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[cellml-dev] cellml_services in java version of the CellML DOM API


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  • From: m.taschuk at newcastle.ac.uk (Morgan Taschuk)
  • Subject: [cellml-dev] cellml_services in java version of the CellML DOM API
  • Date: Tue, 18 May 2010 15:13:27 +0100
Hello all,

I am having the same problem as Allyson is, on two separate machines.
The cellml.jar file is missing the cellml_bootstrap package. I suspect
that it may be related to a non-CellML library update. This machine is
running 32-bit Ubuntu 10 (freshly installed), and the other machine is
running 64-bit Solaris SPARC. Both present with the same problem - the
Java bindings to CellML are not present.

The command I am running to compile the CDA is the following:

> aclocal && autoconf && automake ; ./configure --enable-java
--enable-rdf ;make ; sudo make install

which has previously worked for me. The last working version of the CDA
that I have is changeset 2e4662b7db8c from Wed Apr 14 16:45:41 2010
+1200. I have attempted to pull a fresh copy from the repository of this
revision and attempted to compile it without success. I have also tried
to compile the tip with the same command. Yet, I have on this machine a
fully-compiled CDA with changeset 2e4662b7db8c , so it has worked in the
past.

The only thing I can think of is that the libraries the CDA uses have
been changed somehow. With a brief look through the make output, I see
that /usr/bin/install is run with a -c option. However, if I run
/usr/bin/install --help, it indicates that the -c option is ignored. I'm
not sure if this is relevant at all.

If anyone has any suggestions, they would be welcome, I have saved
the output of the above command with changeset 2e4662b7db8c on Ubuntu 10
and put it online at http://drop.io/ih94gho171/asset/cda-compile-txt
since the file is too large for the mailing list. Thanks in advance.


Cheers,
Morgan


On 17/05/10 14:55, Allyson Lister wrote:
> Hi all,
>
> One final update. To try to solve the problem with the missing classes
> within cellml.jar, I ran the entire build (after a "make clean") using
> this configure command:
>
> ./configure --enable-context=no --enable-annotools --enable-cuses
> --enable-cevas --enable-malaes --enable-ccgs --enable-cis --enable-vacss
> --enable-rdf --enable-celeds --enable-java
>
> However, while a number of new classes appeared within cellml_bootstrap/
> in cellml.jar, none of them were the class I was trying to get built,
> CellMLBootstrap, called in the following bit of code:
>
> bootstrap = cellml_bootstrap.CellMLBootstrap.createCellMLBootstrap();
>
> Can anyone let me know which --enable option I should use to get this class?
>
> And I'm still having the same error with "ld" that I did before. Any
> other ideas on that one?
>
> /usr/bin/ld: cannot find -lannotools
> collect2: ld returned 1 exit status
> libtool: install: error: relink `libcellml_java_bridge.la
> <http://libcellml_java_bridge.la>' with the above command before
> installing it
> make[2]: *** [install-libLTLIBRARIES] Error 1
> make[2]: Leaving directory `/home/allyson/Apps/cellml'
> make[1]: *** [install-am] Error 2
> make[1]: Leaving directory `/home/allyson/Apps/cellml'
> make: *** [install] Error 2
>
> Thanks again,
>
> Allyson
>
> On 17 May 2010 13:59, Allyson Lister <a.l.lister at newcastle.ac.uk
> <mailto:a.l.lister at newcastle.ac.uk>> wrote:
>
> Hi,
>
> I did run a make clean first, and then ran make, which ran with 0
> errors hidden in the output. I did not use a brand-new directory,
> but the one I used before. However, I've just tried with a new
> directory using the following commands:
>
> hg clone http://cellml-api.hg.sourceforge.net:8000/hgroot/cellml-api
> cd cellml-api
> aclocal && autoconf && automake
> ./configure --enable-java --enable-rdf --enable-annotools
> make
> sudo make install
>
> ...and I get the same "ld" error as described before.
>
> As a second problem, while I was waiting for an answer to the "ld"
> error, I thought I'd try to compile my java code with the updated
> cellml.jar file. I got a different error this time:
>
> CellMLReader.java:[36,40] cannot find symbol
> symbol : class CellMLBootstrap
> location: package cellml_bootstrap
>
> Indeed, when I look in the cellml.jar file, while there is a
> cellml_bootstrap directory, the only thing in it is
> AnnoToolsBootstrap.class, and no CellML Bootstrap class. Which extra
> option do I need to get this class? I'm finding the configure
> options really difficult to understand: is there a list somewhere of
> which classes will be created according to which configure options?
> I'd rather not build anything I don't need.
>
> Thanks again!
> Allyson
>
>
> On 17 May 2010 13:45, David Nickerson <david.nickerson at gmail.com
> <mailto:david.nickerson at gmail.com>> wrote:
>
> > Well, I tried just adding the --enable-annotools as suggested
> by Andrew, and
> > I had a successful build all the way through the steps up to
> (and including)
> > the "make" command. When I then tried "sudo make install", I
> got partway
> > through that, and then was presented with the following error:
> >
> > /usr/bin/ld: cannot find -lannotools
> > collect2: ld returned 1 exit status
> > libtool: install: error: relink `libcellml_java_bridge.la
> <http://libcellml_java_bridge.la>' with the above
> > command before installing it
> > make[2]: *** [install-libLTLIBRARIES] Error 1
> >
> > I'm not sure what to do with this error. Does anyone have any
> ideas?
>
> did you do a 'make clean' in your build directory first? or start
> elsewhere from a clean slate?
>
> does doing just a 'make' finish successfully with no error messages
> hidden in the output?
> _______________________________________________
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> <mailto:cellml-tools-developers at cellml.org>
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>
>
>
>
> --
> Allyson Lister
> http://themindwobbles.wordpress.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University
>
>
>
>
> --
> Allyson Lister
> http://themindwobbles.wordpress.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University




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