644 ./interfaces/IfaceDOM_APISPEC.hxx
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./interfaces/IfaceDOM_events.hxx ./interfaces/Ifacexpcom.hxx
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./interfaces/IfaceMathML_content_APISPEC.hxx
>
./interfaces/IfaceCellML_APISPEC.hxx ./interfaces/IfaceRDF_APISPEC.hxx
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./interfaces/IfaceCellML_events.hxx sources/cellml/CellMLBootstrap.hpp
>
cda_config.h sources/cda_compiler_support.h
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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
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./interfaces/IfaceCCGS.hxx ./CCGS/sources/CCGSBootstrap.hpp
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./interfaces/IfaceCeLEDS.hxx ./CeLEDS/sources/CeLEDSBootstrap.hpp
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./interfaces/IfaceCeLEDSExporter.hxx
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./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
>
>
>
_______________________________________________
>
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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