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[cellml-dev] installing the cellmlapi


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  • From: r.britten at auckland.ac.nz (Randall Britten)
  • Subject: [cellml-dev] installing the cellmlapi
  • Date: Fri, 10 Jun 2011 09:39:12 +1200
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
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/d
ownload");

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://www.ncl.ac.uk/>
http://themindwobbles.wordpress.com <http://themindwobbles.wordpress.com/>


_______________________________________________
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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://www.ncl.ac.uk/>
http://themindwobbles.wordpress.com <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://www.ncl.ac.uk/>
http://themindwobbles.wordpress.com <http://themindwobbles.wordpress.com/>



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