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Hi Andrew,

thanks to everyone who replied. Yes, it must be the build script, or the
libraries being used by the build script (not necessarily cellml libraries).
I agree with others, though, who have said that "make install" is a pretty
basic feature that I would guess most people using CellML under linux would
need.

Thanks very much, and I look forward to seeing what you come up with.

:) Allyson

On 17 May 2010 22:06, Andrew Miller <ak.miller at auckland.ac.nz> wrote:

> 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?
>> _______________________________________________
>> cellml-tools-developers mailing list
>> cellml-tools-developers at cellml.org
>> <mailto:cellml-tools-developers at cellml.org>
>>
>> http://www.cellml.org/mailman/listinfo/cellml-tools-developers
>>
>>
>>
>>
>> --
>> Allyson Lister
>> http://themindwobbles.wordpress.com
>>
>> CISBAN, http://www.cisban.ac.uk
>> Newcastle University
>>
>>
>>
>> _______________________________________________
>> cellml-tools-developers mailing list
>> cellml-tools-developers at cellml.org
>> http://www.cellml.org/mailman/listinfo/cellml-tools-developers
>>
>
> _______________________________________________
> cellml-tools-developers mailing list
> cellml-tools-developers at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-tools-developers
>



--
Allyson Lister
http://themindwobbles.wordpress.com

CISBAN, http://www.cisban.ac.uk
Newcastle University
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• [cellml-dev] cellml_services in java version of the CellML DOM API, (continued)
  • [cellml-dev] cellml_services in java version of the CellML DOM API, Allyson Lister, 05/17/2010
    • [cellml-dev] cellml_services in java version of the CellML DOM API, David Nickerson, 05/17/2010
      • [cellml-dev] cellml_services in java version of the CellML DOM API, Andrew Miller, 05/17/2010
        • [cellml-dev] cellml_services in java version of the CellML DOM API, Allyson Lister, 05/18/2010
          • [cellml-dev] cellml_services in java version of the CellML DOM API, Allyson Lister, 05/18/2010
          • [cellml-dev] cellml_services in java version of the CellML DOM API, David Nickerson, 05/18/2010
            • [cellml-dev] cellml_services in java version of the CellML DOM API, Allyson Lister, 05/18/2010
              • [cellml-dev] cellml_services in java version of the CellML DOM API, Allyson Lister, 05/18/2010
              • [cellml-dev] cellml_services in java version of the CellML DOM API, Andrew Miller, 05/18/2010
              • [cellml-dev] cellml_services in java version of the CellML DOM API, David Nickerson, 05/18/2010
              • [cellml-dev] cellml_services in java version of the CellML DOM API, Allyson Lister, 05/19/2010
  • [cellml-dev] cellml_services in java version of the CellML DOM API, Morgan Taschuk, 05/19/2010
    • [cellml-dev] cellml_services in java version of the CellML DOM API, Andrew Miller, 05/19/2010
      • [cellml-dev] cellml_services in java version of the CellML DOM API, Allyson Lister, 05/19/2010

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