First login?
Lost password?
 
 
cellml-tools-developers AT lists.cellml.org 
A list for the developers of CellML tools

Text archives Help


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


Chronological Thread 
  • From: a.l.lister at newcastle.ac.uk (Allyson Lister)
  • Subject: [cellml-dev] cellml_services in java version of the CellML DOM API
  • Date: Wed, 19 May 2010 07:44:42 +0100
Hi Andrew,

Thanks for the info. I've updated my local version of the repo, and followed
your instructions below. The cellml.jar file seems to have all the classes I
need with just --enable-java and --enable-rdf. Thanks!

However, the "sudo make install" command seems to run almost completely
correctly before failing with the following error (tail end of make install
command included):

libtool: install: /usr/bin/install -c .libs/libcellml_java_bridge.so.0.0.0T
/usr/local/lib/libcellml_java_bridge.so.0.0.0
libtool: install: (cd /usr/local/lib && { ln -s -f
libcellml_java_bridge.so.0.0.0 libcellml_java_bridge.so.0 || { rm -f
libcellml_java_bridge.so.0 && ln -s libcellml_java_bridge.so.0.0.0
libcellml_java_bridge.so.0; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f
libcellml_java_bridge.so.0.0.0 libcellml_java_bridge.so || { rm -f
libcellml_java_bridge.so && ln -s libcellml_java_bridge.so.0.0.0
libcellml_java_bridge.so; }; })
libtool: install: /usr/bin/install -c .libs/libcellml_java_bridge.lai
/usr/local/lib/libcellml_java_bridge.la
libtool: install: /usr/bin/install -c .libs/libJavaSupport.a
/usr/local/lib/libJavaSupport.a
libtool: install: chmod 644 /usr/local/lib/libJavaSupport.a
libtool: install: ranlib /usr/local/lib/libJavaSupport.a
libtool: install: /usr/bin/install -c .libs/libcellml.a
/usr/local/lib/libcellml.a
libtool: install: chmod 644 /usr/local/lib/libcellml.a
libtool: install: ranlib /usr/local/lib/libcellml.a
libtool: install: /usr/bin/install -c .libs/libcellml_java_bridge.a
/usr/local/lib/libcellml_java_bridge.a
libtool: install: chmod 644 /usr/local/lib/libcellml_java_bridge.a
libtool: install: ranlib /usr/local/lib/libcellml_java_bridge.a
libtool: finish:
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/sbin"
ldconfig -n /usr/local/lib
----------------------------------------------------------------------
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"
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
./interfaces/IfaceRDF_APISPEC.hxx '/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/Apps/cellml'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/allyson/Apps/cellml'
make: *** [install] Error 2


Is this any cause for worry?

Thanks again,
Allyson

On 18 May 2010 23:27, Andrew Miller <ak.miller at auckland.ac.nz> wrote:

> Morgan Taschuk wrote:
>
>> 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.
>>
>
> Hi Morgan and Allyson,
>
> It was working for me solely because I had an existing javacp directory
> which had been built earlier - which is probably the same reason it worked
> for you.
>
> I have now updated the build system to properly build the bootstrap files
> again.
>
> After updating, you may need to manually delete the javacp directory and
> your cellml.jar file.
>
> make install works for me with this - although it runs into problems if the
> prefix is changed after the first build, unless you remove the .la files and
> build again (I think this is normal libtool behaviour, unfortunately).
>
> Best wishes,
> Andrew
>
>
>
>> 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?
>>> _______________________________________________
>>> 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
>>>
>>>
>>>
>>>
>>> --
>>> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
<http://www.cellml.org/pipermail/cellml-tools-developers/attachments/20100519/9f46ada9/attachment-0001.htm>


Archive powered by MHonArc 2.6.18.

Top of page