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


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  • From: ak.miller at auckland.ac.nz (Andrew Miller)
  • Subject: [cellml-dev] cellml_services in java version of the CellML DOM API
  • Date: Tue, 18 May 2010 09:06:28 +1200
On 18/05/10 00:59, Allyson Lister 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.

Hi Allyson,

You shouldn't need any extra options - obviously something is wrong with
the build script somewhere, which we will look into.

The make install issue can be worked around by copying the required
libraries out of the .libs subdirectory - I think very few people
actually do a make install, which is probably why it has issues we
didn't know about when building AnnoTools.

Best wishes,
Andrew

>
> 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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>
>
>
>
> --
> Allyson Lister
> http://themindwobbles.wordpress.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University
>
>
>
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